gebhart/patrepeval huggingface dataset:
Exploring Dynamics and Structure of Biomolecules, Cryoprotectants, and Water Using Molecular Dynamics Simulations: Implications for Biostabilization and Biopreservation (2018)

Successful stabilization and preservation of biological materials often utilize low temperatures and dehydration to arrest molecular motion. Cryoprotectants are routinely employed to help the biological entities survive the physicochemical and mechanical stresses induced by cold or dryness. Molecular interactions between biomolecules, cryoprotectants, and water fundamentally determine the outcomes of preservation. The optimization of assays using the empirical approach is often limited in structural and temporal resolution, whereas classical molecular dynamics simulations can provide a cost-effective glimpse into the atomic-level structure and interaction of individual molecules that dictate macroscopic behavior. Computational research on biomolecules, cryoprotectants, and water has provided invaluable insights into the development of new cryoprotectants and the optimization of preservation methods. We describe the rapidly evolving state of the art of molecular simulations of these complex systems, summarize the molecular-scale protective and stabilizing mechanisms, and discuss the challenges that motivate continued innovation in this field.
Abstract 237: Enrichment of AXL-high/ MITF-low melanoma cells in the presence of MAPK inhibitors in vitro (2016)

Abstract BRAF and MEK inhibitors have become a standard of care for patients with metastatic BRAF mutant (V600) melanoma. Despite their success, 10- 20% of patients exhibit ‘intrinsic’ resistance and fail to respond to treatment. Recently, distinct transcriptional profiles have been associated with sensitivity to these drugs with intrinsically resistant melanomas exhibiting an AXL-high/ MITF-low phenotype (1). Using melanoma cell lines from the Cancer Cell Line Encyclopedia with matched gene expression data, we confirmed that AXL-high/ MITF-low cell lines had increased resistance to both BRAF (Dabrafenib) and MEK (Trametinib) inhibitors, either singly or in combination. Using flow cytometry with an AXL antibody, we observed that AXL-high/ MITF-low resistant cell lines frequently exhibited a high percentage of AXL+ cells (≥90%) while AXL-low/ MITF-high sensitive cell lines showed the opposite (≤5%). We hypothesized that the small percentage of AXL+ cells in the sensitive cell lines may be responsible for mechanisms of adaptive or acquired resistance (a feature that is frequently observed with the use of BRAF and MEK inhibitors in vitro and in the clinic). To explore this, we cultured sensitive cell lines in vitro for 5 days in the presence of combined Dabrafenib and Trametinib (DT) and performed flow cytometry to determine if there was a change in the percentage of AXL+ cells. All sensitive cell lines exhibited an enrichment of AXL+ cells with increasing concentrations of DT (maximum increase compared to DMSO control across individual cell lines ranged from 10% to 85%). It is unknown whether this phenomenon could be explained by a clonal selection or ‘plastic’ epigenetic reprogramming process and as such, we are currently performing experiments to determine this. Looking to the future, identifying potential dependencies of AXL-low/ MITF-high melanomas will deepen our understanding of the biology supporting this resistant state and provide a platform for the design of future clinical intervention strategies in this subset of patients. 1) Konieczkowski et al. 2014. Cancer Discovery. A melanoma cell state distinction influences sensitivity to MAPK pathway inhibitors. 4(7):816-27. Citation Format: Ken Dutton-Regester, Levi Garraway. Enrichment of AXL-high/ MITF-low melanoma cells in the presence of MAPK inhibitors in vitro. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 237.
Supercharging a MnO2 Nanowire: An Amine-Altered Morphology Retains Capacity at High Rates and Mass Loadings (2017)

The influence of hexamethylenetetraamine (HMTA) on the morphology of δ-MnO<sub>2</sub> and its properties for electrical energy storage are investigated-specifically for ultrathick δ-MnO<sub>2</sub> layers in the micron scale. Planar arrays of gold@δ-MnO<sub>2</sub>, core@shell nanowires, were prepared by electrodeposition with and without the HMTA and their electrochemical properties were evaluated. HMTA alters the MnO<sub>2</sub> in three ways: First, it creates a more open morphology for the MnO<sub>2</sub> coating, characterized by "petals" with a thickness of 6 to 9 nm, rather than much thinner δ-MnO<sub>2</sub> sheets seen in the absence of HMTA. Second, the electronic conductivity of the δ-MnO<sub>2</sub> is increased by an order of magnitude. Third, δ-MnO<sub>2</sub> prepared in HMTA shows a (001) interlayer spacing that is expanded by ≈30% possibly accelerating Li transport. The net effect of "HTMA doping" is to dramatically improve high rate performance, culminating in an increase in the specific capacity for the thickest MnO<sub>2</sub> shells examined here by a factor of 15 at 100 mV/s.
High-level timing analysis using constraint logic programming and interval arithmetic (2002)

This paper addresses the specific problem of true (functional) delay estimation during high-level design. We present a method for modelling and verifying high-level timing specification using CLP (BNR), a constraint logic programming language augmented with relational interval arithmetic.
Photolithographic fabrication of a high-precision bar-code pattern on the surface of a sphere (2005)

Bar-code patterns were produced upon gold-coated glass spheres 8 mm in diameter with a novel projection photolithography exposure system that included a computer-controlled rotation stage-and-shutter arrangement. The patterns extended in an equatorial band about the entire 360 degrees periphery of the sphere. To obtain uniform thickness of the photoresist layer, we dip coated the spheres and removed the excess with an absorption pad. The widths of the bars in the pattern were in the range 21.85 +/- 0.6 microm at the equator, and the relative error in the angular position of the pattern features was less than 0.025 degrees. The patterned spheres are suitable for use in optically interrogated flying spot magnetic heading sensors.
Selective Enhancement of Electrochemical Signal Based on the Size of Alcohols Using Nanoporous Platinum (2021)

Abstract Nanoporous electrodes are representative electrode materials for diverse applications, such as energy conversion devices and sensors. Recently, selectivity based on the size of ions arising from nanoporous structures has been applied to capacitive deionization, electrochemical supercapacitors, and conductometry. Herein, we explored the selectivity based on the size of the redox molecules on the electrochemical reaction at the nanoporous Pt electrode with extremely small (1–2 nm) and uniform pores by linear sweep voltammetry and AC impedance spectroscopy. Among primary alcohols with sizes smaller than that of the pores, we observed exceptional selective enhancement in the case of methanol due to its smallest size, despite all the alcohols having a similar reaction mechanism. These findings may provide an insight into electrochemical analysis and electrocatalysis based on nanoporous structures.
EFFECT OF TWO STOCKING DENSITIES ON THE GROWTH AND MORTALITY OF THE PINK ABALONE HALIOTIS CORRUGATA IN RECIRCULATING AND FLOW-THROUGH SYSTEMS (2007)

Traditional abalone culture is carried out in flow-through systems with water exchange rates between 200 and 2,400% of the total tank volume per day. These high volumes of water associated with abalone culture represents a constraint for the growth of this industry, and recirculating systems can become a viable alternative, because the water exchange rates are less than 10% of the total volume. The objective of this experiment was to evaluate the water quality parameters and the growth rate and mortality of the pink abalone cultured at two different densities, 10% (D1) and 30% (D2) in a flow-through system (S1) and two closed recirculating systems (S2 and S3). A total of 2,400 juvenile abalone (7.11 ± 2.0 g and 37.01 ± 3.4 mm) were distributed among the three experimental systems. The experiment lasted for 127 days. Weight and length of all the abalone were measured at the beginning and end of the experiment. Average water quality parameters for each system (S1, S2, and S3) were respectively: temperature (18.2 ± 1.4, 18.4 ± 1.9, and 18.1 ± 2.0°C); salinity (33.8 ± 1.0, 34.5 ± 1.2, and 34.2 ± 1.5‰); alkalinity (127 ± 13.2, 135 ± 13.7 and 131 ± 14.1 mg of CaCO3/L), total ammonia nitrogen (0.006 ± 0.02, 0.03 ± 0.07, and 0.02 ± 0.08 mg TAN/L) and nitrite (0 ± 0.00, 0.08 ± 0.07, and 0.07 ± 0.05 mg NO2/L). Growth rates in weight (g/d) were for S1D1 (0.027 ± 0.007), S1D2 (0.018 ± 0.001), S2D1 (0.007 ± 0.001), S2D3 (0.005 ± 0.000), S3D1 (0.007 ± 0.000) and S3S2 (0.009 ± 0.003), and growth rates in length (mm/d) were for S1D1 (0.038 ± 0.004), S1D2 (0.031 ± 0.002), S2D1 (0.013 ± 0.001), S2D3 (0.013 ± 0.000), S3D1 (0.002 ± 0.000), and S3D2 (0.024 ± 0.001) respectively. In flow through systems growth in length and width was density dependent. Mortality was higher in S3D2 than in any other treatment. A lower water exchange rate in closed systems could adversely affect growth and mortality. Abalone culture in closed recirculating systems could become another alternative for this industry, but more research is required.
Computational paper-based vertical flow assay for Lyme disease diagnosis (Conference Presentation) (2023)

We demonstrate a computational paper-based vertical flow assay (VFA) for point-of-care serodiagnosis of Lyme Disease (LD). We leveraged the multiplexed nature of the VFA and functionalized it using different antigen panels specific to LD. The paper-based VFA operation takes <20min, after which a hand-held reader captures an image of the sensing membrane. A deep learning-based algorithm processes the signals from multiple immunoreactions to output a diagnostic decision (i.e., positive/negative). This cost-effective computational VFA platform achieved a sensitivity and a specificity of 90.5% and 87%, respectively, demonstrating its promising potential for point-of-care diagnosis of LD even in resource-limited settings.
Functional Analysis of Human Sodium-Phosphate Transporter 4 (NPT4/SLC17A3) Polymorphisms (2011)

We analyzed the functional properties of five nonsynonymous single nucleotide polymorphisms (SNPs) in the sodium-phosphate transporter NPT4 gene (SLC17A3) using the Xenopus oocyte expression system. NPT4 variants carrying SNP V257F, G279R, or P378L exhibited reduced transport of [(14)C]para-aminohippurate, [(3)H]bumetanide, [(3)H]estrone sulfate, and [(14)C]urate, when each variant clone was expressed in the plasma membrane of oocytes. This study suggests the possibility that the genetic variation of NPT4 contributes to inter-individual differences in disposition of anionic drugs such as diuretics as well as certain endogenous organic anions such as urate.
Joint Optimization Framework for Learning with Noisy Labels (2018)

Deep neural networks (DNNs) trained on large-scale datasets have exhibited significant performance in image classification. Many large-scale datasets are collected from websites, however they tend to contain inaccurate labels that are termed as noisy labels. Training on such noisy labeled datasets causes performance degradation because DNNs easily overfit to noisy labels. To overcome this problem, we propose a joint optimization framework of learning DNN parameters and estimating true labels. Our framework can correct labels during training by alternating update of network parameters and labels. We conduct experiments on the noisy CIFAR-10 datasets and the Clothing1M dataset. The results indicate that our approach significantly outperforms other state-of-the-art methods.
Enhanced Lithiation of Doped 6H Silicon Carbide (0001) via High Temperature Vacuum Growth of Epitaxial Graphene (2012)

The electrochemical lithiation capacity of 6H silicon carbide (0001) is found to increase by over 1 order of magnitude following graphitization at 1350 °C in ultrahigh vacuum. Through several control experiments, this Li-ion capacity enhancement is correlated with SiC substrate doping and removal of the native oxide surface layer by thermal annealing, which renders both the bulk and surface electrically conductive. Characterization via multiple depth-resolved spectroscopies shows that lithium penetrates the activated SiC upon lithiation, the bulk lattice spacing does not appreciably change, and the surface structure remains largely intact. The electron energy-loss spectroscopy (EELS) extracted compositional ratio of Li to Si is approximately 1:1, which indicates an intrinsic bulk Li capacity in activated SiC of 670 mAh g–1. In addition, inelastic X-ray scattering spectra show changes in the Si chemical bonding configuration due to lithiation. X-ray scattering data show a decrease in the SiC Bragg peak intensity during lithiation, suggesting changes to the bulk crystallinity, whereas the emergence of a diffuse scattering feature suggests that lithiation is associated with the development of substrate defects. Overall, these results illustrate that the electrochemical capacity of a traditionally inert refractory material can be increased substantially via surface modification, thus suggesting a new strategy for improving the performance of next generation Li-ion battery electrodes.
1.3-μm InGaAlAs MQW RWG DFB lasers for uncooled 10-Gb/s datacom applications (2004)

It was experimentally demonstrated that a 1.3 /spl mu/m InGaAlAs MQW DFB RWG laser with low-resistance notch-free grating was directly modulated at 12.5 Gb/s and 10 Gb/s running at 115/spl deg/C.
Toward Finding Semantic Relations not Written in a Single Sentence: An Inference Method using Auto-Discovered Rules (2011)

Recent advances in automatic knowledge acquisition methods have enabled us to construct massive knowledge bases of semantic relations. Most previous work has focused on semantic relations explicitly expressed in single sentences. Our goal in this work is to obtain valid non-single sentence relation instances, which are not written in any single sentence and may not be even written in a large corpus. We develop a method to infer new semantic relation instances by applying auto-discovered inference rules, and show that our method inferred a considerable number of valid instances that were not written in single sentences even in 600 million Web pages. 1
Stability considerations and performance of wide dynamic range, ambient light active rejection circuits in photodiode receivers (2004)

We discuss several issues in active circuits for the rejection of ambient photocurrent over a wide dynamic range. These circuits are important for diffuse, free-space optical communications that operate over a variety of indoor and outdoor lighting conditions. In addition, we introduce, analyze and demonstrate a second-order rejection circuit based on a low noise gyrator in tandem with the input transimpedance amplifier. Excellent rejection is achieved over three orders of magnitude in ambient photocurrent. The measured transient performance agrees well with theory and simulations, and the rejection circuit was demonstrated with IrDA signals for outdoor applications in direct sunlight.
Selenate-iron complex in functionalized MCM-41 (2003)

Method MCM-41 was prepared by a conventional method using tetraethyl orthosilicate, cetyltrimethylammonium bromide and trimethylammonium hydroxide. The calcined powder was reacted with 3-aminopropyltrimethoxysilane at 383 K. This amino-functionalized MCM41 was treated with 0.1 M 2-propanol solution of FeCl3. The adsorption capacity of selenate was 117 mg (gadsorbent) -1 , when the ratios of N/Fe and Se/Fe were 3.8 and 1.5, respectively. EXAFS spectra of the Fe and Se K edges were measured on a BL-10 B in a transmission mode. The EXAFS spectra were acquired five times under the same measuring conditions and from the extracted spectra, the average χ (k) was calculated. The data were processed by a REX2000 program (Rigaku Co.) The EXAFS oscillation is extracted by fitting a cubic spline function through the post edge region. After normalization using the McMaster tables, the k 3 -weighted EXAFS, k 3 χ(k), in the 3 - 13 A -1 region was Fourier transformed into a radial distribution function. The amplitude and phase functions for Fe-N, Fe-Cl, Fe-Se and Se-O were calculated by FEFF 7.02 code. The curve fitting analysis was carried out between 4 and 12 A -1 in the k-space of inversely Fourier transformed spectra (from FT filtered at 0.77 < r < 3.65 A and 0.89 < r < 3.34 A for Fe K and Se K-edges, respectively.) Results and Discussion Figure 1 shows the EXAFS oscillations of Fe and Se K-edges before and after the adsorption of selenate. A large difference was found between Fe spectra while the profile was almost unchanged in Se spectra, suggesting that the coordination environment of Fe was considerably disturbed by selenate adsorption while Td structure of selenate was not much influenced by anchoring on Fe site.
Midline Body Actions and Leftward Spatial “Aiming” in Patients with Spatial Neglect (2015)

Spatial motor-intentional "Aiming" bias is a dysfunction in initiation/execution of motor-intentional behavior, resulting in hypokinetic and hypometric leftward movements. Aiming bias may contribute to posture, balance, and movement problems and uniquely account for disability in post-stroke spatial neglect. Body movement may modify and even worsen Aiming errors, but therapy techniques, such as visual scanning training, do not take this into account. Here, we evaluated (1) whether instructing neglect patients to move midline body parts improves their ability to explore left space and (2) whether this has a different impact on different patients. A 68-year-old woman with spatial neglect after a right basal ganglia infarct had difficulty orienting to and identifying left-sided objects. She was prompted with four instructions: "look to the left," "point with your nose to the left," "point with your [right] hand to the left," and "stick out your tongue and point it to the left." She oriented leftward dramatically better when pointing with the tongue/nose, than she did when pointing with the hand. We then tested nine more consecutive patients with spatial neglect using the same instructions. Only four of them made any orienting errors. Only one patient made >50% errors when pointing with the hand, and she did not benefit from pointing with the tongue/nose. We observed that pointing with the tongue could facilitate left-sided orientation in a stroke survivor with spatial neglect. If midline structures are represented more bilaterally, they may be less affected by Aiming bias. Alternatively, moving the body midline may be more permissive for leftward orienting than moving right body parts. We were not able to replicate this effect in another patient; we suspect that the magnitude of this effect may depend upon the degree to which patients have directional akinesia, spatial Where deficits, or cerebellar/frontal cortical lesions. Future research could examine these hypotheses.
Highly Sensitive Detection of Non-Labeled Peptides Using UV Excitation Thermal Lens Microscope/Liquid Chromatography (2007)

ペプチド等の生体由来成分の無標識高感度分離分析を目的として，励起光に波長266 nmの紫外光を有する紫外励起熱レンズ顕微鏡（UV-TLM）と液体クロマトグラフィー（LC）を組み合わせた測定システム（LC/UV-TLM）を構築した．構築したシステムの性能を評価するために，グラジエント溶出法を適応した際の熱レンズ信号に対する影響を検討した．熱レンズ信号は溶媒によって信号強度が大きく変化するため，グラジエント溶出法のような溶媒組成が時間とともに変化するような系では，その影響を検討する必要がある．水-アセトニトリル系グラジエントにおいては，アセトニトリルの体積分率が40% 未満では，熱レンズ測定に大きな影響を及ぼさないということが分かった．標準試料を用いてLC/UV-TLMの検出性能を評価したところ，通常の分光光度計を検出器としたシステムに比較して10倍以上高感度であることが分かった．
Pathways to health: a framework for health-focused research and practice (2006)

Public health research and practice is faced with three problems: 1) a focus on disease instead of health, 2) consideration of risk factor/disease relationships one at a time, and 3) attention to individuals with limited regard for the communities in which they live. We propose a framework for health-focused research and practice. This framework encompasses individual and community pathways to health while incorporating the dynamics of context and overall population vulnerability and resilience. Individual pathways to health may differ, but commonalities will exist. By understanding these commonalities, communities can work to support health-promoting pathways in addition to removing barriers. The perspective afforded by viewing health as a dynamic process instead of as a collection of risk factors and diseases expands the number of approaches to improving health globally. Using this approach, multidisciplinary research teams working with active community participants have the potential to reshape health and intervention sciences.
Universal Multi-Stage Precoding with Monomial Phase Rotation for Full-Diversity M2M Transmission (2015)

Machine-to-machine (M2M) communications have been considered as an important application to connect a massively large number of different devices in networks. In particular for M2M wireless networks, low latency and high reliability are of great importance. To fulfill the requirements, a diversity technique exploiting limited resources is proposed in this paper for short-message transmissions. The proposed method uses multiple stages of fast unitary transforms and diagonal phase rotations to achieve full- diversity gain. A monomial phase rotation is also proposed to facilitate an optimization of the precoding matrix. It is verified that the proposed four-stage precoding provides universal diversity gain irrespective of channel selectivity in time and frequency, without changing monomial parameters. In addition, it is shown that the four-stage precoding based on the discrete Haar transform (DHT) achieves a full diversity while the computational complexity is significantly reduced from a log- linear order to a linear order compared to the other unitary transforms such as the discrete Fourier transform (DFT).