gebhart/patrepeval huggingface dataset:
Phase I/II trial of PD-1 antibody nivolumab with peptide vaccine in patients naive to or that failed ipilimumab. (2013)

9011 Background: Nivolumab, an IgG4 fully human monoclonal antibody against checkpoint protein PD-1, is active in metastatic melanoma, renal cell and non-small cell lung cancer. It was administered with a multi-peptide vaccine to patients (pts) with unresectable melanoma who failed at least one regimen for metastatic disease and were ipilimumab naïve, or failed ipilimumab, to assess the toxicity and tolerability of the combination and perform correlative immune assays. Methods: Three cohorts of 10 HLA A0201 positive ipilimumab-naïve pts received nivolumab at 1, 3 or 10 mg/kg, then three additional cohorts of pts who had failed prior ipilimumab received nivolumab at 3 mg/kg: two cohorts of 10 pts each who were A0201 positive and had either grade 2 or less ipilimumab toxicity, or grade 3 dose limiting ipilimumab toxicity; finally 40 pts were treated with antibody who had grade 2 or less ipilimumab toxicity and were not HLA restricted. Pre-treatment archived tumor tissue as well as pre- and post-treatment peripheral blood cells were collected. Results: Median age for all pts was 59;76% were M1c. Response rates by RECIST were 28% in 34 pts naïve to, and 32% for 46 pts who failed prior ipilimumab. Nivolumab did not induce the same irAEs in pts with prior ipilimumab induced toxicity. No cohort had more than one dose limiting toxicity. 2 pts had grade 3 pneumonitis. Three of ten pts who failed nivolumb had stable disease or a partial response to subsequent ipilimumab. Biomarker studies showed that elevated NY-ESO 1 and MART-1 specific CD8 T cells pre-treatment were associated with non-response (p<0.005 and <0.001), and that CTLA-4 positive CD4 T cells and T regulatory cells were elevated after treatment in non-responders (p<0.01). Immunohistochemical analysis of pre-treatment tumors indicated that PD-L1 staining was associated with response, but responses were also observed in pts whose tumors did not stain. Conclusions: Objective responses to nivolumab were observed after failing ipilimumab, and to ipilimumab after failing nivolumab. Elevation of CTLA-4 after nivolumab in non-responders suggest that sequential therapy with the combination should be tested. Tumor PD-L1 was associated with but not predictive of response. Clinical trial information: NCT01176461.
Profiling ribonucleotide modifications at full-transcriptome level: a step toward MS-based epitranscriptomics (2015)

The elucidation of the biological significance of RNA post-transcriptional modifications is hampered by the dearth of effective high-throughput sequencing approaches for detecting, locating, and tracking their levels as a function of predetermined experimental factors. With the goal of confronting this knowledge gap, we devised a strategy for completing global surveys of all ribonucleotide modifications in a cell, which is based on the analysis of whole cell extracts by direct infusion electrospray ionization mass spectrometry (ESI-MS). Our approach eschews chromatographic separation to promote instead the direct application of MS techniques capable of providing detection, differentiation, and quantification of post-transcriptional modifications (PTMs) in complex ribonucleotide mixtures. Accurate mass analysis was used to carry out database-aided identification of PTMs, whereas multistep tandem mass spectrometry (MS n ) and consecutive reaction monitoring (CRM) provided the necessary structural corroboration. We demonstrated that heat-map plots afforded by ion mobility spectrometry mass spectrometry (IMS-MS) can provide comprehensive modification profiles that are unique for different cell types and metabolic states. We showed that isolated tRNA samples can be used as controlled sources of PTMs in standard-additions quantification. Intrinsic internal standards enable direct comparisons of heat-maps obtained under different experimental conditions, thus offering the opportunity to evaluate the global effects of such conditions on the expression levels of all PTMs simultaneously. This type of comparative analysis will be expected to support the investigation of the system biology of RNA modifications, which will be aimed at exploring mutual correlations of their expression levels and providing new valuable insights into their biological significance.
Low-noise wideband ultrasound detection using polymer microring resonators (2008)

Polymer microring resonators for low-noise, wideband ultrasound detection are presented. Using a nanoimprinting technique, we fabricated polymer microring resonators with a quality factor of 6000 resulting in high sensitivity to ultrasound. A noise-equivalent pressure of 0.23 kPa over 1-75 MHz and a detection bandwidth of over 90 MHz at -3 dB were measured. These results demonstrate the potential of polymer microring resonators for high-frequency ultrasound and photoacoustic imaging. For a typical photoacoustic imaging test case, the high sensitivity demonstrated in these devices would increase imaging depth by a factor of 3 compared to state-of-the-art polyvinylidene fluoride detectors.
Amorphous silicon display backplanes on plastic substrates (2005)

Amorphous silicon thin-film transistors and pixel driver circuits for organic light-emitting diode displays have been fabricated on plastic substrates. Pixel circuits demonstrate sufficient current delivery and long-term stable operation.
Structure and content scoring for XML (2005)

XML repositories are usually queried both on structure and content. Due to structural heterogeneity of XML, queries are often interpreted approximately and their answers are returned ranked by scores. Computing answer scores in XML is an active area of research that oscillates between pure content scoring such as the well-known tf*idf and taking structure into account. However, none of the existing proposals fully accounts for structure and combines it with content to score query answers. We propose novel XML scoring methods that are inspired by tf*idf and that account for both structure and content while considering query relaxations. Twig scoring, accounts for the most structure and content and is thus used as our reference method. Path scoring is an approximation that loosens correlations between query nodes hence reducing the amount of time required to manipulate scores during top- query processing. We propose efficient data structures in order to speed up ranked query processing. We run extensive experiments that validate our scoring methods and that show that path scoring provides very high precision while improving score computation time.
Tailoring the Mg-air primary battery performance using strong complexing agents as electrolyte additives (2020)

Mg-air primary battery has become an attractive source of energy due to its economic viability, environmental benignity, and high theoretical specific power density. However, low practical delivered power due to high self-corrosion and fast anode fouling are the main reasons that limit their commercial application. Modification of the electrolyte chemistry in Mg-air batteries plays a crucial role in improving the Mg-air battery performance. In this study, the impact of addition of two strong complexing agents at different concentrations in the aqueous electrolyte of Mg-air battery is investigated. Galvanostatic polarization test is conducted in order to evaluate the discharge performance of the half-cell on the anode side in the presence or absence of strong complexing agents. According to the results, strong complexing agents are able to effectively activate magnesium anode and provide a higher delivered potential. A decrease in the additive concentrations in the electrolyte leads to the attainment of higher utilization efficiency at the expense of slight drop in discharge potential.
Universal turn-on dynamics of superconducing nanowire single-photon detectors (2019)

We model the turn-on dynamics of superconducting nanowire single-photon detectors (SNSPDs), predicting that the rising edge of the readout signal encodes photon number, nanowire length and detector bias current, and experimentally verify these predictions.
Rapid Identification of Immunostimulatory α-Galactosylceramides Using Synthetic Combinatorial Libraries (2007)

Two 60+-membered libraries of alpha-galactosylceramides have been prepared by reactions between activated ester resins and two core, fully deprotected galactosylated sphingoid bases. The libraries were evaluated for their ability to stimulate CD1d-restricted NKT cells, using in vitro stimulation of a murine NKT cell hybridoma line and for their ability to induce the expansion of NKT cells from peripheral blood mononuclear cells (PBMC) of a normal human subject. Our results showed that many compounds constructed on a C18-phytosphingosine base had significant stimulatory activity in both assays. Because no product purification was required, this approach is particularly attractive as a method for rapid synthesis of large libraries of potential immunomodulatory glycosylceramides.
FootprintID (2017)

We present FootprintID, an indoor pedestrian identification system that utilizes footstep-induced structural vibration to infer pedestrian identities for enabling various smart building applications. Previous studies have explored other sensing methods, including vision-, RF-, mobile-, and acoustic-based methods. They often require specific sensing conditions, including line-of-sight, high sensor density, and carrying wearable devices. Vibration-based methods, on the other hand, provide easy-to-install sparse sensing and utilize gait to distinguish different individuals. However, the challenge for these methods is that the signals are sensitive to the gait variations caused by different walking speeds and the floor variations caused by structural heterogeneity. We present FootprintID, a vibration-based approach that achieves robust pedestrian identification. The system uses vibration sensors to detect footstep-induced vibrations. It then selects vibration signals and classifiers to accommodate sensing variations, taking step location and frequency into account. We utilize the physical insight on how individual step signal changes with walking speeds and introduce an iterative transductive learning algorithm (ITSVM) to achieve robust classification with limited labeled training data. When trained only on the average walking speed and tested on different walking speeds, FootprintID achieves up to 96% accuracy and a 3X improvement in extreme speeds compared to the Support Vector Machine. Furthermore, it achieves up to 90% accuracy (1.5X improvement) in uncontrolled experiments.
Evidence for and Characterization of a Liver Cell Proliferation Factor from Blood Plasma of Partially Hepatectomized Rats (1980)

A boiled extract acidified to pH 5.5 from the blood plasma of partially hepatectomized rats was treated with neuraminidase and injected i.p. into untreated rats. The DNA-synthesis of the liver cells showed a four-fold increase in comparison with controls. Extracts from the plasma of partially hepatectomized rats without neuraminidase treatment showed no increase in DNA-synthesis. Injections of boiled acid extracts from plasma of normal rats, however, showed no comparable differences before and after neuraminidase treatment. The activity of neuraminidase treated boiled, plasma extract is lost after treatment both with trypsin-chymotrypsin and with beta-galactosidase. Gel chrmoatography of the factor gave a molecular weight of about 38,000 D. The specific activity of the active extract after chromatography was raised by a factor of 300. According to affinity chromatography the factor was shown to be a glycoprotein containing N-Ac-glucosamine. The factor is inert with respect to the proliferation of spleen and kidney, i.e. it is organ specific. According to these results a regulatory system of hepatopoiesis is proposed.
Synthesis and Testing of Compounds That Inhibit Soybean Cyst Nematode Egg Hatch (1996)

Soybean cyst nematode infestation continues to be a serious agricultural problem. As part of an interdisciplinary effort to identify a biorational solution to the problem, analogs of glycinoeclepin A, a natural hatching stimulus of the nematode, were prepared and tested. Several of the analogs were discovered to inhibit the hatching of soybean cyst nematode eggs. On the basis of the results of egg hatch tests, the minimum functionality for egg hatch inhibition appears to be a keto diacid. Keywords: Nematode; hatching inhibitor; synthesis
Configuration of Highly Reliable Distributed Control System (1984)

Nuclear power plants require a distributed control system to ensure a high ratio of reliability to cost. This paper proposes a flexible configuration control system which is both reliable and economical. This system is capable of continuous plant control owing to a back-up function performed by individual adjacent controllers, even if several controllers fail. To evaluate the system, formulas of Mean Time To Failure (MTTF) and MTTF/redundancy which include the degree of meeting the requirement of control function are prepared as indices of reliability and cost performance respectively, based on the concept of system function reliability. Calculation results clarify that these indices are higher than those of the triple system or n: 1 back-up system.
Improving the test quality for scan-based BIST using a general test application scheme (2003)

In this paper we propose a general test application scheme for existing scan-based BIST architectures. The objective is to further improve the test quality without inserting additional logic to the circuit under test (CUT). The proposed test scheme divides the entire test process into multiple test sessions. A different number of capture cycles is applied after scanning in a test pattern in each test session to maximize the fault detection for a distinct subset of faults. We present a procedure to find the optimal number of capture cycles following each scan sequence for every fault. Based on this information, the number of test sessions and the number of capture cycles after each scan sequence are determined to maximize the random testability of the CUT. We conduct experiments on ISCAS89 benchmark circuits to demonstrate the effectiveness of our approach.
FERROELECTRIC NONVOLATILE MEMORY FIELD-EFFECT TRANSISTORS BASED ON A NOVEL BUFFER LAYER STRUCTURE (2000)

We have proposed and developed a ferroelectric nonvolatile field-effect transistor that incorporates a thin MgO buffer layer between a ferroelectric film and an oxidized Si substrate. The use of an MgO/SiO 2 buffer for a ferroelectric gate is based on the following findings. First, a thin MgO buffer serves well as a template layer allowing the growth of highly oriented ferroelectric films on amorphous substrates. Second, MgO works well as a diffusion barrier between a ferroelectric film and a substrate, protecting the silicon FET channel region from interdiffusion or reaction that may occur during device processing. Third, thermal oxidation of Si is known to be one of the best ways of passivating silicon surfaces, thus to reduce high quality FET channels. The fabricated devices show excellent performance in ferroelectric polarization switching, memory retention, and fatigue resistance. The devices also demonstrate scalability in device dimension and operating voltage, i.e., they are suitable for low voltage operation (3-5 V or below) showing a sufficient memory window (1-2 V).
Time-division multiplexing of pump wavelengths to achieve ultrabroadband, flat, backward-pumped Raman gain (2002)

We describe a simple scheme, which we call the Raman smart pump, to allow for the achievement of flat gain over broad bands with backward-pumped Raman amplification. The proposed method, based on time-division multiplexing, also removes all interaction among the various pump wavelengths and allows for dynamic gain control through simple electronic means.
Clipping and Filtering-Based Adaptive PAPR Reduction Method for Precoded OFDM-MIMO Signals (2013)

This paper presents a new adaptive peak-to-average power ratio (PAPR) reduction method based on clipping and filtering (CF) for precoded orthogonal frequency division multiplexing (OFDM)-multiple-input multiple-output (MIMO) transmission. While the conventional CF method adds roughly the same interference power to each of the transmission streams, the proposed method suppresses the addition of interference power to the streams with good channel conditions. Since the sum capacity is dominated by the capacity of the streams under good channel conditions and the interference caused by the PAPR reduction process severely degrades the achievable capacity for these streams, the proposed method significantly improves the achievable sum capacity compared to the conventional CF method for a given PAPR. Simulation results show the capacity gain by using the proposed method compared to the conventional method.
Beat to beat volumetric analysis in arrhythmia using real time CMR (2015)

Background ECG-gated cardiac MRI is the gold standard for volumetric evaluation of patients, and clinically, ejection fraction is used as a surrogate for function. We hypothesized that the use of arrhythmia rejection in the presence of ectopic beats compromises the accuracy of hemodynamic measurements. Real-time MRI, coupled with ECG telemetry and semi-automated LV endocardial segmentation, can be used to identify multiple beat morphologies and derive global hemodynamic measurements for each beat. Methods Short-axis golden angle radial bSSFP projections (8000 projections/slice) were reconstructed using Gadgetron (non-Cartesian, iterative SENSE) with 34 projections per frame, and slice volume was measured via segmentation of LV endocardial contour with ITK-SNAP. ECG was synchronously recorded with the acquisition, and each image frame was assigned a time point on the ECG (~22 seconds/slice). QRS detection was used to identify cardiac cycles, and similar beats (across slices) were grouped via RR-duration of the beat of interest as well as the previous (loading) beat. The use of the loading beat duration allowed for accurate grouping of premature ventricular contractions (PVCs). For each beat morphology, global volume was obtained by summation of slice volume curves allowing for hemodynamic evaluation via EDV, ESV, SV, and EF.
Generating Peptide Titration-Type Curves Using Polymeric Reverse Micelles As Selective Extraction Agents along with Matrix-Assisted Laser Desorption Ionization-Mass Spectrometry Detection (2009)

Amphiphilic homopolymers that self-assemble into reverse micelles in nonpolar solvents have been used by us in the context of a two-phase liquid-liquid extraction protocol to selectively extract peptides from aqueous solution for MALDI-MS detection. In this manuscript, we investigate the scope of these materials in terms of its extraction capabilities, using compounds with varying isoelectric points (pI) and pK(a) values over a range of aqueous solution pHs. We find that the aqueous solution pH and analyte pK(a) values are the major factors controlling extraction selectivity. We also find that the experimental extraction efficiencies correspond very well with the fractional compositions of species calculated using analyte pK(a) values, indicating that these extraction materials can be used to simultaneously generate titration-type curves for each individual peptide in a mixture. We predict that such titration curves, along with accurate mass measurements, could represent a new way of improving protein identification procedures.
Microbial Oxidation of Methane and Methanol: Isolation of Methane-Utilizing Bacteria and Characterization of a Facultative Methane-Utilizing Isolate (1978)

A methane-utilizing organism capable of growth both on methane and on more complex organic substrates as a sole source of carbon and energy, has been isolated and studied in detail. Suspensions of methane-grown cells of this organism oxidized C-1 compounds (methane, methanol, formaldehyde, formate); hydrocarbons (ethane, propane); primary alcohols (ethanol, propanol); primary aldehydes (acetaldehyde, propionaldehyde); alkenes (ethylene, propylene); dimethylether; and organic acids (acetate, malate, succinate, isocitrate). Suspensions of methanol-or succinate-grown cells did not oxidize methane, ethane, propane, ethylene, propylene, or dimethylether, suggesting that the enzymatic systems required for oxidation of these substrates are induced only during growth on methane. Extracts of methane-grown cells contained a particulate reduced nicotinamide adenine dinucleotide-dependent methane monooxygenase activity. Oxidation of methanol, formaldehyde, and primary alcohols was catalyzed by a phenazine methosulfate-linked, ammonium ion-requiring methanol dehydrogenase. Oxidation of primary aldehydes was catalyzed by a phenazine methosulfate-linked, ammonium ion-independent aldehyde dehydrogenase. Formate was oxidized by a nicotinamide adenine dinucleotide-specific formate dehydrogenase. Extracts of methane-grown, but not succinate-grown, cells contained the key enzymes of the serine pathway, hydroxypyruvate reductase and malate lyase, indicating that the enzymes of C-1 assimilation are induced only during growth on C-1 compounds. Glucose-6-phosphate dehydrogenase was induced during growth on glucose. Extracts of methane-grown cells contained low levels of enzymes of the tricarboxylic acid cycle, including alpha-keto glutarate dehydrogenase, relative to the levels found during growth on succinate.
Treatment of Neurodegenerative Disorders with Radical Nanomedicine (2007)

In engineering and materials science, nanotechnology has provided many advances that effectively reduce oxidative damage generated by free radical production. Despite such advances, there has been little application to biomedical problems. Increased oxidative stress and free radical production are associated with neurodegenerative conditions, including aging, trauma, Alzheimer's and Parkinson's diseases, and many others. The antioxidant properties of cerium oxide nanoparticles show promise in the treatment of such diseases. Here, we summarize the work on the biological antioxidant actions of cerium oxide nanoparticles in extension of cell and organism longevity, protection against free radical insult, and protection against trauma-induced neuronal damage. We discuss establishment of effective dosing parameters, along with the physicochemical properties that regulate the pharmacological action of these new nanomaterials. Taken together, these studies suggest that nanotechnology can take pharmacological treatment to a new level, with a novel generation of nanopharmaceuticals.
Botulinum toxin type A (botox) for treatment of migraine headaches (2001)

The aim of the clinical experiment was to evaluate the correlation between the administration of pericranial botulinum toxin type A (botox) and the relief of migraine symptoms.