gebhart/patrepeval huggingface dataset:
The role of crystallization and phase separation in the formation of physically cross-linked PVA hydrogels (2012)

The biocompatibility, processing ease, and mechanical properties of freeze-thawed poly(vinyl alcohol) (PVA)-based hydrogels have encouraged significant research toward developing this material for various biomedical applications. Crystallization that occurs during the freeze-thawing process is cited in the literature as the primary mechanism responsible for the resultant mechanical properties. Further analysis, however, shows the presence of two unique mechanisms that contribute to PVA's mechanical properties. During freeze–thaw cycling water freezes causing phase separation, which facilitates crystallization. The impact of phase separation during freeze–thaw cycling was investigated by comparing freeze-thawed and aged PVA hydrogels. Aged hydrogels were not prepared by freezing and, therefore, did not exhibit significant phase separation. The amount of phase separation was discerned using optical microscopy in the hydrated state. Crystallinity and mechanical properties were also evaluated as a function of the number of cycles (for freeze-thawed gels) and aging time (for aged gels). For freeze-thawed hydrogels, crystallinity deviated significantly from the trend observed in compressive modulus, indicating that crystallinity was not the only factor determining the hydrogel's mechanical properties. Phase separation was found to occur during freeze–thaw cycling independently of crystallization, especially at later freeze–thaw cycles (after the third). The trends observed for both crystallinity and modulus for aged hydrogels, however, were in better agreement with each other. Further evaluation of the mechanical properties of aged and freeze-thawed hydrogels with similar crystallinities indicated that freeze-thawed hydrogels have significantly higher modulus values (p < 0.05). As a result, phase separation, independently of crystallization, was determined to have a significant effect on gelation during freeze–thaw cycling. In particular, PVA-rich regions that are formed during phase separation, without additional cross-linking, are believed to have a significant effect on the resultant mechanical properties.
A Time-Resolved Four-Tap Lock-In Pixel CMOS Image Sensor for Real-Time Fluorescence Lifetime Imaging Microscopy (2018)

A programmable sub-nanosecond time-gated four-tap CMOS lock-in pixel (LIP) image sensor that uses an in-pixel pulse generator (PG) is developed for time-resolved (TR) biomedical imaging applications, such as a fluorescence lifetime imaging microscopy (FLIM). We demonstrate the system's effectiveness with simulations and measurements. Using pixel-level PG circuits, very narrow time windows (TWs) that are less than 0.8 ns can be used for charge modulation. This rapid gating allows very weak signals from living cells to be captured with a high signal-to-noise ratio (SNR). The prototype CMOS imaging system displays a fast intrinsic response of 170 ps at 472 nm and a very low temporal random noise of 0.85 e-rms at 45 frames/s under truly correlated-double-sampling operation using two-stage charge transfer. Four outputs from the LIPs allow real-time fluorescence lifetimes (FLTs) measurement, even from samples with multiple FLT components.
Initial association of NR2E1 with bipolar disorder and identification of candidate mutations in bipolar disorder, schizophrenia, and aggression through resequencing (2008)

Nuclear receptor 2E1 gene (NR2E1) resides within a 6q21-22 locus for bipolar disorder and schizophrenia. Mice deleted for Nr2e1 show altered neurogenesis, cortical and limbic abnormalities, aggression, hyperexcitability, and cognitive impairment. NR2E1 is therefore a positional and functional candidate for involvement in mental illness. We performed association analyses in 394 patients with bipolar disorder, 396 with schizophrenia, and 479 controls using six common markers and haplotypes. We also performed a comprehensive mutation screen of NR2E1, resequencing its entire coding region, complete 5' and 3' untranslated regions, consensus splice-sites, and evolutionarily conserved regions in 126 humans with bipolar disorder, schizophrenia, or aggressive disorders. NR2E1 was associated with bipolar disorder I and II [odds ratio (OR = 0.77, P = 0.013), bipolar disorder I (OR = 0.77, P = 0.015), bipolar disorder in females (OR = 0.72, P = 0.009), and with age at onset < or = 25 years (OR = 0.67, P = 0.006)], all of which remained significant after correcting for multiple comparisons. We identified eight novel candidate mutations that were absent in 325 controls; four of these were predicted to alter known neural transcription factor binding sites. Analyses of NR2E1 mRNA in human brain revealed forebrain-specific transcription. The data presented support the hypothesis that genetic variation at NR2E1 may be associated with susceptibility to brain-behavior disorders.
Structural–functional interactions of NS1-BP protein with the splicing and mRNA export machineries for viral and host gene expression (2018)

The influenza virulence factor NS1 protein interacts with the cellular NS1-BP protein to promote splicing and nuclear export of the viral M mRNAs. The viral M1 mRNA encodes the M1 matrix protein and is alternatively spliced into the M2 mRNA, which is translated into the M2 ion channel. These proteins have key functions in viral trafficking and budding. To uncover the NS1-BP structural and functional activities in splicing and nuclear export, we performed proteomics analysis of nuclear NS1-BP binding partners and showed its interaction with constituents of the splicing and mRNA export machineries. NS1-BP BTB domains form dimers in the crystal. Full-length NS1-BP is a dimer in solution and forms at least a dimer in cells. Mutations suggest that dimerization is important for splicing. The central BACK domain of NS1-BP interacts directly with splicing factors such as hnRNP K and PTBP1 and with the viral NS1 protein. The BACK domain is also the site for interactions with mRNA export factor Aly/REF and is required for viral M mRNA nuclear export. The crystal structure of the C-terminal Kelch domain shows that it forms a β-propeller fold, which is required for the splicing function of NS1-BP. This domain interacts with the polymerase II C-terminal domain and SART1, which are involved in recruitment of splicing factors and spliceosome assembly, respectively. NS1-BP functions are not only critical for processing a subset of viral mRNAs but also impact levels and nuclear export of a subset of cellular mRNAs encoding factors involved in metastasis and immunity.
Aqueous-phase reforming of xylitol over Pt/C and Pt/TiC-CDC catalysts: catalyst characterization and catalytic performance (2013)

The aqueous phase reforming (APR) of xylitol was studied over five Pt/C catalysts. The correlation between physico-chemical properties of the catalysts and catalytic performance was established. The Pt/C catalysts have different textural properties as well as different mean Pt cluster sizes and surface acidity. The average Pt cluster size was investigated by means of CO chemisorption as well as by TEM. The reaction was found to be structure sensitive and TOF linearly increases with increasing average Pt cluster size in the studied domain. The catalysts which possess higher surface acidity favoured higher rates of hydrocarbon production. On the contrary the Pt/C materials with lower acidities generated hydrogen with high selectivity and TOF.
Mechanical properties of α‐tricalcium phosphate‐based bone cements incorporating regenerative biomaterials for filling bone defects exposed to low mechanical loads (2015)

Calcium phosphate-based cements with enhanced regenerative potential are promising biomaterials for the healing of bone defects in procedures such as percutaneous vertebroplasty. With a view to the use of such cements for low load bearing applications such as sinus augmentation or filling extraction sites. However, the inclusion of certain species into bone cement formulations has the potential to diminish the mechanical properties of the formulations and thereby reduce their prospects for clinical translation. Consequently, we have prepared α-tricalcium phosphate (α-TCP)-based bone cements including materials that we would expect to improve their regenerative potential, and describe the mechanical properties of the resulting formulations herein. Formulations incorporated α-TCP, hydroxyapatite, biopolymer-thickened wetting agents, sutures, and platelet poor plasma. The mechanical properties of the composites were composition dependent, and optimized formulations had clinically relevant mechanical properties. Such calcium phosphate-based cements have potential as replacements for cements such as those based on polymethylmethacrylate.
Regulation and function of the extracellular matrix protein tenascin-C in ovarian cancer cell lines (1999)

The extracellular matrix glycoprotein tenascin-C (TN) is overexpressed in the stroma of malignant ovarian tumours particularly at the interface between epithelia and stroma leading to suggestions that it may be involved in the process of invasion (Wilson et al (1996) Br J Cancer 74: 999-1004). To define regulation of TN further and investigate its function in ovarian cancer, a range of cell line models were studied. Concentrations of secreted TN in media from cultures of ovarian fibroblast cell lines were at least 100-fold greater than from carcinoma cell lines. Evidence for paracrine regulation of TN secretion was obtained by co-culture of carcinoma cells with fibroblast cells wherein secretion into the media was greater than from fibroblasts alone. Transforming growth factor (TGF)-beta1, insulin-like growth factor (IGF)-II and progesterone all stimulated TN secretion while human choriogonadotropin (hCG), follicle-stimulating hormone (FSH) and gamma-interferon inhibited secretion. TGF-beta1 produced the greatest stimulation of TN in cultured fibroblasts and its co-expression with TN was examined in primary ovarian tumours. There was a significant association between the presence of moderate-strong expression of TN and TGF-beta1. Evidence for TN having a functional role in ovarian carcinoma was obtained from adhesion and migration assays. The PE01, PE04, SKOV-3 and 59M cell lines all demonstrated marked adhesion to plastic coated with TN relative to the control protein bovine serum albumin (BSA) and expressed alpha2beta1 and alpha3beta1 integrins. The SKOV-3 cell line migrated more rapidly through TN than through BSA indicating that TN can facilitate migration of ovarian carcinoma cells.
Improved single-cell ATAC-seq reveals chromatin dynamics of in vitro corticogenesis (2019)

Abstract Development is a complex process that requires the precise modulation of regulatory gene networks controlled through dynamic changes in the epigenome. Single-cell-omic technologies provide an avenue for understanding the mechanisms of these processes by capturing the progression of epigenetic cell states during the course of cellular differentiation using in vitro or in vivo models 1 . However, current single-cell epigenomic methods are limited in the information garnered per individual cell, which in turn limits their ability to measure chromatin dynamics and state shifts. Single-cell combinatorial indexing (sci-) has been applied as a strategy for identifying single-cell-omic originating libraries and removes the necessity of single-cell, single-compartment chemistry 2 . Here, we report an improved sci-assay for transposase accessible chromatin by sequencing (ATAC-seq), which utilizes the small molecule inhibitor Pitstop 2™ (scip-ATAC-seq) 3 . We demonstrate that these improvements, which theoretically could be applied to any in situ transposition method for single-cell library preparation, significantly increase the ability of transposase to enter the nucleus and generate highly complex single-cell libraries, without altering biological signal. We applied sci-ATAC-seq and scip-ATAC-seq to characterize the chromatin dynamics of developing forebrain-like organoids, an in vitro model of human corticogenesis 4 . Using these data, we characterized novel putative regulatory elements, compared the epigenome of the organoid model to human cortex data, generated a high-resolution pseudotemporal map of chromatin accessibility through differentiation, and measured epigenomic changes coinciding with a neurogenic fate decision point. Finally, we combined transcription factor motif accessibility with gene activity (GA) scores to directly observe the dynamics of complex regulatory programs that regulate neurogenesis through developmental pseudotime. Overall, scip-ATAC-seq increases information content per cell and bolsters the potential for future single-cell studies into complex developmental processes.
A Measurement-Driven Anti-Jamming System for 802.11 Networks (2011)

Dense, unmanaged IEEE 802.11 deployments tempt saboteurs into launching jamming attacks by injecting malicious interference. Nowadays, jammers can be portable devices that transmit intermittently at low power in order to conserve energy. In this paper, we first conduct extensive experiments on an indoor 802.11 network to assess the ability of two physical-layer functions, rate adaptation and power control, in mitigating jamming. In the presence of a jammer, we find that: 1) the use of popular rate adaptation algorithms can significantly degrade network performance; and 2) appropriate tuning of the carrier sensing threshold allows a transmitter to send packets even when being jammed and enables a receiver to capture the desired signal. Based on our findings, we build ARES, an Anti-jamming REinforcement System, which tunes the parameters of rate adaptation and power control to improve the performance in the presence of jammers. ARES ensures that operations under benign conditions are unaffected. To demonstrate the effectiveness and generality of ARES, we evaluate it in three wireless test-beds: 1) an 802.11n WLAN with MIMO nodes; 2) an 802.11a/g mesh network with mobile jammers; and 3) an 802.11a WLAN with TCP traffic. We observe that ARES improves the network throughput across all test-beds by up to 150%.
Al-2.54 Exposure Latitude (2021)

As increasingly smaller molecular materials and material structures are devised or developed for technological applications, the demands on the processes of lithography now routinely include feature sizes that are of the order of 10 nm. In reaching such a fine level of resolution, the methods of lithography have increased markedly in sophistication and brought into play 2terminology that is unfamiliar, on the one hand, to scientists tasked with the development of new lithographic materials or, on the other, to the engineers who design and operate the complex equipment that is required in modern-day processing. Publications produced by scientists need to be understood by engineers and vice versa, and these commonly arise from collaborative research that draws heavily on the terminology of two or more of the traditional disciplines. It is developments in polymer science and material science that lead progress in areas that cross traditional boundaries, such as microlithography. This document provides the exact definitions of a selection of unfamiliar terms that researchers and practitioners from different disciplines might encounter.
Characterization of new scintillators: SrI2:Eu, CeBr3, GYGAG:Ce and CLYC:Ce (2015)

We measured the performance of a 2"×2" tapered cylindrical SrI2:Eu, a 2" × 3" cylindrical CeBr3, a 2" × 0.3" cylindrical GYGAG:Ce. The gamma-ray energy resolution was measured up to 9 MeV. A scan along three axes of each scintillator was performed using a collimated source of 137Cs. The signals of the detectors were also digitized and compared. We tested two 1" × 1" cylindrical CLYC crystals. One was enriched with 6Li at 95% while the other was enriched with 99% of 7Li. The response of the two detectors to gamma rays, thermal and fast neutrons was measured. The PSD performances have been tested with a different types of PMTs.
Stretchable and Transparent Electrodes using Hybrid Structures of Graphene–Metal Nanotrough Networks with High Performances and Ultimate Uniformity (2014)

Transparent electrodes that can maintain their electrical and optical properties stably against large mechanical deformations are essential in numerous applications of flexible and wearable electronics. In this paper, we report a comprehensive analysis of the electrical, optical, and mechanical properties of hybrid nanostructures based on graphene and metal nanotrough networks as stretchable and transparent electrodes. Compared to the single material of graphene or the nanotrough, the formation of this hybrid can improve the uniformity of sheet resistance significantly, that is, a very low sheet resistance (1 Ω/sq) with a standard deviation of less than ±0.1 Ω/sq, high transparency (91% in the visible light regime), and superb stretchability (80% in tensile strain). The successful demonstration of skin-attachable, flexible, and transparent arrays of oxide semiconductor transistors fabricated using hybrid electrodes suggests substantial promise for the next generation of electronic devices.
Biocompatibility of Human Collagen Type IV Intracorneal Implants (1989)

A new biomaterial made from human placental collagen type IV has been developed in corneal inlays for refractive keratoplasty. Eight dogs received intracorneal lenses to investigate biocompatibility. Postoperative follow-up observation of 2 years revealed that the eyes remained clear and without inflammatory reaction. Endothelial cells were unaltered. Histological and ultrastructural studies showed no signs of inflammation, ulceration, or encapsulation. No fibroblastic activity was evident at the lens stroma interface.
An oxime–carbapalladacycle complex covalently anchored to silica as an active and reusable heterogeneous catalyst for Suzuki cross-coupling in water (2003)

A preformed oxime-carbapalladacycle complex covalently anchored onto mercaptopropyl modified silica is highly active (> 99%) for the Suzuki reaction of p-chloroacetophenone and phenylboronic acid in water; no leaching occurs and the same catalyst sample was reused eight times without decreased activity.
Maximum Likelihood Estimation of a Stochastic Integrate-and-Fire Neural Model (2003)

Recent work has examined the estimation of models of stimulus-driven neural activity in which some linear filtering process is followed by a nonlinear, probabilistic spiking stage. We analyze the estimation of one such model for which this nonlinear step is implemented by a noisy, leaky, integrate-and-fire mechanism with a spike-dependent aftercurrent. This model is a biophysically plausible alternative to models with Poisson (memory-less) spiking, and has been shown to effectively reproduce various spiking statistics of neurons in vivo. However, the problem of estimating the model from extracellular spike train data has not been examined in depth. We formulate the problem in terms of maximum likelihood estimation, and show that the computational problem of maximizing the likelihood is tractable. Our main contribution is an algorithm and a proof that this algorithm is guaranteed to find the global optimum with reasonable speed. We demonstrate the effectiveness of our estimator with numerical simulations.
Simultaneous Orthogonalizing and Shaping of Multiple LG Beams to Mitigate Crosstalk and Power Loss by Transmitting Each of Four Data Channels on Multiple Modes in a 400-Gbit/s Free-Space Link (2020)

We experimentally utilize orthogonal combinations of multiple Laguerre-Gaussian modes in a 400-Gbit/s free-space link with limited-size aperture or misalignment. Power loss and crosstalk could be reduced by up tô15 dB and ~40 dB, respectively.
Evaluating Paint-Sludge Chars for Adsorption of Selected Paint Solvents (1996)

At Ford, a study had been carried out to investigate the technical feasibility of converting paint sludge to activated char and reusing the char in paint spray-booth water to capture paint solvents from spray-booth air. As part of the study, several chars were made from a paint sludge and six dried paints to evaluate their effectiveness as adsorbents by conducting a series of liquid-phase adsorption experiments. Three commonly-used paint solvents and p-nitrophenol were selected as adsorbates. The three paint solvents were toluene, 2-methyl-1-propanol (iso-butanol), and 2-butoxyethanol (butylcellosolve). In this paper, the results of the pyrolysis and adsorption experiments are presented along with practical implications. The primary findings include the following: (1) Black-paint chars showed substantially larger surface area and higher adsorption capacity (based on total weight) than white-paint chars which had high ash contents due to the white pigment, titanium dioxide; (2) the adsorption capacity of the paint-sludge char was between those of black-paint and white-paint chars, and was 5–20% that of a commercial activated carbon; (3) titanium dioxide in white-paint chars did not improve the chars' affinity for hydrophilic compounds such as 2-methyl-1-propanol and 2-butoxyethanol; (4) coal could be added to paint sludge to improve the quality of the resulting char and to reduce ash content; and (5) the pyrolysis of paint sludge could present an attractive opportunity for reusing and recycling a waste product for pollution abatement and as a vehicle component.
Physically derived geometric models for polarized reflection and emission from rough surfaces (2000)

This thesis studies reflection and emission of light from rough surfaces. Geometric models for the reflection and emission of light are developed based on the precise physical geometry of rough surfaces. The predictions of the models are compared to experimentally measured results. These models may be applied to generating highly accurate image creation in computer graphics, and image analysis in computer vision. 
Physical reflectance models use the physics of light and reflection theory to accurately model the reflection from rough surfaces. Although the precise interaction of light and a reflecting (or emitting) rough surface can be precisely computed, those computations are extremely complex and cannot be solved for use as a rendering technique for the near future. For this reason, physical reflectance models use simplifying assumptions to make the problem of rough surface reflection tractable. Geometric reflectance models consider the reflection of light from a rough surface as the summation of reflections from small smooth facets on the surface. The reflections from these smooth facets of the surface are computed according to Fresnel theory, which also predicts the polarization of the reflected light. The goal of the geometric reflectance model is to describe the reflected light from a rough surface accurately using only the reflection geometry and the physical description of the surface roughness. 
We use experimental measurements of reflection from several surfaces, both smooth and rough to test the accuracy of established geometric reflection models. We also physically measure the rough surfaces at sub-micron detail to determine and verify the geometric surface parameters of the reflection model. 
From the comparison of past reflection models to our experimental data, we conclude that the parameterization of these models is insufficient to accurately model reflectance. Our new model, the surface function reflectance model, derived from the combined results of the reflection measurements and the physical measurements of the surface geometry, models the surface reflection with much higher accuracy than has previously been obtained from a tractable geometric reflectance model.