gebhart/patrepeval huggingface dataset:
Mutational spectra of aflatoxin B 1 in vivo establish biomarkers of exposure for human hepatocellular carcinoma (2017)

Aflatoxin B<sub>1</sub> (AFB<sub>1</sub>) and/or hepatitis B and C viruses are risk factors for human hepatocellular carcinoma (HCC). Available evidence supports the interpretation that formation of AFB<sub>1</sub>-DNA adducts in hepatocytes seeds a population of mutations, mainly G:C→T:A, and viral processes synergize to accelerate tumorigenesis, perhaps via inflammation. Responding to a need for early-onset evidence predicting disease development, highly accurate duplex sequencing was used to monitor acquisition of high-resolution mutational spectra (HRMS) during the process of hepatocarcinogenesis. Four-day-old male mice were treated with AFB<sub>1</sub> using a regimen that induced HCC within 72 wk. For analysis, livers were separated into tumor and adjacent cellular fractions. HRMS of cells surrounding the tumors revealed predominantly G:C→T:A mutations characteristic of AFB<sub>1</sub> exposure. Importantly, 25% of all mutations were G→T in one trinucleotide context (C<u>G</u>C; the underlined G is the position of the mutation), which is also a hotspot mutation in human liver tumors whose incidence correlates with AFB<sub>1</sub> exposure. The technology proved sufficiently sensitive that the same distinctive spectrum was detected as early as 10 wk after dosing, well before evidence of neoplasia. Additionally, analysis of tumor tissue revealed a more complex pattern than observed in surrounding hepatocytes; tumor HRMS were a composite of the 10-wk spectrum and a more heterogeneous set of mutations that emerged during tumor outgrowth. We propose that the 10-wk HRMS reflects a short-term mutational response to AFB<sub>1</sub>, and, as such, is an early detection metric for AFB<sub>1</sub>-induced liver cancer in this mouse model that will be a useful tool to reconstruct the molecular etiology of human hepatocarcinogenesis.
Purification of groundwater contaminated with iron and manganese by effective cost filter materials for households in rural areas (2018)

This research investigated the feasibility of effective cost filter materials for groundwater purification in the small and medium scale households in Vietnamese rural areas. The trial models could treat 30 L of groundwater with aeration flow 5 L/min for 15 min. After 24 h of sedimentation, the water was filtered through layers of gravel (h = 11 cm), sea sand (h = 11 cm), activated carbon (h = 15 cm), manganese sand (h = 12 cm), sea sand (h = 11 cm) and gravel (h = 11 cm). After treatment process, the concentration of Fe and Mn ions of the output trial models was lower than the Vietnamese standard for drinking water. The model has a simple structure and easy assembly for washing the filter materials which continued to be used for the next filtration process. These models provide in rural areas, where it promising solutions for supplying drinking water to households is difficult to get clean ground water.
Myogenic gene expression signature establishes that brown and white adipocytes originate from distinct cell lineages (2007)

Attainment of a brown adipocyte cell phenotype in white adipocytes, with their abundant mitochondria and increased energy expenditure potential, is a legitimate strategy for combating obesity. The unique transcriptional regulators of the primary brown adipocyte phenotype are unknown, limiting our ability to promote brown adipogenesis over white. In the present work, we used microarray analysis strategies to study primary preadipocytes, and we made the striking discovery that brown preadipocytes demonstrate a myogenic transcriptional signature, whereas both brown and white primary preadipocytes demonstrate signatures distinct from those found in immortalized adipogenic models. We found a plausible SIRT1-related transcriptional signature during brown adipocyte differentiation that may contribute to silencing the myogenic signature. In contrast to brown preadipocytes or skeletal muscle cells, white preadipocytes express Tcf21, a transcription factor that has been shown to suppress myogenesis and nuclear receptor activity. In addition, we identified a number of developmental genes that are differentially expressed between brown and white preadipocytes and that have recently been implicated in human obesity. The interlinkage between the myocyte and the brown preadipocyte confirms the distinct origin for brown versus white adipose tissue and also represents a plausible explanation as to why brown adipocytes ultimately specialize in lipid catabolism rather than storage, much like oxidative skeletal muscle tissue.
An integrated model for statistical and vision monitoring in manufacturing transitions (2003)

Abstract Manufacturing transitions have been increasing due to higher pressures for product variety. One dimension of this variety is color. A major quality control challenge is to regulate the color by capturing data on color in real‐time during the operation and to use it to assess the opportunities for good parts. Control charting, when applied to a stable state process, is an effective monitoring tool to continuously check for process shifts or upsets. However, the presence of transition events can impede the normal performance of a traditional control chart. In this paper, we present an integrated model for statistical and vision monitoring using a tracking signal to determine the start of the transition and a confirmation signal to ensure that any process oscillation has concluded. We also developed an automated color analysis and forecasting system (ACAFS) that we can adjust and calibrate to implement this methodology in different production processes. We use a color transition process in plastic extrusion to illustrate a transition event and demonstrate our proposed methodology. Copyright © 2003 John Wiley &amp; Sons, Ltd.
Cloud SLAs (2012)

The variability in the service level agreements (SLAs) of cloud providers prompted us to ask the question how do the SLAs compare and how should the SLAs be defined for future cloud services. We break down a cloud SLA into easy to understand components and use it to compare SLAs of public cloud providers. Our study indicates that none of the surveyed cloud providers offer any performance guarantees for compute services and leave SLA violation detection to the customer. We then provide guidance on how SLAs should be defined for future cloud services.
Data from AMG 479, a fully human anti–insulin-like growth factor receptor type I monoclonal antibody, inhibits the growth and survival of pancreatic carcinoma cells (2023)

&lt;div&gt;Abstract&lt;p&gt;Pancreatic carcinoma is a leading cause of cancer deaths, and recent clinical trials of a number of oncology therapeutics have not substantially improved clinical outcomes. We have evaluated the therapeutic potential of AMG 479, a fully human monoclonal antibody against insulin-like growth factor (IGF) type I receptor (IGF-IR), in two IGF-IR–expressing pancreatic carcinoma cell lines, BxPC-3 and MiaPaCa2, which also differentially express insulin receptor (INSR). AMG 479 bound to IGF-IR (&lt;i&gt;K&lt;/i&gt;&lt;sub&gt;D&lt;/sub&gt; 0.33 nmol/L) and blocked IGF-I and IGF-II binding (IC&lt;sub&gt;50&lt;/sub&gt; &lt; 0.6 nmol/L) without cross-reacting to INSR. AMG 479 completely inhibited ligand-induced (IGF-I, IGF-II, and insulin) activation of IGF-IR homodimers and IGF-IR/INSR hybrids (but not INSR homodimers) leading to reduced cellular viability in serum-deprived cultures. AMG 479 inhibited &gt;80% of basal IGF-IR activity in BxPC-3 and MiaPaCa2 xenografts and prevented IGF-IR and IGF-IR/INSR hybrid activation following challenge with supraphysiologic concentrations of IGF-I. As a single agent, AMG 479 inhibited (∼80%) the growth of pancreatic carcinoma xenografts, and long-term treatment was associated with reduced IGF-IR signaling activity and expression. Efficacy seemed to be the result of two distinct biological effects: proapoptotic in BxPC-3 and antimitogenic in MiaPaCa2. The combination of AMG 479 with gemcitabine resulted in additive inhibitory activity both &lt;i&gt;in vitro&lt;/i&gt; and &lt;i&gt;in vivo&lt;/i&gt;. These results indicate that AMG 479 is a clinical candidate, both as a single agent and in combination with gemcitabine, for the treatment of patients with pancreatic carcinoma.[Mol Cancer Ther 2009;8(5):1095–105]&lt;/p&gt;&lt;/div&gt;
Modulation of murine tumor major histocompatibility antigens by cytokines in vivo and in vitro. (1988)

The capacity of different cytokines to upregulate major histocompatibility complex (MHC) expression on murine tumor cells in vitro, and on s.c. tumors or pulmonary metastases in vivo has been examined. Interleukins-1, -2, and -4 (IL-1, -2, -4), tumor necrosis factor-alpha (TNF-alpha), alpha-interferon (IFN-alpha), and gamma-interferon (IFN-gamma), were incubated with tissue culture lines of murine tumor cells displaying low (MCA-101), intermediate (MCA-102, -106), or high (MCA-105) Class I expression. IFN-alpha and IFN-gamma significantly increased Class I but not Class II antigens on all lines. TNF-alpha, IL-1, -2, and -4 had no significant effect on Class I or II expression in vitro. Mice bearing pulmonary metastases or s.c. lesions generated by MCA-101 and -102 were treated with IFN-alpha or IFN-gamma i.p. or i.v., or with a single dose of TNF-alpha i.v. Immunoperoxidase staining of lung metastases or subcutaneous tumors showed an increase in Class I but not Class II expression on MCA-102 tumors treated with IFN-alpha or IFN-gamma. IL-1, -2, or TNF-alpha had no effect on MHC Class I or II expression in vivo. None of the cytokines tested could upregulate MHC Class I or II expression on MCA-101 tumors in vivo. Flow cytometry analysis demonstrated an increase in Class I but not Class II expression on MCA-102 and MCA-106 tumor cells from s.c. tumor treated with IFN-alpha or IFN-gamma. A kinetic analysis of the flow cytometry data revealed that augmented MCA-102 Class I levels persisted for several days after cessation of in vivo therapy with IFN-alpha. Our data suggest one possible mechanism for the synergistic antitumor effects of IL-2 and IFN-alpha.
Melt versus solvent coating: Structure and properties of block–copolymer‐based pressure‐sensitive adhesives (2002)

Abstract Pressure‐sensitive adhesives (PSAs) composed of a styrene–isoprene–styrene triblock copolymer and a midblock‐associating resin were prepared via solvent and hot‐melt coating. The formulations and thermal histories up to the point of coating were identical, yet significant differences in the properties were observed as a function of the coating method. The solvent‐coated PSA showed superior shear holding power, and the hot‐melt‐coated PSA performed better in tack and peel tests. Two factors resulting from the processing conditions were responsible for these property differences. The quick cooling process occurring after hot‐melt coating led to a poorly defined microstructure and, therefore, less physical crosslinking. Rheological data for melt‐pressed and solvent‐cast PSA films confirmed these microstructural differences. The increased solubility of the tackifier in the solvent additionally created a composition gradient in the solvent coating. Annealing improved the long‐range order of both hot‐melt and solvent coatings, producing a body‐centered cubic microstructure identified by small‐angle X‐ray scattering. This microstructure improved the shear strength of both types of adhesive coatings, whereas the peel and tack properties of the solvent coatings remained inferior to those of the hot‐melt coatings because of differences in the surface compositions. © 2002 Wiley Periodicals, Inc. J Appl Polym Sci 86: 3355–3367, 2002
A Neural Network Model of Temporal Code Generation and Position-Invariant Pattern Recognition (1999)

Numerous studies have suggested that the brain may encode information in the temporal firing pattern of neurons. However, little is known regarding how information may come to be temporally encoded and about the potential computational advantages of temporal coding. Here, it is shown that local inhibition may underlie the temporal encoding of spatial images. As a result of inhibition, the response of a given cell can be significantly modulated by stimulus features outside its own receptive field. Feedforward and lateral inhibition can modulate both the firing rate and temporal features, such as latency. In this article, it is shown that a simple neural network model can use local inhibition to generate temporal codes of handwritten numbers. The temporal encoding of a spatial pattern has the interesting and computationally beneficial feature of exhibiting position invariance. This work demonstrates a manner by which the nervous system may generate temporal codes and shows that temporal encoding can be used to create position-invariant codes.
Constraints on the Efficiency of Electromicrobial Production (2020)

Abstract Electromicrobial production technologies (EMP) aim to combine renewable electricity and microbial metabolism. We have constructed molecular to reactor scale models of EMP systems using H 2 -oxidation and extracellular electron transfer (EET). We predict the electrical-to-biofuel conversion efficiency could rise to ≥ 52% with in vivo CO 2 -fixation. H 2 and EET-mediated EMP both need reactors with high surface areas. H 2 -diffusion at ambient pressure requires areas 20 to 2,000 times that of the solar photovoltaic (PV) supplying the system. Agitation can reduce this to less than the PV area, and the power needed becomes negligible when storing ≥ 1.1 megawatts. EET-mediated systems can be built that are ≤ 10 times the PV area and have minimal resistive energy losses if a conductive extracellular matrix (ECM) with a resistivity and height seen in natural conductive biofilms is used. The system area can be reduced to less than the PV area if the ECM conductivity and height are increased to those of conductive artificial polymers. Schemes that use electrochemical CO 2 -fixation could achieve electrical-to-fuel efficiencies of almost 50% with no complications of O 2 -sensitivity.
Structural and Electrical Properties of MoTe2 and MoSe2 Grown by Molecular Beam Epitaxy (2016)

We demonstrate the growth of thin films of molybdenum ditelluride and molybdenum diselenide on sapphire substrates by molecular beam epitaxy. In situ structural and chemical analyses reveal stoichiometric layered film growth with atomically smooth surface morphologies. Film growth along the (001) direction is confirmed by X-ray diffraction, and the crystalline nature of growth in the 2H phase is evident from Raman spectroscopy. Transmission electron microscopy is used to confirm the layered film structure and hexagonal arrangement of surface atoms. Temperature-dependent electrical measurements show an insulating behavior that agrees well with a two-dimensional variable-range hopping model, suggesting that transport in these films is dominated by localized charge-carrier states.
WayPoint: Scaling coherence to 1000-core architectures (2010)

In this paper, we evaluate a set of coherence architectures in the context of a 1024-core chip multiprocessor (CMP) tailored to throughput-oriented parallel workloads. Based on our analysis, we develop and evaluate two techniques for scaling coherence to thousand-core CMPs. We find that a broadcast-based probe filtering scheme provides reasonable performance up to 128 cores for some benchmarks, but is not generally scalable. We propose a broadcast-collective network for accelerating probe filter misses, which extends scalability but falls short of supporting 1024 cores. We find that a sparse directory with an invalidate-on-evict policy can work well for many throughput-oriented workloads. However, the on-die structures required to achieve good performance carry a large performance and power overhead. To achieve thousand-core scalability with smaller and less associative sparse directories, we introduce WayPoint, a mechanism that increases directory associativity and capacity dynamically. Using less than 3% of total die area, WayPoint achieves performance within 4% of an infinitely large on-die directory.
Special Issue in Honor of Professor Jon Clardy (2020)

ADVERTISEMENT RETURN TO ISSUEEditorialNEXTSpecial Issue in Honor of Professor Jon ClardyMohammad R. SeyedsayamdostMohammad R. SeyedsayamdostPrinceton University, Princeton, New Jersey, United StatesLeibniz Institute for Natural Product Research and Infection Biology, Jena, GermanyMore by Mohammad R. Seyedsayamdosthttp://orcid.org/0000-0003-2707-4854 and Pierre StallforthPierre StallforthPrinceton University, Princeton, New Jersey, United StatesLeibniz Institute for Natural Product Research and Infection Biology, Jena, GermanyMore by Pierre Stallforthhttp://orcid.org/0000-0001-7260-9921Cite this: J. Nat. Prod. 2020, 83, 3, 565–568Publication Date (Web):March 27, 2020Publication History Published online27 March 2020Published inissue 27 March 2020https://pubs.acs.org/doi/10.1021/acs.jnatprod.0c00199https://doi.org/10.1021/acs.jnatprod.0c00199editorialACS PublicationsCopyright © 2020 American Chemical Society and American Society of Pharmacognosy. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views2904Altmetric-Citations2LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail PDF (1 MB) Get e-AlertscloseSUBJECTS:Chemical structure,Crystal structure,Pharmaceuticals,Protein structure Get e-Alerts
Some observations on the dynamics of a congestion control algorithm (1990)

We use simulation to make some observations about the behavior of the congestion control algorithm currently embedded in the 4.3-Tahoe BSD TCP implementation. We investigate a simple case of a few TCP connections, originating and terminating at the same pair of hosts, using a single bottleneck link. Our simulations reveal two unexpected phenomena. First, packets from the individual connections, rather than being mixed together, completely separate into individual clusters. Second, every connection loses a single packet during each congestion epoch. As a way of exploring the cause of these phenomena, we discuss how the behavior is altered by modifications to the congestion control algorithm and to the switch queue control algorithm .
Three‐dimensional tomography of composite fracture surfaces (2005)

The goal of this project was to image the three-dimensional fracture interface of a dental composite with the use of X-ray tomography. With the use of the Advanced Photon Source (APS) at Argonne National Laboratory, three-dimensional images were obtained of the crack interface of a dental composite material that had been subjected to three different treatments: a control, cycled in air, and cycled in a 50/50 mixture by volume of ethanol and distilled water. The cycle-loaded treatments were for 100,000 cycles at a load between 80 and 100 N at 5 Hz. The crack interface extended over 28 slices for the control, 96 for the air-cycled specimen, and 83 slices for the 50/50 solution cycle specimen. It would appear that the fatiguing of the specimens allowed for an increase in the crack interface as demonstrated by the 3D tomographical analysis. This volume increase in the crack interface is attributed to a separation of the filler fiber from the resin matrix. Three-dimensional tomography provides an excellent method to observe crack interfaces of dental composites subjected to different types of mechanical and environmental conditions.
Advanced Uncertainty Quantification Methods Deployed on Electromagnetic Dataset for Reservoir Saturation Mapping (2017)

This work introduces a novel approach that will aid the interpretation of the resistivity distribution maps obtained from electromagnetic surveys to produce more robust saturation maps. Fluid flow simulation and advanced uncertainty quantification methods are extensively applied. Two main uncertainty quantification methods are introduced; the probabilistic collocation method (PCM) and the Multi-Level Monte Carlo (MLMC) method. These methods were used to quantify the uncertainty in the permeability distribution in a synthetic reservoir. The results from this study are benchmarked against a reference case Monte Carlo Simulation (MCS) run over a large number of permeability realizations. The obtained results prove that it is possible to investigate a wide range of uncertainty in a spatial parameter in a more computationally efficient manner than current practices.
BGP Link State Extensions for SRv6 (2019)

Segment Routing IPv6 (SRv6) allows for a flexible definition of end-
to-end paths within various topologies by encoding paths as sequences
of topological or functional sub-paths, called segments. These
segments are advertised by the various protocols such as BGP, ISIS and
OSPFv3. BGP Link-state (BGP-LS) address-family solution for SRv6 is
similar to BGP-LS for SR for MPLS dataplane. This draft defines
extensions to the BGP-LS to advertise SRv6 Segments along with their
functions and other attributes via BGP.