gebhart/patrepeval huggingface dataset:
INTEGRATIVE ANALYSIS OF TWO CELL LINES DERIVED FROM A NON-SMALL-LUNG CANCER PATIENT – A PANOMICS APPROACH (2013)

Cancer cells derived from different stages of tumor progression may exhibit distinct biological properties, as exemplified by the paired lung cancer cell lines H1993 and H2073. While H1993 was derived from chemo-naive metastasized tumor, H2073 originated from the chemo-resistant primary tumor from the same patient and exhibits strikingly different drug response profile. To understand the underlying genetic and epigenetic bases for their biological properties, we investigated these cells using a wide range of large-scale methods including whole genome sequencing, RNA sequencing, SNP array, DNA methylation array, and de novo genome assembly. We conducted an integrative analysis of both cell lines to distinguish between potential driver and passenger alterations. Although many genes are mutated in these cell lines, the combination of DNA- and RNA-based variant information strongly implicates a small number of genes including TP53 and STK11 as likely drivers. Likewise, we found a diverse set of genes differentially expressed between these cell lines, but only a fraction can be attributed to changes in DNA copy number or methylation. This set included the ABC transporter ABCC4, implicated in drug resistance, and the metastasis associated MET oncogene. While the rich data content allowed us to reduce the space of hypotheses that could explain most of the observed biological properties, we also caution there is a lack of statistical power and inherent limitations in such single patient case studies.
Experiments with random projections for machine learning (2003)

Dimensionality reduction via Random Projections has attracted considerable attention in recent years. The approach has interesting theoretical underpinnings and offers computational advantages. In this paper we report a number of experiments to evaluate Random Projections in the context of inductive supervised learning. In particular, we compare Random Projections and PCA on a number of different datasets and using different machine learning methods. While we find that the random projection approach predictively underperforms PCA, its computational advantages may make it attractive for certain applications.
Comparison of Polymyxin E and Polymyxin B as an Additive to Pulmonary Surfactant in Escherichia coli Pneumonia of Ventilated Neonatal Rabbits (2017)

Addition of polymyxin to SF effectively promotes antimicrobial treatment and improves lung function in neonatal pneumonia of rabbits.
A background model initialization algorithm for video surveillance (2002)

Many motion detection and tracking algorithms rely on the process of background subtraction, a technique which detects changes from a model of the background scene. We present a new algorithm for the purpose of background model initialization. The algorithm takes as input a video sequence in which moving objects are present, and outputs a statistical background model describing the static parts of the scene. Multiple hypotheses of the background value at each pixel are generated by locating periods of stable intensity in the sequence. The likelihood of each hypothesis is then evaluated using optical flow information from the neighborhood around the pixel, and the most likely hypothesis is chosen to represent the background. Our results are compared with those of several standard background modeling techniques using surveillance video of humans in indoor environments.
Design of 2.87 GHz Frequency Synthesizer with Programmable Sweep for Diamond Color Defect based CMOS Quantum Sensing Applications (2022)

Recently, diamond color defect based quantum sensing applications such as nitrogen-vacancy (NV) center magnetometry have emerged in CMOS technology, which use optically detected magnetic resonance (ODMR) for sensing magnetic field strengths $(|\tilde{\mathrm{B}}|)$ from different environmental physical quantities. For ODMR based sensing, CMOS quantum sensors seek an onchip 2.87 GHz microwave (MW) signal generator. Moreover, in order to sense smaller $|\tilde{\mathrm{B}}|$, these CMOS quantum sensors also require that MW signal should be swept with sufficiently small step-size near 2.87 GHz. In this work, we present a fractional-N synthesizer based 2.87 GHz MW-generator (MWG) with an extremely small programmable sweep step-size for improved sensitivity of $|\tilde{\mathrm{B}}|$ measurements in CMOS NV magnetometry. The proposed MWG is implemented in 180 nm CMOS technology and simulations were done to validate the proposed design. Post-layout simulation results show that the proposed MWG achieves a minimum sweep-step size of 50 kHz, which can be used to sense $|\tilde{\mathrm{B}}|\lt 0.9\;\mu \mathrm{T}$ and exhibits a phase noise of −114.5 dBc/Hz at an offset of 1 MHz near 2.87 GHz center frequency.
A Prototype Pyrolysis / Oxidation System for Solid Waste Processing (2005)

&lt;div class="htmlview paragraph"&gt;Pyrolysis is a very versatile waste processing technology which can be tailored to produce a variety of solid liquid and/or gaseous products. The main disadvantages of pyrolysis processing are: (1) the product stream is more complex than for many of the alternative treatments; (2) the product gases cannot be vented directly into the cabin without further treatment because of the high CO concentrations. One possible solution is to combine a pyrolysis step with catalytic oxidation (combustion) of the effluent gases. This integration takes advantage of the best features of each process, which is insensitivity to product mix, no O&lt;sub&gt;2&lt;/sub&gt; consumption, and batch processing, in the case of pyrolysis, and simplicity of the product effluent stream in the case of oxidation. In addition, this hybrid process has the potential to result in a significant reduction in Equivalent System Mass (ESM) and system complexity. This paper describes the development of a prototype hybrid pyrolysis/oxidation system which can process up to 100 grams of material. The prototype includes a multi-stage reactor and product collection, process monitoring and process control systems. Initial experiments have been done with wheat straw, as well as with chicken litter and chicken manure as analogs for human waste.&lt;/div&gt;
A monoclonal antibody that neutralizes SARS-CoV-2 variants, SARS-CoV, and other sarbecoviruses (2021)

The repeated emergence of highly pathogenic human coronaviruses as well as their evolving variants highlight the need to develop potent and broad-spectrum antiviral therapeutics and vaccines. By screening monoclonal antibodies (mAbs) isolated from COVID-19-convalescent patients, we found one mAb, 2-36, with cross-neutralizing activity against SARS-CoV. We solved the cryo-EM structure of 2-36 in complex with SARS-CoV-2 or SARS-CoV spike, revealing a highly conserved epitope in the receptor-binding domain (RBD). Antibody 2-36 neutralized not only all current circulating SARS-CoV-2 variants and SARS-COV, but also a panel of bat and pangolin sarbecoviruses that can use human angiotensin-converting enzyme 2 (ACE2) as a receptor. We selected 2-36-escape viruses <i>in vitro</i> and confirmed that K378 T in SARS-CoV-2 RBD led to viral resistance. Taken together, 2-36 represents a strategic reserve drug candidate for the prevention and treatment of possible diseases caused by pre-emergent SARS-related coronaviruses. Its epitope defines a promising target for the development of a pan-sarbecovirus vaccine.
Histamine Blocks Interleukin 2 (IL-2) Gene Expression and Regulates IL-2 Receptor Expression (1990)

Histamine inhibited the proliferative response of human peripheral blood mononuclear cells (PBMC) to the T cell mitogen Phytohemagglutinin-P (PHA-P) in a dose-dependent fashion. This inhibition was mediated via the H2 receptor since cimetidine, a known H2 antagonist, removed the inhibition, whereas the addition of the H1 antagonist Diphenhydramine did not. Inhibition occurred during the inductive phase of the cell cycle, since histamine added 24 hours after PHA-P stimulation had no effect on subsequent T cell proliferation, and was attributable to inhibition of interleukin-2 (IL-2) gene expression. Both secreted IL-2 and messenger RNA coding for IL-2 were inhibited by histamine. In contrast, histamine exerted no inhibitory effect on the expression of cell surface receptors for IL-2 as determined by flow cytometry. Furthermore, histamine-treated cells retained full responsiveness to exogenously administered IL-2, which completely reversed the anti-proliferative effect of histamine. In some donors, histamine enhanced the percentage of IL-2 receptor positive cells. Stimulated PBMC from AIDS KS patients as a group, displayed a lower percentage of IL-2 receptor bearing cells, which was significantly increased by the addition of histamine even at concentrations as low as 10(-6) M and peaking at 10(-3) M. These findings indicate that histamine exerts its anti-proliferative effects on T cells by inhibiting IL-2 production, via blockade of IL-2 gene expression. In addition, histamine seems to exert immunomodulating effects on IL-2 receptor expression, particularly in those individuals with AIDS-KS.
Performance analysis of feedback synchronization for multicast ABR flow control (2003)

We present a balanced and unbalanced binary-tree model to explore the delay performance of feedback synchronization algorithms for multicast ABR flow control. Using this model, we analyze the feedback-delay performance scalability of the soft-synchronization protocol (SSP), which derives a single "consolidated" RM (resource management) cell at each multicast branch-point from feedback RM cells of different downstream branches that are not necessarily responses to the same forward RM cell. In contrast with the other existing schemes, SSP is shown to be able to effectively support synchronization of feedback RM cell and make the effective RM cell roundtrip time (RTT) virtually independent of the multicast tree's topology. Also derived is the optimal RM-cell update interval for SSP to minimize RM-cell RTTs for a given multicast tree.
Mixed Potential Hydrogen Sensor Combining Oxide Ion Conductor with Oxide Electrode (1996)

A zirconia‐based electrochemical device attached with an oxide electrode was developed for the detection of in air at elevated temperature. The sensing mechanism was confirmed to involve a mixed potential at the oxide sensing electrode. Among the oxides tested, ZnO was the best suited for the sensing electrode, giving a sharp selective response to 50 ∼ 500 ppm in air at 450 to 600°C.
In vitro Antilisterial Effects of Citrus Oil Fractions in Combination with Organic Acids (2009)

The objectives of this study were to screen activity of citrus essential oil fractions (EOs) alone and in combination with organic acids against 2 species of Listeria. Five citrus EOs were initially screened by disc diffusion assay for antibacterial activity. Cold pressed terpeneless Valencia orange oil (CP terpeneless oil) had the strongest bacteriostatic (MIC) and bactericidal (MBC) properties at 0.55% and 1.67%, respectively. Four organic acids were tested for effectiveness against Listeria. Citric and malic acids proved to be the most effective with MBC of 1.1% alone. Assays were conducted to determine synergistic effects of EOs and citric or malic acids. There was a significant decrease in MIC and MBC to 0.04% EO plus 0.12% malic or citric acid. EOs from citrus paired with organic acids offer the potential as an all-natural antimicrobial for improving the safety of all-natural foods.
Gerüstumlagerungen an Clustern: Zur Reaktion von [(tBuP)Fe3(CO)10] mit Diphenylacetylen (1986)

Sehr ähnliche Energien von PC-, PFe-, CFe- und FeFe-Bindungen in Clustern werden durch die Bildung der Verbindungen 2 und 3 aus 1 und PhCCPh nahegelegt. Durch weitere Umsetzungen von 2 und 3 kommt eine in der Clusterchemie kaum jemals so vollständig beobachtete geschlossene Folge von Gerüstumlagerungen zustande.
Surface Carbon as a Reactive Intermediate in Dry Reforming of Methane to Syngas on a 5% Ni/MnO Catalyst (2018)

A 5% Ni/MnO catalyst has been tested for the dry reforming of methane at different temperatures and reactant partial pressures. Changing the reactant ratio with time on stream results in a decrease in the deactivation rate of the catalyst. Graphitic carbon growth and metal particle sintering have been observed by applying in situ transmission XRD using synchrotron radiation under actual reaction conditions. Both methane and carbon monoxide separately result in graphitic surface carbon, which can then be oxidized by carbon dioxide. The morphology of the surface carbon has been analyzed by TEM, and the reactions of both methane and carbon monoxide result in the same graphitic multiwalled carbon nanotubes. The present combination of catalytic experiments and in situ techniques suggests that surface carbon acts as an intermediate in the formation of CO and that catalyst deactivation happens via metallic particle sintering. These results enable a more rational choice of reaction conditions to ensure high catalyst activity and long-term stability. Future catalyst advances must aim to prevent metal particle sintering.
Vertically integrated double-layer on-chip crystalline silicon nanomembranes based on adhesive bonding (2013)

In this paper we demonstrate a three-dimensional (3D) photonic integration scheme based on crystalline silicon. We develop a process using SU-8 based adhesive bonding to fabricate vertically stacked, double-layer silicon nanomembranes. A single-layer silicon photonic integrated circuit fabricated on a silicon-on-insulator (SOI) chip and a bare SOI chip are bonded together, followed by removal of the bare SOI chip’s silicon substrate and buried oxide layer, to form a silicon nanomembrane as a platform for additional photonic layer. We designed and fabricated subwavelength nanostructure based fiber-to-chip grating coupler on the bonded silicon nanomembrane, and also inter-layer grating coupler for coupling between two silicon nanomembranes. The fiber-to-chip grating coupler has a peak efficiency of -3.9 dB at 1545 nm operating wavelength with transverse-electric (TE) polarization. The inter-layer grating coupler has a peak efficiency of -6.8 dB at 1533 nm operating wavelength with TE polarization. The demonstrated approach serves as a potential solution for 3D photonic integration and novel 3D photonic devices.
Adolescent idiopathic scoliosis: etiology, anatomy, natural history, and bracing. (2005)

Adolescent idiopathic scoliosis is a three-dimensional deformity of the spine. Despite active efforts by different research teams, the etiology of scoliosis remains unclear. Treatment of scoliosis requires a solid understanding of the natural history of the disorder as well as sound clinical judgment. The evaluation, monitoring, and institution of conservative treatment such as bracing can present a challenge to the orthopaedic surgeon. Clinical monitoring is the only intervention necessary in most patients. A detailed review of the patient's history as well as a careful physical examination can help establish the diagnosis and the risk for progression. Skeletal maturity, gender; growth velocity, curve location, and magnitude are factors that can help assess the likelihood of progression. Bracing is the only nonsurgical measure proven to have any effect on halting the progression of scoliosis. Other forms of conservative treatment have not been shown to significantly modify the natural history of idiopathic scoliosis. Bracing results are directly related to compliance with brace treatment; therefore, optimal results cannot be achieved without the patient's cooperation and family support.
A locally adaptive window for signal matching (2002)

The authors presents a signal matching algorithm that can select an appropriate window size adaptively so as to obtain both precise and stable estimation of correspondences. A statistical model is presented for disparity variation within a window, and it is used to establish a link between the window size and the uncertainty of the computed disparity. This makes it possible to choose the window size that minimizes uncertainty in the disparity computed at each point. A theory is presented for the model and the resultant algorithm, together with analytical and experimental results that demonstrate their effectiveness.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Solid polymer electrolyte and method of preparation (2023)

Disclosed is an improved solid electrolyte made of an interpenetrating network type solid polymer comprised of two compatible phases: a crosslinked polymer for mechanical strength and chemical stability, and an ionic conducting phase. The highly branched siloxane polymer of the present invention has one or more poly(ethylene oxide) (“PEO”) groups as a side chain. The PEO group is directly grafted to silicon atoms in the siloxane polymer. This kind of branched type siloxane polymer is stably anchored in the network structure and provides continuous conducting paths in all directions throughout the IPN solid polymer electrolyte. Also disclosed is a method of making an electrochemical cell incorporating the electrolyte. A cell made accordingly has an extremely high cycle life and electrochemical stability.
The Impact of Different Intraoperative Fluid Administration Strategies on Postoperative Extubation Following Multilevel Thoracic and Lumbar Spine Surgery: A Propensity Score Matched Analysis (2018)

PSM analysis of patients undergoing multilevel thoracic and/or lumbar spine fusion demonstrated that increased administration of crystalloid to colloid ratio is independently associated with delayed extubation. With increasing EBL, a proportionate reduction of crystalloids facilitates early extubation.
Anti-wrinkle activity of hydrolyzed ginseng saponins. (2003)

<i>Puccinia coronata</i> f. sp. <i>avenae</i> (<i>Pca</i>) is an important fungal pathogen causing crown rust that impacts oat production worldwide. Genetic resistance for crop protection against <i>Pca</i> is often overcome by the rapid virulence evolution of the pathogen. This study investigated the factors shaping adaptive evolution of <i>Pca</i> using pathogen populations from distinct geographic regions within the United States and South Africa. Phenotypic and genome-wide sequencing data of these diverse <i>Pca</i> collections, including 217 isolates, uncovered phylogenetic relationships and established distinct genetic composition between populations from northern and southern regions from the United States and South Africa. The population dynamics of <i>Pca</i> involve a bidirectional movement of inoculum between northern and southern regions of the United States and contributions from clonality and sexuality. The population from South Africa is solely clonal. A genome-wide association study (GWAS) employing a haplotype-resolved <i>Pca</i> reference genome was used to define 11 virulence-associated loci corresponding to 25 oat differential lines. These regions were screened to determine candidate <i>Avr</i> effector genes. Overall, the GWAS results allowed us to identify the underlying genetic factors controlling pathogen recognition in an oat differential set used in the United States to assign pathogen races (pathotypes). Key GWAS findings support complex genetic interactions in several oat lines, suggesting allelism among resistance genes or redundancy of genes included in the differential set, multiple resistance genes recognizing genetically linked <i>Avr</i> effector genes, or potentially epistatic relationships. A careful evaluation of the composition of the oat differential set accompanied by the development or implementation of molecular markers is recommended. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
Allergen-induced airway inflammation and bronchial responsiveness in interleukin-5 receptor alpha chain-deficient mice. (2000)

These findings indicate that IL-5Ralpha plays an important role in the development of antigen-induced airway eosinophilia and BHR in mice.
The CREAM-III Calorimeter (2008)

After successful recovery of the first CREAM (Cosmic Ray Energetics And Mass) instrument during the 2004/5 Antarctic campaign, the calorimeter was refurbished for a third flight, planned for December 2007. In this CREAM-III calorimeter, the optics were replaced with multi-clad fiber ribbons to enhance the light signal, and new readout electronics boards reduce noise even further than the previous low-noise version. These improvements allow increased sensitivity to low energy showers. A new assembly structure has also been fabricated for ease of recovery. This refurbished calorimeter was calibrated at a CERN test beam in October 2006, and is now being integrated with the rest of the CREAM detector suite. The construction of the calorimeter and tests of its optical and electronic components will be discussed.
Lasing in chiral microlasers (2003)

Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text A. Genack, V. Milner, V. I. Kopp, P. V. Shibaev, and J. Singer, "Lasing in chiral microlasers," in Frontiers in Optics, OSA Technical Digest (CD) (Optica Publishing Group, 2003), paper TuT1. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Performance Analysis of Slotted Carrier Sense IEEE 802.15.4 Acknowledged Uplink Transmissions (2008)

Advances in low-power and low-cost sensor networks have led to solutions mature enough for use in a broad range of applications, requiring various degrees of reliability. To facilitate this, a broad range of options are possible to tune reliability, throughput or energy cost in the IEEE 802.15.4 standard defining the medium access control (MAC) and physical layer for sensor networks. Knowing how to tune those knobs however requires detailed models of the protocol behavior under different conditions. In our earlier work, we have proposed a very accurate model for the slotted Carrier Sense Multiple Access with Collision Avoidance (CSMA/CA) access scheme of the IEEE 802.15.4 standard for the unacknowledged transmission mode. Because of the design of the 802.15.4 carrier sensing mechanism, modeling the performance of the network in case of acknowledged transmissions is not a trivial extension. In this paper, we hence derive such model and illustrate through simulations that it is extremely accurate. Next, using the model, guidelines are derived to optimize the energy or throughput performance of sensor networks using the IEEE 802.15.4 standard.
An Activatable siRNA Probe: Trigger‐RNA‐Dependent Activation of RNAi Function (2009)

Einfangen und Freisetzen: Eine Haarnadel-siRNA-Sonde aus einem „Sense“- und einem „Antisense“-Strang (rot bzw. blau) wurde entwickelt, die mit einer Auslöser-RNA aktiviert werden kann. In Gegenwart der Auslöser-RNA wurde ein stark sequenzabhängiges An- und Ausschalten der RNAi-Aktivität beobachtet (siehe Schema). Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.