gebhart/patrepeval huggingface dataset:
Soluble RAGE Is a Biomarker for Idiopathic Pulmonary Fibrosis (2021)

The receptor for advanced glycosylated end products (RAGE) mediates inflammation and injury response through ligand binding and signal transduction. A soluble form (sRAGE) of RAGE, a decoy receptor, is readily detectable in peripheral blood and has been associated with lung diseases including COPD and idiopathic pulmonary fibrosis (IPF). A recent report has demonstrated association of lower level of sRAGE with severe disease and worse outcomes in IPF patients. We have validated these findings in an independent cohort and demonstrated differential expression levels of AGER gene (encoding for RAGE) in lung tissue and sRAGE protein in bronchoalveolar lavage (BAL) of IPF patients and controls. METHODS: We have analyzed expression of AGER in IPF and control lungs using the LGRC (Lung Tissue Research Consortium) dataset and analyzed plasma and BAL levels of sRAGE using an IPF cohort and a multiplex Luminex assay. Levels of sRAGE were compared between the IPF and control groups and correlated with pulmonary function and outcomes in IPF subjects. We also explored the utility of sRAGE as a marker predicting patient outcomes. RESULTS: We have identified that AGER is 2.62-fold decreased in IPF lungs (N=134) compared to controls (N=108, P<0.0001). The levels of AGER in IPF were directly correlated with FVC (r=0.38, P<0.0001), DLCO (r=0.48, P=<0.0001) and inversely correlated with calculated GAP mortality prediction scores (Spearman rho=-0.42, P<0.0001). It was further confirmed by plasma levels of sRAGE protein in IPF (N=74) and controls (N=38). The sRAGE levels were lower in IPF (median 868 pg/mL) compared to controls (median 1176 pg/mL), P=0.001. In IPF, plasma sRAGE levels are correlated with FVC (r=0.28, P<0.01) and DLCO (r=0.33, P<0.01). We explored the utility of sRAGE as a predictive biomarker for patient reported outcomes and found a borderline correlation of sRAGE levels with shortness of breath (N=59, r=-0.23, P=0.009). Finally, in an independent cohort, the expression levels of sRAGE in BAL of IPF patients were also reduced compared to controls with median 475 pg/mL in IPF (N=131) and 957 pg/mL in unaffected controls (N=18), P<0.0001. CONCLUSIONS: AGER expression is reduced in IPF lungs and sRAGE level is also reduced in IPF blood and BAL samples. AGER gene expression levels inversely correlate with disease severity and the GAP mortality predictor score. Plasma levels of sRAGE are also inversely correlated with disease severity and borderline with patient reported shortness of breath. Our study confirmed sRAGE and AGER expression as predictive biomarkers for IPF.
<title>Integrating optical wave simulation into microsystems CAD tools</title> (2001)

A method for integrating optical wave propagation into electrical simulators is presented. For this purpose the Beam Propagation Method has been implemented using the HDL-A<SUP>TM</SUP> language. This enables the simulation of optical wave propagation on the system level, using current Microsystems CAD tools. Some typical optical components have been simulated using this technique and satisfactory results were obtained. This enables the analysis of MOEMS components into standard Microsystems CAD tools using electrical simulators.
Gegenwart und Zukunft der molekularen Therapie – vom Genom zum Antigenom (2003)

Zusammenfassung Genchips erlauben die Analyse des mehr oder weniger kompletten Genexpressionsprofils von Tumorzellen und normalen Geweben in einem einzigen Experiment. Drei Hauptmotive rufen unser Interesse an der Genchipanalyse wach: (i) Die Genchiptechnologie bietet eine neue diagnostische Zusatzuntersuchung. (ii) Wir erhoffen uns, mehr über die Biologie der Tumorzelle zu erfahren. (iii) Wir hoffen mit Hilfe dieser Technologie neue therapeutische Zielstrukturen zu finden. Ein Hauptziel dieser Studien ist die Identifikation geeigneter Antigene für immunologische Therapieansätze.
Supplementary Figure Legends 1-7 from A Smac Mimetic Rescue Screen Reveals Roles for Inhibitor of Apoptosis Proteins in Tumor Necrosis Factor-α Signaling (2023)

Supplementary Figure Legends 1-7 from A Smac Mimetic Rescue Screen Reveals Roles for Inhibitor of Apoptosis Proteins in Tumor Necrosis Factor-α Signaling
Copper‐Decorated Iron Carbide Nanoparticles Heated by Magnetic Induction as Adaptive Multifunctional Catalysts for the Selective Hydrodeoxygenation of Aldehydes (2022)

Abstract Copper‐decorated iron carbide nanoparticles (Cu@ICNPs) are prepared following an organometallic approach, producing a multifunctional catalytic system that can be heated magnetically. ICNPs act as heating agents, generating thermal energy from the alternating current magnetic field in an extremely localized, rapid, and efficient manner, thereby heating and activating the catalytically active Cu‐containing NPs present at their surface. Upon exposure to magnetic induction, the Cu@ICNPs catalyst is capable of selectively hydrodeoxygenating aromatic aldehydes under mild observable conditions (≈100 °C, 3 bar H 2 ), without hydrogenation of the aromatic ring. A large scope of benzylic and non‐benzylic aldehydes including key biomass‐derived platform chemicals could be effectively converted to valuable aromatic alkanes. In addition, the Cu@ICNPs catalytic system is found adaptive to intermittent electricity supply, which is of great interest when considering the use of alternative renewable energy sources. In contrast, Cu@ICNPs, ICNPs, or Cu NPs show low activity when heated conventionally, even up to 200 °C. This work demonstrates the possibility to use magnetic induction heating to perform challenging hydrodeoxygenation reactions at mild pressure and temperature with noble metal‐free catalysts, while being able to cope with fluctuating energy sources.
Design and evaluation of a 3D video system based on H.264 view coding (2006)

Recent advances in video compression and 3D displays have necessitated a further understanding and development of 3D video coding algorithms. The emergence of low cost autostereoscopic displays is expected to drive the growth of 3DTV services. This paper discusses key issues that affect the quality of 3D video experience on autostereoscopic displays. The characteristics of the human visual system can be exploited to compress individual stereo views at different qualities without affecting the perceptual quality of the 3D video. The H.264/AVC video coding algorithm was used to compress each view. We examine the bounds of asymmetric stereo view compression and its relationship to eye-dominance based on a user study. This paper also presents the design and development of a modular video player with stereoscopic and multi-view capabilities including a discussion of useful tools for accelerating the development and enhancing flexibility. The experimental results indicate that eye-dominance influences 3D perception and as a result will impact the coding efficiency of 3D video.
Fiber-Optic Based Laser Wakefield Accelerated Electron Beams and Potential Applications in Radiotherapy Cancer Treatments (2022)

Ultra-compact electron beam technology based on laser wakefield acceleration (LWFA) could have a significant impact on radiotherapy treatments. Recent developments in LWFA high-density regime (HD-LWFA) and low-intensity fiber optically transmitted laser beams could allow for cancer treatments with electron beams from a miniature electronic source. Moreover, an electron beam emitted from a tip of a fiber optic channel could lead to new endoscopy-based radiotherapy, which is not currently available. Low-energy (10 keV–1 MeV) LWFA electron beams can be produced by irradiating high-density nano-materials with a low-intensity laser in the range of ~1014 W/cm2. This energy range could be useful in radiotherapy and, specifically, brachytherapy for treating superficial, interstitial, intravascular, and intracavitary tumors. Furthermore, it could unveil the next generation of high-dose-rate brachytherapy systems that are not dependent on radioactive sources, do not require specially designed radiation-shielded rooms for treatment, could be portable, could provide a selection of treatment energies, and would significantly reduce operating costs to a radiation oncology clinic.
BatchDB (2017)

In this paper we present BatchDB, an in-memory database engine designed for hybrid OLTP and OLAP workloads. BatchDB achieves good performance, provides a high level of data freshness, and minimizes load interaction between the transactional and analytical engines, thus enabling real time analysis over fresh data under tight SLAs for both OLTP and OLAP workloads.
Protection against retroviral diseases after vaccination is conferred by interference to superinfection with attenuated murine leukemia viruses (1993)

Cell cultures expressing a retroviral envelope are relatively resistant to superinfection by retroviruses which bear envelopes using the same receptor. We tested whether this phenomenon, known as interference to superinfection, might confer protection against retroviral diseases. Newborn mice first inoculated with the attenuated strain B3 of Friend murine leukemia virus (F-MuLV) were protected against severe early hemolytic anemia and nonacute anemiant erythroleukemia induced by the virulent strain 57 of F-MuLV. Vaccinated animals were also protected as adults against acute polycythemic erythroleukemia induced upon inoculation with the viral complex containing the defective spleen focus-forming virus and F-MuLV 57 as helper virus. Animals were inoculated as newborns, which is known to induce immune tolerance in mice, and the rapid kinetics of protection, incompatible with the delay necessary for the immune response to develop, indicated that protection was not due to an immune mechanism but rather was due to the rapid and long-lasting phenomenon of interference. This result was confirmed by combining parental and envelope chimeric MuLV from different interference groups as vaccinal and challenge viruses. Although efficient protection could be provided by vaccination by interference, we observed that attenuated replication-competent retroviruses from heterologous interference groups might exert deleterious synergistic effects.
Exploring the dynamic knowledge structure of studies on the Internet of things: Keyword analysis (2018)

A wide range of studies in various disciplines has focused on the Internet of Things (IoT) and cyber‐physical systems (CPS). However, it is necessary to summarize the current status and to establish future directions because each study has its own individual goals independent of the completion of all IoT applications. The absence of a comprehensive understanding of IoT and CPS has disrupted an efficient resource allocation. To assess changes in the knowledge structure and emerging technologies, this study explores the dynamic research trends in IoT by analyzing bibliographic data. We retrieved 54,237 keywords in 12,600 IoT studies from the Scopus database, and conducted keyword frequency, co‐occurrence, and growth‐rate analyses. The analysis results reveal how IoT technologies have been developed and how they are connected to each other. We also show that such technologies have diverged and converged simultaneously, and that the emerging keywords of trust, smart home, cloud, authentication, context‐aware, and big data have been extracted. We also unveil that the CPS is directly involved in network, security, management, cloud, big data, system, industry, architecture, and the Internet.
Differences in the Performance of Allyl Based Palladium Precatalysts for Suzuki-Miyaura Reactions (2020)

We evaluate the activity of different allyl-based precatalysts in Suzuki-Miyaura reactions as the ancillary ligand (NHC or phosphine), reaction conditions, and substrates are varied. In some cases, we connect relative activity to both the mechanism of activation and the prevalence of the formation of inactive palladium(I) dimers.
DrawFromDrawings: 2D Drawing Assistance via Stroke Interpolation with a Sketch Database (2016)

We present DrawFromDrawings, an interactive drawing system that provides users with visual feedback for assistance in 2D drawing using a database of sketch images. Following the traditional imitation and emulation training from art education, DrawFromDrawings enables users to retrieve and refer to a sketch image stored in a database and provides them with various novel strokes as suggestive or deformation feedback. Given regions of interest (ROIs) in the user and reference sketches, DrawFromDrawings detects as-long-as-possible (ALAP) stroke segments and the correspondences between user and reference sketches that are the key to computing seamless interpolations. The stroke-level interpolations are parametrized with the user strokes, the reference strokes, and new strokes created by warping the reference strokes based on the user and reference ROI shapes, and the user study indicated that the interpolation could produce various reasonable strokes varying in shapes and complexity. DrawFromDrawings allows users to either replace their strokes with interpolated strokes (deformation feedback) or overlays interpolated strokes onto their strokes (suggestive feedback). The other user studies on the feedback modes indicated that the suggestive feedback enabled drawers to develop and render their ideas using their own stroke style, whereas the deformation feedback enabled them to finish the sketch composition quickly.
High Efficiency Stacked Organic Light-Emitting Diodes Employing Li2O as a Connecting Layer (2006)

We demonstrate the high-efficiency stacked organic light-emitting diodes (OLEDs) introducing new connecting layers. In the green stacked OLEDs, the external efficiencies increase proportionally to the number of the stacked units without suffering the decrease in power efficiency. The current, power and external efficiencies at 0.5 mA/cm 2 of the stacked OLED with six stacked units (6-stacked OLED) have reached 235 cd/A, 46.6 lm/W, and 65.8%, respectively. Furthermore, we have applied the connecting layers to a white stacked OLED and fabricated an active-matrix full-color display with a low temperature polysilicon thin film transistor backplane. In the device, the current efficiency of the white 2-stacked OLED is enhanced by a factor of 2.2. The initial luminance drop is significantly suppressed for the white 2-stacked OLED compared to 1-stacked OLED. The proposed white stacked OLED technology can be applied to a full-color display for a practical use.
Suppression of impairment due to intra-channel crosstalk using wavelength selective filter with broadband channel isolation (2008)

We quantitatively show suppression of intra-channel crosstalk using wavelength selective filter with broadband channel isolation, and confirm that 24 nodes can be used in a 50 GHz-spaced 44 Gbps transmission system with OSNR penalty of 0.5 dB.
Tracheostomy – percutaneous dilatational or standard surgical? Are there any helpful prognostic aids? (2018)

Patients in need for longterm tracheal cannula benefit from a surgical tracheostomy. For choosing the tracheostomy procedure (percutaneous dilatational tracheostomy (PDT) or standard surgical (sT)) a prognostic aid about the perspective cannulation period would be helpful. The aim was to identify prognostic parameters.
IDES: a progress report (Intrusion-Detection Expert System) (2002)

Describes a real-time intrusion-detection expert system (IDES), that observes user behavior on a monitored computer system and adaptively learns what is normal for individual users, groups, remote hosts, and the overall system behavior. Observed behavior is flagged as a potential intrusion if it deviates significantly from the expected behavior or if it triggers a rule in the expert-system rule base.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Improved Prediction of Antisense Oligonucleotide Efficacy for Exon Skipping Using Ensemble Learning and Feature Selection (2023)

Antisense oligonucleotide (ASO)-mediated exon skipping has become a valuable tool for investigating gene function and developing gene therapy. Machine learning-based computational methods such as eSkip-Finder have been developed to predict the efficacy of ASOs via exon skipping. However, these methods are computationally demanding, and the accuracy of predictions remains suboptimal. In this study, we propose a new approach to reduce computational burden and improve prediction performance by using feature selection within machine learning algorithms and ensemble learning techniques. We evaluated our approach using a dataset of experimentally validated exon skipping events, dividing it into training and testing sets. Our results demonstrate that using a 3-way voting approach with random forest, gradient boosting, and XGBoost can significantly reduce computation time to under ten seconds while improving prediction performance, as measured by R2 for both 2&amp;rsquo;-O-methyl nucleotides (2OMe) and phosphorodiamidate morpholino oligomers (PMOs). Additionally, the feature importance ranking derived from our approach is in good agreement with previously published results. Our findings suggest that our approach has the potential to enhance the accuracy and efficiency of predicting ASO efficacy via exon skipping. It could also facilitate the development of novel therapeutic strategies. This study could contribute to the ongoing efforts to improve ASO design and optimize gene therapy approaches.
Cyclin-dependent Kinase-mediated Sox2 Phosphorylation Enhances the Ability of Sox2 to Establish the Pluripotent State (2015)

Sox2 is a key factor in maintaining self-renewal of embryonic stem cells (ESCs) and adult stem cells as well as in reprogramming differentiated cells back into pluripotent or multipotent stem cells. Although previous studies have shown that Sox2 is phosphorylated in human ESCs, the biological significance of Sox2 phosphorylation in ESC maintenance and reprogramming has not been well understood. In this study we have identified new phosphorylation sites on Sox2 and have further demonstrated that Cdk2-mediated Sox2 phosphorylation at Ser-39 and Ser-253 is required for establishing the pluripotent state during reprogramming but is dispensable for ESC maintenance. Mass spectrometry analysis of purified Sox2 protein has identified new phosphorylation sites on two tyrosine and six serine/Threonine residues. Cdk2 physically interacts with Sox2 and phosphorylates Sox2 at Ser-39 and Ser-253 in vitro. Surprisingly, Sox2 phosphorylation at Ser-39 and Ser-253 is dispensable for ESC self-renewal and cell cycle progression. In addition, Sox2 phosphorylation enhances its ability to establish the pluripotent state during reprogramming by working with Oct4 and Klf4. Finally, Cdk2 can also modulate the ability of Oct4, Sox2, and Klf4 in reprogramming fibroblasts back into pluripotent stem cells. Therefore, this study has for the first time demonstrated that Sox2 phosphorylation by Cdk2 promotes the establishment but not the maintenance of the pluripotent state. It might also help explain why the inactivation of CDK inhibitors such as p53, p21, and Arf/Ink4 promotes the induction of pluripotent stem cells.
Direct Optical Link between a mmWave Optical Frequency Comb and a Chip-Scale Mode-Locked Laser (2019)

A 10GHz MLL-PIC is synchronized to an optical frequency comb at 120GHz using harmonic injection locking. After injection, the Allan Deviation in the repetition rate of the MLL-PIC is 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-11</sup> at 1s. The mmWave comb features an intracavity high-finesse etalon to enhance its frequency stability.
Stereocontrolled synthesis of calyculin A: construction of the C(26)–C(37) amide-oxazole unit (1992)

A. G. M. Barrett, J. J. Edmunds, J. A. Hendrix, J. W. Malecha and C. J. Parkinson, J. Chem. Soc., Chem. Commun., 1992, 1240 DOI: 10.1039/C39920001240
Isolation and Identification of Antimicrobial Compounds in Brazilian Propolis (1994)

Three distinct antimicrobial compounds were isolated from Brazilian propolis. These compounds were identified as 3,5-diprenyl-4-hydroxycinnamic acid (1), 3-prenyl-4-dihydrocinnamoloxycinnamic acid (2), and 2,2-dimethyl-6-carboxyethenyl-2H-1-benzopyran (3). The respective antimicrobial activity, expressed as MIC in μg/ml, 1–3 against Bacillus cereus was 15.6, 31.3, and 125; that against Enterobacter aerogenes was 31.3, 62.5, and 125; and that against Arthroderma benhamiae was 15.6, > 250, and 62.5. Compound 1 is likely to be one of the major antimicrobial compounds in Brazilian propolis.
319 Reflections at the Halfway Point of a Multi-Institutional Comprehensive Usda Sustainable Agriculture Systems Project: Empowering the US Broiler Industry for Transformation and Sustainability (2022)

Abstract We received funding for a USDA SAS project that began in September (2019) that involves 7 institutions and approximately 30 faculty. Overarching goals of the project are to improve the system wide efficiency of nutrient and water use in broiler production through a) a better understanding and manipulation of the host physiology and microbial influence on water and nutrient efficiency, b) implementation of novel algal-based technology, and c) effecting educational-behavioral changes through enhanced education and extension programs. To date: a) We have had group progress report meetings 6-8 times per year, and b) we have supported or involved 19 undergraduate students, 22 grad students, and 6 post-docs on the project. The group collectively has published 15 book chapters, 74 refereed publications, 7 theses/dissertations, and filed 2 patents. We also had a symposium at a national meeting. Despite restrictions due to Covid, we have been able to have students take part in internships at U of A and Cornell. A minor in Sustainable Agriculture Systems has been established at Cornell. A class offered by Cornell (The global food, energy, and water nexus – engaging students from the US, China, and India to Chart a Sustainable Future) enables students to participate in the class and receive credit from their home institution. This class incorporates faculty involved in the SAS grant as well as many international guest speakers who are experts in their field. An area we hope to improve upon is getting our message out to our clientele and general public via several different methods.
Hybrid Models of Physical Systems and Discrete Controllers (2000)

A unifying modeling method is presented that (1) extends the declarative, equation based, object oriented modeling approach by discontinuous and variable structure components which arise from abstractions in physical system models and (2) combines this with imperative, reactive, discrete event controllers based on the statechart and the sequential function chart formalisms.