gebhart/patrepeval huggingface dataset:
Immunogenicity and tolerogenicity of self-major histocompatibility complex peptides. (1990)

Mechanisms involved in self-antigen processing and presentation are crucial in understanding the induction of self-tolerance in the thymus. We examined the immunogenicity of determinants from major histocompatibility complex (MHC) molecules that are expressed in the thymus and have tested peptides derived from the polymorphic regions of class I and class II molecules. We found that two peptides corresponding to NH2 termini of the class II alpha and beta chains (Ak alpha 1-18 and Ak beta 1-16) could bind to self-Ak molecules with high affinity and, surprisingly, were immunogenic in that they could elicit strong proliferative T cell responses in B10.A mice (Ak, Ek). Neonatal injection of peptide Ak beta 1-16 resulted in complete unresponsiveness to this peptide at 8 wk of age showing that these T cells were susceptible to tolerance induction. We have also tested certain class I MHC peptides and showed that some can interact efficiently with class II MHC peptides to induce an autoreactive T cell proliferative response. Among these class I peptides is one (Dd 61-85) that has the capacity to bind to self-Ia without being immunogenic, and therefore represents an MHC determinant that had induced thymic self-tolerance. We conclude that some self-MHC molecules can be processed into peptides that can be presented in the context of intact class II molecules at the surface of antigen-presenting cells. Autoreactive T cells recognizing optimally processed self-peptide/MHC complexes are eliminated during development, whereas other potentially autoreactive T cells escape clonal inactivation or deletion. Incomplete tolerance to self-antigens enriches the T cell repertoire despite the fact that such T cells may eventually become involved in autoimmune disease.
<title>Quantitative comparison of temperature/emissivity algorithm performance using SEBASS data</title> (1999)

Algorithms have been developed for estimating temperature and emissivity of terrestrial targets from airborne LWIR hyperspectral radiance data. This report documents a performance comparison of these algorithms. Data collected at the Department of Energy's Atmospheric Radiation Measurement Site by the Spatially-Enhanced Broadband Array Spectrograph System (SEBASS) was used. SEBASS is a 128-band hyperspectral instrument covering a wavelength range of 7.3 to 13.6 micrometers. Spectra of natural and man-made objects were processed by Thermal Log Residual, Alpha Log Residual, Normalized Emissivity, Inverse Wave, Graybody, EOS/ASTER, N- Temperature, and Max-Min Difference methods. Temperature and emissivity estimates are compared to ground truth measurements. Sample results and performance statistics are presented.
Secret key generation using channel quantization with SVD for reciprocal MIMO channels (2016)

The generation of secret keys from reciprocal wireless channel by exploiting their randomness nature, is an emerging area of interest to provide secure communication. One of the main challenges in this domain is to increase the secret key length, extracted from the shared channel coefficients between two legitimate communication parties, while maintaining its randomness and uniformity. In this work, we develop a practical key generation method, based on channel quantization with singular value decomposition (CQSVD), which is capable of significantly increasing the generated secret key in MIMO systems. This is achieved through quantizing the phases and amplitudes of the estimated MIMO channel coefficient's matrix by using an alternative form of SVD, where the key sequence is extracted from the orthogonal basis functions of the decomposed channel. In this method, it is shown that for an M ×M antenna system, with M <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> independent channel fading coefficients, a secret key sequence of length 2M <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> can be generated. The extracted key sequence is transformed to a random phase sequence, which is then used to manipulate the transmitted data on a symbol level basis rather than bit level-basis, to provide more secure communication. The comparative simulation results show that the proposed CQSVD method outperforms the state of the art secret key generation methods.
Hypoxia signaling during acute lung injury (2015)

Acute lung injury (ALI) is an inflammatory lung disease that manifests itself in patients as acute respiratory distress syndrome and thereby contributes significantly to the morbidity and mortality of patients experiencing critical illness. Even though it may seem counterintuitive, as the lungs are typically well-oxygenated organs, hypoxia signaling pathways have recently been implicated in the resolution of ALI. For example, functional studies suggest that transcriptional responses under the control of the hypoxia-inducible factor (HIF) are critical in optimizing alveolar epithelial carbohydrate metabolism, and thereby dampen lung inflammation during ALI. In the present review we discuss functional roles of oxygenation, hypoxia and HIFs during ALI, mechanisms of how HIFs are stabilized during lung inflammation, and how HIFs can mediate lung protection during ALI.
Clinician predictions of intensive care unit mortality* (2004)

Physician estimates of intensive care unit survival < 10% are associated with subsequent life support limitation and more powerfully predict intensive care unit mortality than illness severity, evolving or resolving organ dysfunction, and use of inotropes or vasopressors.
Ensemble Modeling of Substrate Binding to Cytochromes P450:  Analysis of Catalytic Differences between CYP1A Orthologs<sup>,</sup> (2007)

A novel application of modeling and docking approaches involving ensembles of homology models is used to understand structural bases underlying subtle catalytic differences between related cytochromes P450 (CYPs). Mammalian CYP1A1s and fish CYP1As are orthologous enzymes with similar substrate preferences. With some substrates (3,3',4,4'-tetrachlorobiphenyl, TCB) oxidation rates differ by orders of magnitude, while others (e.g., benzo[a]pyrene; B[a]P) are oxidized at similar rates but with somewhat differing regiospecificity. These two environmental chemical substrates (TCB and B[a]P) as well as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) were docked to multiple models of rat, human, scup, and/or killifish CYP1As, based on multiple templates, retaining multiple poses from each model, giving ensembles of docked poses for each species. With TCB, more poses were observed closer to the heme in ensembles of rat or human CYP1A1 than of killifish CYP1A. Analysis of interacting residues suggested that differences in TCB pose distributions are due primarily to Leu387 and Val230 in killifish CYP1A. In silico mutations L387V and V230G enabled TCB to dock closer to the heme in killifish CYP1A. Mutating additional interacting residues (Ala127, Thr233, Asn317, and Tyr386) of killifish CYP1A to the corresponding residues of human CYP1A1 resulted in TCB pose distributions nearly identical with those of human CYP1A1. Docking of TCDD to sets of consensus models of killifish, rat, and human CYP1As showed species differences similar to those with TCB, but with further structural constraints possibly contributing to slower oxidation of TCDD. Docking B[a]P to sets of consensus models of the human and fish CYP1As yielded frequencies of substrate orientations correlating with known regiospecificities for metabolism of B[a]P by these enzymes. The results demonstrate the utility of this ensemble modeling method, which can account for uncertainty inherent in homology modeling and docking by producing statistical distributions of ligand positions.
Molecular tectonics: heterometallic (Ir,Cu) grid-type coordination networks based on cyclometallated Ir(<scp>iii</scp>) chiral metallatectons (2015)

A chiral-at-metal Ir(III) organometallic metallatecton was synthesised as a racemic mixture and as enantiopure complexes and combined with Cu(II) to afford a heterobimetallic (Ir,Cu) grid-type 2D coordination network.
Field controlled thyristors-a new family of power semiconductors with advanced circuitry (2003)

Field-controlled thyristors (FCTs) exhibiting true normally-off characteristics without deterioration of the on-state are reported. Snubberless switching capability has been extended to 1200 V and 16 A (200 A/cm/sup 2/, dynamic avalanche). A novel latching mechanism, called current punchthrough, that limits the turn-off current is presented. Typical devise characteristics are reported for both a normally-on FCT with lifetime control (dV/dt=10 kV/ mu s) and a normally-off FCT without lifetime control (dV/dt=600 V/ mu s). The influence of the drive circuit (MOSFET-FCT and thyristor-FCT cascades) is discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Continuous Blood Pressure Measurement From Invasive to Unobtrusive: Celebration of 200th Birth Anniversary of Carl Ludwig (2016)

The year 2016 marks the 200th birth anniversary of Carl Friedrich Wilhelm Ludwig (1816-1895). As one of the most remarkable scientists, Ludwig invented the kymograph, which for the first time enabled the recording of continuous blood pressure (BP), opening the door to the modern study of physiology. Almost a century later, intraarterial BP monitoring through an arterial line has been used clinically. Subsequently, arterial tonometry and volume clamp method were developed and applied in continuous BP measurement in a noninvasive way. In the last two decades, additional efforts have been made to transform the method of unobtrusive continuous BP monitoring without the use of a cuff. This review summarizes the key milestones in continuous BP measurement; that is, kymograph, intraarterial BP monitoring, arterial tonometry, volume clamp method, and cuffless BP technologies. Our emphasis is on recent studies of unobtrusive BP measurements as well as on challenges and future directions.
The Holdout Randomization Test: Principled and Easy Black Box Feature Selection (2018)

We consider the problem of feature selection using black box predictive models. For example, high-throughput devices in science are routinely used to gather thousands of features for each sample in an experiment. The scientist must then sift through the many candidate features to find explanatory signals in the data, such as which genes are associated with sensitivity to a prospective therapy. Often, predictive models are used for this task: the model is fit, error on held out data is measured, and strong performing models are assumed to have discovered some fundamental properties of the system. A model-specific heuristic is then used to inspect the model parameters and rank important features, with top features reported as discoveries. However, such heuristics provide no statistical guarantees and can produce unreliable results. We propose the holdout randomization test (HRT) as a principled approach to feature selection using black box predictive models. The HRT is similar to a permutation test, where each random reshuffling is a draw from the complete conditional distribution of the feature being tested. The HRT is model agnostic and produces a valid $p$-value for each feature, enabling control over the false discovery rate (or Type I error) for any predictive model. Further, the HRT is computationally efficient and, in simulations, has greater power than a competing knockoffs-based approach. Code is available at this https URL.
Multibeam antenna using a phased array fed reflector (2002)

Communication satellites achieve global communication coverage by using high gain multibeam satellite antennas. In geostationary satellites, large reflector antennas fed by cluster feeds arranged on the focal plane are common to meet the requirement of high gain and fixed multibeams. Adopting phased array antennas for a geostationary satellite is attractive because they offer power reallocation according to traffic demand, reconfigurability of beams, and maintainability of beam pointing. This paper provides an analytical study of the phased array fed single reflector antenna and clarifies that the feed element number is the most important design parameter Calculated radiation properties prove the usefulness of the antenna as a large scale multibeam antenna.
On Multihop Distances in Wireless Sensor Networks with Random Node Locations (2009)

Location and intersensor distance estimations are important functions for the operation of wireless sensor networks, especially when protocols can benefit from the distance information prior to network deployment. The maximum multihop distance that can be covered in a given number of hops in a sensor network is one such parameter related with coverage area, delay, and minimal multihop transmission energy consumption estimations. In randomly deployed sensor networks, intersensor distances are random variables. Hence, their evaluations require probabilistic methods, and distance models should involve investigation of distance distribution functions. Current literature on analytical modeling of the maximum distance distribution is limited to 1D networks using the Gaussian pdf. However, determination of the maximum multihop distance distribution in 2D networks is a quite complex problem. Furthermore, distance distributions in 2D networks are not accurately modeled by the Gaussian pdf. Hence, we propose a greedy method of distance maximization and evaluate the distribution of the obtained multihop distance through analytical approximations and simulations.
Berberine affects mitochondrial activity and cell growth of leukemic cells from chronic lymphocytic leukemia patients (2020)

B-cell chronic lymphocytic leukemia (CLL) results from accumulation of leukemic cells that are subject to iterative re-activation cycles and clonal expansion in lymphoid tissues. The effects of the well-tolerated alkaloid Berberine (BRB), used for treating metabolic disorders, were studied on ex-vivo leukemic cells activated in vitro by microenvironment stimuli. BRB decreased expression of survival/proliferation-associated molecules (e.g. Mcl-1/Bcl-xL) and inhibited stimulation-induced cell cycle entry, irrespective of TP53 alterations or chromosomal abnormalities. CLL cells rely on oxidative phosphorylation for their bioenergetics, particularly during the activation process. In this context, BRB triggered mitochondrial dysfunction and aberrant cellular energetic metabolism. Decreased ATP production and NADH recycling, associated with mitochondrial uncoupling, were not compensated by increased lactic fermentation. Antioxidant defenses were affected and could not correct the altered intracellular redox homeostasis. The data thus indicated that the cytotoxic/cytostatic action of BRB at 10-30 μM might be mediated, at least in part, by BRB-induced impairment of oxidative phosphorylation and the associated increment of oxidative damage, with consequent inhibition of cell activation and eventual cell death. Bioenergetics and cell survival were instead unaffected in normal B lymphocytes at the same BRB concentrations. Interestingly, BRB lowered the apoptotic threshold of ABT-199/Venetoclax, a promising BH3-mimetic whose cytotoxic activity is counteracted by high Mcl-1/Bcl-xL expression and increased mitochondrial oxidative phosphorylation. Our results indicate that, while CLL cells are in the process of building their survival and cycling armamentarium, the presence of BRB affects this process.
New Predictive Equations for Dynamic Modulus and Phase Angle Using a Nonlinear Least-Squares Regression Model (2014)

The sigmoidal equation is usually used to make predictions for dynamic modulus (|E*|), but equations to predict phase angle are still unavailable. In this study, equations to predict both the |E*| and phase angle for asphalt mixtures were proposed. The expression for the |E*| prediction in the proposed model is the same as the sigmoidal equation, while the predictive equation for the phase angle was derived based on the Kramers-Kronig equation, which reveals the relation between the |E*| and phase angle. The new predictive equation set is called the initial proposed (IP) model, as differentiated from the modified proposed (MP) model, in which an additional coefficient was given to the equation. To validate the IP and MP models, the equations were used to fit the |E*| and phase angle data at a wide range of temperatures and frequencies from 14 different asphalt mixtures. The coefficients and shift factors in the equations were obtained from a nonlinear least-squares optimization using optimization software. The predicted results using the sigmoidal equation and the IP and MP models were compared through the measured |E*| and phase angle values, |E*| and phase angle master curves, shift factors, Cole-Cole plots, and black space diagrams. The results showed that both the IP and MP models predicted the |E*| and phase angle well, and the MP model made more precise predictions for both the |E*| and phase angle as compared to the IP model. The MP model and the sigmoidal equation obtained close |E*| master curves and shift factors but slightly differed from the IP model. In addition, the IP and MP models successfully predicted the existence of the maximum and minimum values of the |E*| and phase angle through the construction of master curves. The proposed models developed in this study can be an effective approach to predict the |E*| and phase angle in a wide range of temperatures and frequencies for asphalt mixtures.
ANALYSIS AND VISUALIZATION OF FLOW FIELDS USING INFORMATION-THEORETIC TECHNIQUES AND GRAPH-BASED REPRESENTATIONS (2015)

Three-dimensional flow visualization plays an essential role in many areas of science and engineering, such as aero- and hydro-dynamical systems which dominate various physical and natural phenomena. For popular methods such as the streamline visualization to be effective, they should capture the underlying flow features while facilitating user observation and understanding of the flow field in a clear manner. My research mainly focuses on the analysis and visualization of flow fields using various techniques, e.g. information-theoretic techniques and graph-based representations. Since the streamline visualization is a popular technique in flow field visualization, how to select good streamlines to capture flow patterns and how to pick good viewpoints to observe flow fields become critical. We treat streamline selection and viewpoint selection as symmetric problems and solve them simultaneously using the dual information channel [81]. To the best of my knowledge, this is the first attempt in flow visualization to combine these two selection problems in a unified approach. This work selects streamline in a view-independent manner and the selected streamlines will not change for all viewpoints. My another work [56] uses an information-theoretic approach to evaluate the importance of each streamline under various sample viewpoints and presents a solution for view-dependent streamline selection that guarantees coherent streamline update when the view changes gradually. When projecting 3D streamlines to 2D images for viewing, occlusion and clutter become inevitable. To address this challenge, we design FlowGraph [57, 58], a novel compound graph representation that organizes field line clusters and spatiotemporal regions hierarchically for occlusion-free and controllable visual exploration. We enable observation and exploration of the relationships among field line clusters, spatiotemporal regions and their interconnection in the transformed space. Most viewpoint selection methods only consider the external viewpoints outside of the flow field. This will not convey a clear observation when the flow field is clutter on the boundary side. Therefore, we propose a new way to explore flow fields by selecting several internal viewpoints around the flow features inside of the flow field and then generating a B-Spline curve path traversing these viewpoints to provide users with closeup views of the flow field for detailed observation of hidden or occluded internal flow features [54]. This work is also extended to deal with unsteady flow fields. Besides flow field visualization, some other topics relevant to visualization also attract my attention. In iGraph [31], we leverage a distributed system along with a tiled display
ABNER: an open source tool for automatically tagging genes, proteins and other entity names in text (2005)

ABNER (A Biomedical Named Entity Recognizer) is an open source software tool for molecular biology text mining. At its core is a machine learning system using conditional random fields with a variety of orthographic and contextual features. The latest version is 1.5, which has an intuitive graphical interface and includes two modules for tagging entities (e.g. protein and cell line) trained on standard corpora, for which performance is roughly state of the art. It also includes a Java application programming interface allowing users to incorporate ABNER into their own systems and train models on new corpora.
Retention Behavior of Linear and Ring Polystyrene at the Chromatographic Critical Condition (2001)

Chromatographic retention of linear and ring polystyrene was investigated near the chromatographic critical condition. Reversed phase silica columns of four different pore sizes were employed to examine the pore size dependence. Adjusting the column temperature, the critical condition for linear polystyrene was searched for each column with a mixed mobile phase of CH2Cl2/CH3CN (57/43 v/v). It was practically impossible to establish an unambiguous critical condition with a single pore size column for a wide molecular weight range of polystyrenes, in particular with narrow pore size columns. At the best available condition, retentions of nine different molecular weight ring polystyrenes were measured relative to their linear precursors for each pore-sized column. As predicted theoretically, the partition coefficient (K) of ring polymers vs the size ratio of polymer chain to pore (R/d) shows a good linear relationship in the large pore regime (R/d ≪ 1). This linearity is found to be universal for all the pore sizes, which is consistent with the theoretical prediction. However, the K vs R/d dependency at the large pore regime did not follow the theoretical prediction quantitatively. In the narrow-pore regime (R/d ≫ 1) the experimental results did not follow the theory for ideal-chain ring macromolecules even qualitatively. To explain the observed chromatographic behavior at R/d ≫ 1, the scaling theory accounting for the polymer excluded volume was used, and the definition of the critical condition was revised. This analysis gave some keys for understanding the results at R/d ≫ 1 and revealed the possible nonequivalence of the conditions for theory and experiment as the most probable reason for observed discrepancies.
A 125MHz 8b digital-to-phase converter (2003)

A digital-to-phase converter (DPC) generates a 125MHz clock with phase shift controlled by an 8b digital input. Averaging resistor rings are used for phase interpolation and phase error reduction by averaging. Implemented in a standard 0.35 /spl mu/m CMOS technology, the DPC achieves /spl plusmn/1 LSB differential nonlinearity and /spl plusmn/2 LSB integral nonlinearity. Power dissipation is 110mW with a 3.3V supply.
Simple and Efficient: Validation of a Cotton Wick Electrode for Animal Electroretinography (2010)

This cotton electrode is simple to make and easy to place. It provides reliable recordings during the entire life span of the animal and reliable comparisons between contralateral eyes, thus providing a powerful tool for ERG studies.