gebhart/patrepeval huggingface dataset:
Biomarkers are used to predict quantitative metabolite concentration profiles in human red blood cells (2017)

Deep-coverage metabolomic profiling has revealed a well-defined development of metabolic decay in human red blood cells (RBCs) under cold storage conditions. A set of extracellular biomarkers has been recently identified that reliably defines the qualitative state of the metabolic network throughout this metabolic decay process. Here, we extend the utility of these biomarkers by using them to quantitatively predict the concentrations of other metabolites in the red blood cell. We are able to accurately predict the concentration profile of 84 of the 91 (92%) measured metabolites (p < 0.05) in RBC metabolism using only measurements of these five biomarkers. The median of prediction errors (symmetric mean absolute percent error) across all metabolites was 13%. The ability to predict numerous metabolite concentrations from a simple set of biomarkers offers the potential for the development of a powerful workflow that could be used to evaluate the metabolic state of a biological system using a minimal set of measurements.
Figure S1 from Identification of Recurrent <i>FGFR3–TACC3</i> Fusion Oncogenes from Lung Adenocarcinoma (2023)

&lt;p&gt;Figure S1. Sequencing chromatogram of the two RIT1mutations identified. A. D51Y mutation identified in sample J2-113, occurring in the Switch I domain in the RIT1 gene. B. M90V mutation identified in sample CG-67, occurring in the Switch II domain of the RIT1 gene.&lt;/p&gt;
Di-μ-chlorodichlorobis(η2-ethene)-diplatinum (2014)

[12073-36-8] C4H8Cl4Pt2 (MW 588.10) InChI = 1S/2C2H4.4ClH.2Pt/c2*1-2;;;;;;/h2*1-2H2;4*1H;;/q;;;;;;2*+2/p-4 InChIKey = XBLBDYCZFZESPN-UHFFFAOYSA-J (reagent for cyclopropane isomerization and cleavage, synthesis of platinacyclobutanes, hydration of alkynes) Alternate Name: Zeise's dimer. Form Supplied in: commercially available as orange crystals. Preparative Methods: although commercially available, the title compound is also readily prepared by stirring an acidic aqueous solution of [PtCl4]2− under an atmosphere of ethylene (100 psi) at rt for 48 h to give Zeise's salt K[Pt(η2-C2H4)Cl3]·H2O. This salt is then dissolved in EtOH and treated with concentrated HCl. After shaking for 2 min the mixture is then filtered to remove KCl, and evaporated while slowly warming to 60 °C. This gives an essentially quantitative yield of Zeise's dimer based on [PtCl4]2−.1
Impaired Ionizing Radiation-induced Activation of a Nuclear Signal Essential for Phosphorylation of c-Jun by Dually Phosphorylated c-Jun Amino-terminal Kinases in Ataxia Telangiectasia Fibroblasts (1998)

The c-Jun amino-terminal kinases (JNKs) participate in intracellular signaling in response to cytokines and cellular stresses. JNKs are activated by phosphorylation on two critical residues, the threonine 183 and tyrosine 185, within the TPY motif. The activated JNKs, in turn, phosphorylate the nuclear protein c-Jun, a major component of the transcription factor AP1. In vitro studies have revealed a defect in ionizing radiation-induced activation of the JNK signaling pathway in lymphoblastoid cells from individuals with ataxia telangiectasia (AT). However, the biochemical basis for this signaling defect is not clear. Here, we show that ionizing radiation induces the phosphorylation of endogenous c-Jun in normal fibroblasts but not in AT fibroblasts. The p46 isoforms of dually phosphorylated JNKs were detected in the nuclei of both normal and AT fibroblasts following exposure to ionizing radiation or sham radiation. However, c-Jun kinase activity was detected in normal cells but not in AT cells. Furthermore, an exogenous purified active JNK protein was able to phosphorylate endogenous c-Jun in nuclear extracts only of normal cells and only after the cells were irradiated. Electrophoretic mobility shift assays also showed that the ionizing radiation-induced increase in the DNA binding activity of AP1 observed in normal cells was absent or markedly reduced in AT cell lines. These data suggest that the defect in ionizing radiation-induced signaling through c-Jun in AT cells is the result of impaired function of an unknown nuclear protein or proteins that negatively regulate both JNK and c-Jun.
Data from Dolaflexin: A Novel Antibody–Drug Conjugate Platform Featuring High Drug Loading and a Controlled Bystander Effect (2023)

&lt;div&gt;Abstract&lt;p&gt;After significant effort over the last 30 years, antibody–drug conjugates (ADC) have recently gained momentum as a therapeutic modality, and nine ADCs have been approved by the FDA to date, with additional ADCs in late stages of development. Here, we introduce dolaflexin, a novel ADC technology that overcomes key limitations of the most common ADC platforms with two key features: a higher drug-to-antibody ratio and a novel auristatin with a controlled bystander effect. The novel, cell permeable payload, auristatin F-hydroxypropylamide, undergoes metabolic conversion to the highly potent, but less cell permeable auristatin F to balance the bystander effect through drug trapping within target cells. We conducted studies in mice, rats, and cynomolgus monkeys to complement &lt;i&gt;in vitro&lt;/i&gt; characterization and contrasted the performance of dolaflexin with regard to antitumor activity, pharmacokinetic properties, and safety in comparison with the ADC platform utilized in the approved ADC ado-trastuzumab emtansine (T-DM1). A HER2-targeted dolaflexin ADC was shown to have a much lower threshold of antigen expression for potent cell killing &lt;i&gt;in vitro&lt;/i&gt;, was effective &lt;i&gt;in vivo&lt;/i&gt; in tumors with low HER2 expression, and induced tumor regressions in a xenograft model that is resistant to T-DM1.&lt;/p&gt;&lt;/div&gt;
Overall Survival and Durable Responses in Patients With BRAF V600–Mutant Metastatic Melanoma Receiving Dabrafenib Combined With Trametinib (2016)

Dabrafenib plus trametinib results in a median OS of more than 2 years in BRAF inhibitor-naive patients with BRAF V600 mutation-positive metastatic melanoma, and approximately 20% were progression free at 3 years. Durable responses occurred in patients with good prognostic features at baseline, which may be predictive.
Controlling the Emission of Blue-Emitting Complexes by Encapsulation within Zeolite Cavities (2004)

Blue light-emitting boron 8-hydroxyquinolinate and 8-hydroxyquinaldinate complexes have been formed inside boron zeolites Beta, MCM-22, and ferrierite, and on layered ITQ-2 and ITQ-6 zeolites starting from the corresponding ligands and boron dislodged from framework positions. The luminescence properties, i.e., emission intensity, maximum wavelength, and lifetime of the ship-in-a-bottle quinolinate complexes are strongly modulated by the zeolite host. Besides the species responsible for the photoluminescence, other longer-lived transient species, presumably related to electron transport, are also photochemically generated and have been detected by laser flash photolysis.
Immunoglobulin gene rearrangements in remission bone marrow specimens from patients with acute lymphoblastic leukemia (1986)

Recombinant DNA probes for the joining (JH) segment of the immunoglobulin heavy chain gene were used to detect molecular rearrangements of this gene in the DNA of bone marrow cells obtained during remission of acute lymphoblastic leukemia (ALL). This molecular approach was optimized and found to exceed the sensitivity of conventional morphologic screening for detecting residual leukemia cells; one leukemic cell in 500 normal nucleated bone marrow cells was easily detected using this approach. In the present study, bone marrow from three of seven patients in complete clinical remission (defined morphologically) contained leukemic cells in these proportions. This analysis may be of use in evaluating the status of clinical remission in selected ALL patients.
Coking-Resistant Iron Catalyst in Ethane Dehydrogenation Achieved through Siliceous Zeolite Modulation (2020)

Nonoxidative dehydrogenation is promising for production of light olefins from shale gas, but current technology relies on precious Pt or toxic Cr catalysts and suffers from thermodynamically oriented coke formation. To solve these issues, the earth-abundant iron catalyst is employed, where Fe species are effectively modulated by siliceous zeolite, which is realized by the synthesis of Fe-containing MFI siliceous zeolite in the presence of ethylenediaminetetraacetic sodium (FeS-1-EDTA). Catalytic tests in ethane dehydrogenation show that this catalyst has a superior coke resistance in a 200 h run without any deactivation with extremely high activity and selectivity (e.g., 26.3% conversion and over 97.5% selectivity to ethene in at 873 K, close to the thermodynamic equilibrium limitation). Multiple characterizations demonstrate that the catalyst has uniformly and stably isolated Fe sites, which improves ethane dehydrogenation to facilitate the fast desorption of hydrogen and olefin products in the zeolite micropores and hinders the coke formation, as also identified by density functional calculations.
Plasma Extracellular Vesicles Play a Role in Immune System Modulation in Minimal Hepatic Encephalopathy (2022)

Minimal hepatic encephalopathy (MHE) is associated with changes in the immune system including an increased pro-inflammatory environment and altered differentiation of CD4+ T lymphocytes. The mechanisms remain unknown. Changes in extracellular vesicle (EV) cargo including proteins and miRNAs could play a main role as mediators of immune system changes associated with MHE. The aim was to assess whether plasma EVs from MHE patients played a role in inducing the pro-inflammatory environment and altered differentiation of CD4+ T lymphocyte subtypes in MHE patients. We characterized the miRNA and protein cargo of plasma EVs from 50 cirrhotic patients (27 without and 23 with MHE) and 24 controls. CD4+ T cells from the controls were cultured with plasma EVs from the three groups of study, and the cytokine release and differentiation to CD4+ T-cell subtypes were assessed. Plasma EVs from MHE patients had altered miRNA and protein contents, and were enriched in inflammatory factors compared to the controls and patients without MHE. EVs from MHE patients modulated the expression of pro-inflammatory IL-17, IL-21, and TNF-α and anti-inflammatory TGF-β in cultured CD4+ T lymphocytes, and increased the proportion of Th follicular and Treg cells and the activation of Th17 cells. In conclusion, plasma EVs could play an important role in the induction of immune changes observed in MHE.
Extended Phase-Matching of High Harmonics Driven by Focusing Light in Planar Waveguide (2012)

We show, theoretically and experimentally, that the regime of pressure-tuning phase-matching in high harmonic generation is extended to shorter wavelengths when the process is driven by focusing light (positive intensity gradient) within a planar waveguide.
Will Systems Biology Deliver Its Promise and Contribute to the Development of New or Improved Vaccines? (2017)

During the last decade, several high-throughput technologies have been applied to gather deeper understanding on the biological events elicited by vaccination. The main goal of systems biology is to integrate different sources of data and extract biologically meaningful information. This holistic approach has provided new insights on the impact that the innate immune status has on vaccine responsiveness. Other factors like chronic infections, age, microbiome, and metabolism can influence the outcome of vaccination, and systems biology offers unique opportunities to expand our understanding of their role on the immune response. However, a few challenges that still need to be overcome will be discussed.
A Facile Solution‐Doping Method to Improve a Low‐Temperature Zinc Oxide Precursor: Towards Low‐Cost Electronics on Plastic Foil (2014)

Optimization of thin‐film transistors performance is usually accompanied by an increase of the process temperature. This work presents a method to raise the field effect mobility by a factor of 3 without a change of the process parameters. The modification involves a solution doping process where an ammine zinc complex is formed in the presence of metal ions of the 13 th group, namely gallium and indium. Morphological studies, including scanning electron microscopy and atomic force microscopy, reveal the difference among the resulting films. Moreover, X‐ray diffraction results show that the doping affects the preferred orientation of the zinc oxide crystals in the resulting film. The electrical properties vary distinctly and are best for a solution doped with both gallium and indium. With a double‐layer system the performance of this new precursor exceeds field effect mobility values of 1 cm 2 V −1 s −1 after a maximum process temperature of 160 °C.
Harmonic Envelope Detection and Amplitude Estimation Using Map Seeking Circuits (2006)

In this paper we introduce the use of map-seeking circuits for auditory pattern detection and classification. A map-seeking circuit is a signal processing structure used to detect a desired feature in a mixture by iteratively transforming, superposing, and comparing the composite mixture with a pattern template. The result is a mapping between the template and the position of the matched feature in the mixture. The iterative detection process is inspired by the neural connections in the human visual system. A particularly important feature of map-seeking classification is that the search operates on an additive superposition of allowable transformations of the desired feature vector, giving a linear increase in computation with increasing image complexity, rather than a brute-force feature detection that increases in computation geometrically
Rivaroxaban vs. vitamin K antagonists for cardioversion in atrial fibrillation (2014)

NCT01674647.
Aminoglycoside-modifying enzyme of an antibiotic-producing bacterium acts as a determinant of antibiotic resistance in Escherichia coli. (1977)

Bacillus circulans NRRL B-3312, a nonpathogenic bacterium that produces the aminoglycoside antibiotic butirosin, is known to contain an aminoglycoside phosphotransferase that is similar to the neomycin phosphotransferases of clinically isolated antibiotic-resistant bacteria. Purified DNAs from B. circulans and the plasmid ColE1-ApR were digested with EcoRI endonuclease and the resulting fragments covalently joined with polynucleotide ligase. The recombined DNA was used to transform E. coli and ampicillin-neomycin resistant colonies were selected. Analysis of several clones indicated that neomycin resistance in the E. coli transformants was due to the presence of the B. circulans phosphotransferase gene. This observation is consistent with the notion that anitbiotic-modifying enzymes from antibiotic-producing organisms may be the sources of antibiotic resistance in plasmid-containing bacteria.
Doubly-selective channels: estimation, capacity, and space-time coding (2003)

High data rates give rise to frequency-selective propagation, while carrier frequency-offsets and mobility-induced Doppler shifts introduce time-selectivity in wireless communication links. As the transmission rates and mobility increase, future generations of wireless communication systems will have to cope with critical performance-limiting challenges that originates from propagation channels exhibiting time- and frequency-selectivity (double-selectivity). This research investigation focuses on the basic properties and principles of doubly-selective channels: modeling, estimation, diversity, and capacity. In a nutshell, the research in this dissertation includes: (i) derivation of a basis expansion to model physical doubly-selective channels; (ii) design of linearly coded transmissions with maximum diversity to combat fading of doubly-selective channels; (iii) development of data-aided (training-based) channel estimation and delineation of information-theoretic aspects of doubly-selective propagation with non-coherent receivers; (iv) study of multi-antenna space-time coded transmissions over doubly-selective channels to collect multi-dimensional diversity; and (v) design for multi-antenna systems to achieve full rate and full diversity. The findings impact the basic research, and facilitate the design of mobile wireless systems communicating over interference-rich propagation media.
Segmentation of plaques in sequences of ultrasonic B-mode images of carotid arteries based on motion estimation and Nakagami distributions (2009)

The goal of this work was to perform a segmentation of atherosclerotic plaques in view of evaluating its burden and to provide boundaries for computing properties such as the plaque elasticity distribution (elastogram). The echogenicity of a region of interest comprising the plaque, the lumen, and the adventitia in an ultrasonic B-mode image was modeled by a mixture of three Nakagami distributions. To each of these three tissues corresponds a specific weighted sum of these three distributions, which yields the likelihood of a Bayesian model. The prior of that model includes a geometrical smoothness constraint, as well as an original spatio-temporal cohesion constraint, based on the estimation of the motion field of the plaque in the video sequence. The Maximum A Posteriori (MAP) of the proposed model was computed with a variant of the Exploration/Selection (ES) algorithm. The starting point is a manual segmentation of the first frame. The main contribution of this paper is the estimation of the motion field and its integration into the prior of the Bayesian model. The proposed method was quantitatively compared with manual segmentations of all frames by an expert technician. Various measures were used for this evaluation, including the sensitivity and specificity of the receiver operating characteristic (ROC) analysis, and the error of area of the plaque. Results were evaluated on 21 sequences of 18 symptomatic patients (for a total of 2078 images). We report a sensitivity of 87.7 ± 5.9%, a specificity of 94.6 ± 3.2%, a kappa index of 88.1 ± 4.7%, an error of the plaque area of -0.79 ± 8.0%, and an absolute error of the plaque area of 6.61 ± 4.8%, which compare favorably with previous studies.
A Novel Channel Estimation in T-DMB Receivers (2007)

This paper proposes noise reduction methods to improve the channel estimation performance in terrestrial-digital multimedia broadcasting (T-DMB) receivers. In the T-DMB, the channel estimation is performed by the pilot signal extraction and the channel coefficient estimation. Since the performance of the channel estimation highly depends on the estimated channel coefficients whose accuracy is associated with the received signal-to-noise ratio (SNR), it is important to reduce noise existing at the estimated channel coefficients. To reduce such noise components, various noise reduction methods of the estimated channel coefficients based on the Ad-point weighted moving average are proposed. Computer simulations show that the proposed methods improve the estimation performance by more than 2 to 3 dB in terms of the symbol error rate after equalization.
Bit Whisperer: Enabling Ad-hoc, Short-range, Walk-Up-and-Share Data Transmissions via Surface-restricted Acoustics (2021)

Bluetooth requires device pairing to ensure security in data transmission, encumbering a number of ad-hoc, transactional interactions that require both ease-of-use and “good enough” security: e.g., sharing contact information or secure links to people nearby. We introduce Bit Whisperer, an ad-hoc short-range wireless communication system that enables “walk up and share” data transmissions with “good enough” security. Bit Whisperer transmits data to proximate devices co-located on a solid surface through high frequency, inaudible acoustic signals. The physical surface has two benefits: it enhances acoustic signal transmission by reflecting sound waves as they propagate; and, it makes the domain of communication visible, helping users identify exactly with whom they are sharing data without prior pairing. Through a series of technical evaluations, we demonstrate that Bit Whisperer is robust for common use-cases and secure against likely threats. We also implement three example applications to demonstrate the utility of Whisperer: 1-to-1 local contact sharing, 1-to-N private link sharing to open a secure group chat, and 1-to-N local device authentication.
Design and Optimization of High Performance Adsorption-Based Thermal Battery (2013)

Electric vehicle (EV) technology faces a substantial challenge in terms of driving range, especially when the vehicle's climate control system relies entirely on the onboard electric battery. Therefore, we are developing an advanced adsorption-based thermal battery (ATB) capable of delivering both heating and cooling for electric vehicles with minimal use of the electric battery bank. While adsorption based climate control systems offer the advantage of direct usage of primary thermal energy sources for operation, they typically have low COP values, and are often bulky and heavy. A compact and lightweight ATB is necessary to replace existing climate control systems in EVs that use electric battery for operation. In this paper, we present a detailed computational analysis of adsorption kinetics taking place within an adsorption bed that is capable of delivering large cooling and heating capacities by making use of novel adsorbents. The overall design of the adsorption bed, which is a critical element in achieving a high performance thermal battery, is also discussed. To make performance predictions, we characterized the adsorbents to obtain their thermophysical and transport properties as well as adsorption characteristics. The model consequently incorporates these measured properties to predict the performance variation as a function of time. This work provides the critical parameters affecting heating and cooling rates, and identifies avenues for further improvement in the overall performance of the thermal battery.
Closed Brayton cycle power system with a high temperature pellet bed reactor heat source for NEP applications (1993)

Capitalizing on past and future development of high temperature gas reactor (HTGR) technology, a low mass 15 MWe closed gas turbine cycle power system using a pellet bed reactor heating helium working fluid is proposed for Nuclear Electric Propulsion (NEP) applications. Although the design of this directly coupled system architecture, comprising the reactor/power system/space radiator subsystems, is presented in conceptual form, sufficient detail is included to permit an assessment of overall system performance and mass. Furthermore, an attempt is made to show how tailoring of the main subsystem design characteristics can be utilized to achieve synergistic system level advantages that can lead to improved reliability and enhanced system life while reducing the number of parasitic load driven peripheral subsystems.