gebhart/patrepeval huggingface dataset:
Targeting Keratin 17 in Pancreatic Cancer: A Novel Rewired Pathway of Nucleotide Metabolism that Drives Chemoresistance (2022)

Pancreatic ductal adenocarcinoma (PDAC) is characterized by two molecular subtypes, of which the basal‐like subtype is associated with the worst survival and is highly resistant to the first‐line chemotherapy. We previously reported that keratin 17 (K17), a signature gene in basal‐like subtype, is a novel negative‐prognostic and predictive biomarker, whose overexpression results in resistance to Gemcitabine (Gem) and 5‐fluorouracil, the major chemotherapeutic agents in standard‐of‐care treatments, and leads to shortened patient survival. Here, we set out to uncover the mechanisms of chemoresistance and explore targeted therapies for K17‐expressing PDAC. We hypothesized that K17 reprograms cancer metabolism and leads to therapeutic resistance. We manipulated the expression of K17 in multiple in vitro and in vivo models of PDAC, spanning human and murine PDAC cells and orthotopic xenografts, for drug‐testing, metabolomic and mechanistic studies. To uncover the mechanisms associated with K17‐induced chemoresistance, we performed unbiased metabolomic studies in isogenic PDAC cell lines and found that compared to control cells, K17 increases intracellular levels of deoxycytidine (dC) by four‐fold that promote Gem (dC analogue) resistance. Interestingly, K17‐expressing cells are more sensitive to a compound that targets de novo pyrimidine biosynthesis. Based on previous findings that K17 enters nucleus to regulate gene expression, weexplored whether K17 triggers metabolic reprogramming at the transcriptional level and found that enzymes involved in pyrimidine biosynthesis are positively correlated with K17 expression in PDAC cells. Given that it is still poorly understood how K17 regulates gene expression, we performed domain‐prediction analyses. We discovered and validated a novel chromatin remodeling domain in K17 that is required for metabolic reprogramming. Importantly, mice bearing tumors with the deletion of the chromatin remodeling domain in K17 survived significantly longer than those with tumors expressing wild type K17. We are now performing ATAC‐seq, ChIP‐Seq and RNA‐Seq to understand how this domain alters pyrimidine biosynthesis. In summary, we identified a novel pathway of chemoresistance that could result in developing a biomarker‐based personalized therapy.
A Novel Collection of snRNA-Like Promoters with Tissue-Specific Transcription Properties (2012)

We recently identified a novel dataset of snRNA-like trascriptional units in the human genome. The investigation of a subset of these elements showed that they play relevant roles in physiology and/or pathology. In this work we expand our collection of small RNAs taking advantage of a newly developed algorithm able to identify genome sequence stretches with RNA polymerase (pol) III type 3 promoter features thus constituting putative pol III binding sites. The bioinformatic analysis of a subset of these elements that map in introns of protein-coding genes in antisense configuration suggest their association with alternative splicing, similarly to other recently characterized small RNAs. Interestingly, the analysis of the transcriptional activity of these novel promoters shows that they are active in a cell-type specific manner, in accordance with the emerging body of evidence of a tissue/cell-specific activity of pol III.
Receptor binding site-deleted foot-and-mouth disease (FMD) virus protects cattle from FMD (1995)

Binding of foot-and-mouth disease virus (FMDV) to cells requires an arginine-glycine-aspartic acid (RGD) sequence in the capsid protein VP1. We have genetically engineered an FMDV in which these three amino acids have been deleted, producing a virus particle which is unable to bind to cells. Cattle vaccinated with these receptor binding site-deleted virions were protected from disease when challenged with a virulent virus, demonstrating that these RGD-deleted viruses could serve as the basis for foot-and-mouth disease vaccines safer than those currently in use. This strategy may prove useful in the development of vaccines for other viral diseases.
Reverberation suppression in cochlear implants using a blind channel-selection strategy (2013)

Reverberation severely degrades speech intelligibility for cochlear implant (CI) users. The ideal reverberant mask (IRM), a binary mask for reverberation suppression which is computed using signal-to-reverberant ratio, was found to yield substantial intelligibility gains for CI users even in highly reverberant environments (e.g., T60 = 1.0 s). Motivated by the intelligibility improvements obtained from IRM, a monaural blind channel-selection criterion for reverberation suppression is proposed. The proposed channel-selection strategy is blind, meaning that prior knowledge of neither the room impulse response nor the anechoic signal is required. By the use of a residual signal obtained from linear prediction analysis of the reverberant signal, the residual-to-reverberant ratio (RRR) of individual frequency channels was employed as the channel-selection criterion. In each frame, the channels with RRR less than an adaptive threshold were retained while the rest were zeroed out. Performance of the proposed strategy was evaluated via intelligibility listening tests conducted with CI users in simulated rooms with two reverberation times of 0.6 and 0.8 s. The results indicate significant intelligibility improvements in both reverberant conditions (over 30 and 40 percentage points in T60 = 0.6 and 0.8 s, respectively). The improvement is comparable to that obtained with the IRM strategy.
Measurement of air refractive index fluctuation based on a laser synthetic wavelength interferometer (2014)

A novel method for measuring air refractive index fluctuation based on a laser synthetic wavelength interferometer is proposed. The change of air refractive index is regarded as an equivalent measured displacement in the measurement arm, which can be realized by tracking a large compensative displacement of the reference mirror in the reference arm of the laser synthetic wavelength interferometer. The merit of the proposed method is that the slight air refractive index fluctuation is magnified to a large displacement on the order of millimeters or micrometers. To verify the feasibility of the proposed method, the correlation experiment between the displacement of the reference mirror and the air refractive index fluctuation and the comparison experiments with Edl?n equations?both in short time and long time were performed. Experimental results show that the measurement accuracy of the air refractive index fluctuation is better than 3.7???10?8.
Rapid fault detection and recovery for IP telephony (2004)

Short, low-bandwidth keep-alive packets can be injected into VoIP packet streams to rapidly detect faults and deteriorating network conditions (e.g., increasing delay, jitter, or loss). The keep-alive packets can be duplicated and also used to continuously monitor and compare the delay and loss characteristics of primary and alternate network paths, and thereby help control the rapid switchover of calls (in-progress and future) to alternate routing paths (or the circuit-switched PSTN) when faults or deteriorating QoS conditions are detected. By simultaneously transmitting copies of keep-alive packets over multiple paths to make the differential delay measurements and comparisons, the proposed techniques avoid many common synchronization and timing errors. We examine various performance tradeoffs and describe several ways to implement the proposed architectures and techniques.
Industrial Geospatial Analysis Tool for Energy Evaluation (IGATE-E) (2013)

IGATE-E is an energy analysis tool for industrial energy evaluation. The tool applies statistical modeling to multiple publicly available datasets and provides information at the geospatial resolution of zip code using bottom up approaches. Within each zip code, the current version of the tool estimates electrical energy consumption of manufacturing industries based on each type of industries using DOE s Industrial Assessment Center database (IAC-DB) and DOE s Energy Information Administration Manufacturing Energy Consumption Survey database (EIA-MECS DB), in addition to other commercially available databases such as the Manufacturing News database (MNI, Inc.). Ongoing and future work include adding modules for the predictions of fuel energy consumption streams, manufacturing process steps energy consumption, major energy intensive processes (EIPs) within each industry type among other metrics of interest. The tool provides validation against DOE s EIA-MECS state level energy estimations and permits several statistical examinations. IGATE-E is intended to be a decision support and planning tool to a wide spectrum of energy analysts, researchers, government organizations, private consultants, industry partners, and alike.
Phosphate Glass as a Phosphate Source in High Cell Density Escherichia coli Fermentations (1996)

Polyphosphate glass (sodium hexametaphosphate, sodium polyphosphate, glassy) was identified and tested as a source of phosphate that supports growth of recombinant Escherichia coli to cell densities over 110 g dry wt/L. Polyphosphate glasses cost no more than sodium and potassium phosphates, are more soluble than any other inorganic phosphate source, and do not form metallophosphate precipitates when mixed with other nutrients in proportions found in fermentation medias. Using a typical fermentation medium, 40% higher cell densities were obtained using polyphosphate glass rather than orthophosphate. Polyphosphate glasses will allow more flexibility in designing and executing high cell density fermentations.
Frequency modulation based angular rate sensor (2011)

We report, for the first time, a quasi-digital angular rate sensor based on mechanical frequency modulation (FM) of the input rotation rate. The new approach relies on tracking of the resonant frequencies of two ultra-high Q-factor mechanical modes of vibration in a MEMS vibratory gyroscope to produce a frequency based measurement of the input angular rate. Rate table characterization of the new FM angular rate sensor with quality factors of 1 million revealed a linear dynamic range of 2000 deg/s limited by the setup, with a fundamental performance limit in excess of 72,000 deg/s. Temperature characterization of the FM rate sensor exhibited less than 0.2 % variation of the angular rate response between 25 °C and 70 °C environments, enabled by the self-calibrating differential frequency detection.
Design of photonic crystal microcavities for cavity QED (2001)

We discuss the optimization of optical microcavity designs based on two-dimensional photonic crystals for the purpose of strong coupling between the cavity field and a single neutral atom trapped within a hole. We present numerical predictions for the quality factors and mode volumes of localized defect modes as a function of geometric parameters, and discuss some experimental challenges related to the coupling of a defect cavity to gas-phase atoms.
Abstract 1502: Three intrinsic subtypes of prostate cancer with distinct pathway activation profiles differ in prognosis and treatment response (2016)

Abstract In the era of precision medicine, genomic classifications of prostate cancer (PC) have not broadly impacted patient care. Here we present an integrative transcriptome analysis of 14 disease-related pathways in over 4,600 clinical specimens and 25 PC preclinical models. This approach provides a novel classification scheme, inclusive of 3 PC subtypes (PCS1-3), which predict disease progression and drug resistance. The PCS1 and PCS2 categories possess characteristics of luminal cells, while PCS3 exhibits basal features. Castration-resistant and metastatic cancers are over-represented in PCS1 and PCS3 tumors. All 3 subtypes are represented in commonly used PC cell lines; however, none of the mouse models we analyzed resembles PCS3. PCS classification using RNA expression data appears to be stable across primary and metastatic human tumors, cell lines, xenografts and mouse models. This new subtyping method provides novel opportunities for patient stratification that reflect specific features of tumor biology and may influence therapeutic decisions. Citation Format: Sungyong You, Beatrice Knudsen, Nicholas Erho, Mohammed Alshalalfa, Mandeep Takhar, Hussam Al-deen Ashab, Elai Davicioni, Robert Jeffrey Karnes, Eric A. Klein, Robert B. Den, Ashley E. Ross, Edward M. Schaeffer, Isla P. Garraway, Jayoung Kim, Michael R. Freeman. Three intrinsic subtypes of prostate cancer with distinct pathway activation profiles differ in prognosis and treatment response. [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 1502.
A Proposed Speech Discrimination Assessment Methodology Based on Event-Related Potentials to Visual Stimuli (2012)

Objective and quantitative assessment methods are needed for the fitting of hearing aid parameters. This paper proposes a novel speech discrimination assessment method using electroencephalograms (EEGs). The method utilizes event-related potentials (ERPs) to visual stimuli instead of the conventionally used auditory stimuli. A spoken letter is played through a speaker as an initial auditory stimulus. The same letter can then be visually displayed on a screen as a match condition, or a different letter is displayed (mismatch condition). The participant determines whether the two stimuli represent the same letter or not. The P3 component or late positive potential (LPP) component are elicited when a participant detects either a match or mismatch between the auditory and visual stimuli, respectively. The hearing ability of each participant can be estimated objectively via analysis of these ERP components.
Quantitative Secretome Analysis Reveals that COL6A1 is a Metastasis-Associated Protein Using Stacking Gel-Aided Purification Combined with iTRAQ Labeling (2010)

In cancer metastasis, secreted proteins play an important role in promoting cancer cell migration and invasion and thus also in the increase of cancer metastasis in the extracellular microenvironment. In this study, we developed a strategy that combined a simple gel-aided protein purification with iTRAQ labeling to quantify and discover the metastasis-associated proteins in the lung cancer cell secretome. Secreted proteins associated with lung cancer metastasis were produced using CL1-0 and CL1-5 cells with different metastatic abilities. Quantitative secretomics analysis identified a total of 353 proteins, 7 of which were considered to be metastasis-associated proteins. These included TIMP1, COL6A1, uPA, and AAT, all of which were higher in CL1-5, and AL1A1, PRDX1, and NID1, which were higher in CL1-0. Six of these metastasis-associated proteins were validated with Western blot analysis. In addition, pathway analysis was performed in building the interaction network between the identified metastasis-associated proteins. Further functional analysis of COL6A1 on the metastatic abilities of CL1 cells was also carried out. An RNA interference-based knock-down of COL6A1 suppressed the metastatic ability of CL1-5 cells; in contrast, a plasmid-transfected overexpression of COL6A1 increased the metastatic ability of CL1-0 cells. This study describes a simple and high throughput sample purification method that can be used for the quantitative secretomics analysis of metastasis-associated proteins.
Helping Video Games Rewire "Our Minds" (2001)

Biofeedback-modulated video games are games that respond to physiological signals as well as mouse, joystick or game controller input; they embody the concept of improving physiological functioning by rewarding specific healthy body signals with success at playing a video game. The NASA patented biofeedback-modulated game method blends biofeedback into popular off-the- shelf video games in such a way that the games do not lose their entertainment value. This method uses physiological signals (e.g., electroencephalogram frequency band ratio) not simply to drive a biofeedback display directly, or periodically modify a task as in other systems, but to continuously modulate parameters (e.g., game character speed and mobility) of a game task in real time while the game task is being performed by other means (e.g., a game controller). Biofeedback-modulated video games represent a new generation of computer and video game environments that train valuable mental skills beyond eye-hand coordination. These psychophysiological training technologies are poised to exploit the revolution in interactive multimedia home entertainment for the personal improvement, not just the diversion, of the user.
Exact score distribution computation for ontological similarity searches (2011)

The new algorithm enables for the first time exact P-value calculation via exact score distribution computation for ontology similarity searches. The approach is applicable to any ontology for which the annotation-propagation rule holds and can improve any bioinformatic method that makes only use of the raw similarity scores. The algorithm was implemented in Java, supports any ontology in OBO format, and is available for non-commercial and academic usage under: https://compbio.charite.de/svn/hpo/trunk/src/tools/significance/
Large-Pore Mesoporous Materials with Semi-Crystalline Zeolitic Frameworks (2001)

Crystallizing walls: Following the templated solid-state secondary crystallization of an amorphous mesoporous material the amorphous pore walls of the mesoporous precursor are partially reorganized into a crystalline material, the zeolite ZSM-5, as indicated by the dark-field transmission electron micrograph image shown. The bright spots correspond to the ZSM-5 nanocrystals.
Metallurgical Design of Newly Developed Material for Seamless Pipes of X80–X100 Grades (2007)

With the increasing development of oil and gas fields in deepwater or ultra-deepwater with deep well depth, the development of high strength seamless pipe has become necessary. This paper describes a metallurgical design of seamless pipe with high strength reaching X80–X100 grade (minimum yield strength, 552 MPa–689 MPa) manufactured by steel containing very low carbon and with a microstructure of uniform bainite. The effect of microstructure of quenched and tempered (QT) steel on strength and toughness is investigated in laboratory. Uniform bainitic structure without coarse martensite-austenite constituent (M-A) is obtained by lowering bainite transformation temperature during quenching process by controlling the alloying elements. Moreover the structure is very effective in obtaining good toughness for tempered steel even with the high strength X100 grade. Sufficiently low hardness and good toughness in heat affected zone (HAZ) are confirmed by welding tests. The trial production of developed steel is conducted by applying inline QT process in medium-size seamless mill according to an alloying design obtained in laboratory tests. The seamless pipes of the trial production achieve grades X80 to X100 by changing tempering temperature. Some data of mechanical properties of the produced pipes is introduced.
A novel seizure detection algorithm informed by hidden Markov model event states (2016)

This algorithm represents a computationally inexpensive, individualized, real-time detection method suitable for implantable antiepileptic devices that may considerably reduce false positive rate relative to current industry standards.
Fabrication of moiré on curved surfaces (2020)

Moiré is an appealing visual effect observable when two or more repetitive patterns are superposed. Fabrication of moiré effects has already proven to be useful in a range of applications, from art to engineering. Here, we introduce a method for designing and fabricating level-line moirés on curved surfaces. These moiré shapes are obtained by superposing a partly absorbing layer and a layer formed by an array of cylindrical lenses or by two layers of cylindrical lenses. We formulate the problem of placing an array of cylindrical lenses on a curved surface as a design problem with a small number of dimensions. The range of possible solutions can therefore be explored by a human observer. We demonstrate the quality of our method by rendered simulations and by fabrication. The resulting static displays can be manufactured using different fabrication techniques, from multi-material 3D printing to molding.
Role of ultrathin Alq3 and LiF layers in conjugated polymer light-emitting diodes (2003)

We report that an ultrathin layer of tris-(8-hydroxyquinoline) aluminum (Alq3) interposed between a bilayer cathode of LiF/Al and an emissive layer can significantly improve electroluminescence efficiency in a polymer light-emitting device (PLED). At a current density of 35 mA/cm2, a poly[2-methoxy-5-(2′-ethyl-hexyloxy)-1,4-phenyl-enevinylene] (MEH-PPV)-based PLED with a cathode of Alq3/LiF/Al has a quantum efficiency of 2.5%, considerably higher than that of a MEH-PPV-based PLED with a bare Al or a LiF/Al cathode. Interfacial characteristics of MEH-PPV/LiF/Al and MEH-PPV/Alq3/LiF/Al were investigated by photoelectron spectroscopy, and the results were used to explain the difference in device performance.
Simple Length Determination of Single-Walled Carbon Nanotubes by Viscosity Measurements in Dilute Suspensions (2007)

We describe a fast, reproducible method to accurately measure the length of single-walled carbon nanotubes (SWNTs). The method is based on measuring the viscosity of a macroscopic sample of dilute suspended SWNTs. The average length is determined from the difference between the zero-shear viscosity of the suspension and that of the solvent. Using the relationship between viscosity and length, the average length of HiPco SWNTs is found to range from 400 to 700 nm, in agreement with atomic force microscopy (AFM) measurements. Compared to AFM, length determination by viscosity is faster and appears more reproducible.
Use of NH<sub>4</sub>OAc and BMIM Br in Staged Oxidation of <i>p</i>-Xylene and Oxidative Treatment of CTA for Obtaining TPA with a Low Content of 4-CBA (2019)

Synthesis of terephthalic acid (TPA) with a low content of p-toluic acid and 4-carboxybenzaldehyde (4-CBA) intermediates through only oxidative procedures without hydrogenation purification is a promising approach to simplify commercial production. Here, addition of ammonium acetate (NH4OAc) and 1-butyl-3-methylimidazolium bromide (BMIM Br) has been proposed to conduct two-step oxidation of p-xylene and oxidative treatment of crude terephthalic acid (CTA) using conventional conditions and a Co/Mn/Br catalyst. The additives enabled an efficient oxidation of undesirable intermediates due to an increase in their solubility under reaction conditions. Concentration of the catalyst, temperature and duration of the procedure were important factors affecting the oxidation. Subsequent recrystallization was advisable for further removal of the intermediates, as well as for the hydrolysis of the impure amide that was caused by bringing them into contact with nitrogen compounds. BMIM Br required a higher temperature than NH4OAc to oxidize the intermediates, but did not generate colored impurities during the oxidation. The oxidative treatment of CTA in the presence of BMIM Br allowed to obtain an absolute white TPA with a content of 4-CBA below 300 ppm that corresponded to medium quality TPA.