gebhart/patrepeval huggingface dataset:
Metabolic modeling of polyhydroxybutyrate biosynthesis (1998)

A mathematical model describing intracellular polyhydroxybutyrate (PHB) synthesis in Alcaligenes eutrophus has been constructed. The model allows investigation of issues such as the existence of rate-limiting enzymatic steps, possible regulatory mechanisms in PHB synthesis, and the effects different types of rate expressions have on model behavior. Simulations with the model indicate that activities of all PHB pathway enzymes influence overall PHB flux and that no single enzymatic step can easily be identified as rate limiting. Simulations also support regulatory roles for both thiolase and reductase, mediated through AcCoA/CoASH and NADPH/NADP+ ratios, respectively. To make the model more realistic, complex rate expressions for enzyme-catalyzed reactions were used which reflect both the reversibility of the reactions and the reaction mechanisms. Use of the complex kinetic expressions dramatically changed the behavior of the system compared to a simple model containing only Michaelis-Menten kinetic expressions; the more complicated model displayed different responses to changes in enzyme activities as well as inhibition of flux by the reaction products CoASH and NADP+. These effects can be attributed to reversible rate expressions, which allow prediction of reaction rates under conditions both near and far from equilibrium.
Solution processed uniaxially oriented thin film of tert -butyl-substituted phthalocyanine (2019)

Abstract Uniaxially orientated thin film of phthalocyanine with bulky tert -butyl substituents ( t -BuPcH 2 ) was fabricated by bar-coating method. The thin film exhibited high dichroic ratio of more than 50 in the polarized absorption. Molecular packing structure of t -BuPcH 2 in the thin film was suggested by using the results of XRD measurements, in which the molecular plane of t -BuPcH 2 was determined to be perpendicular to the substrate and bar-sweep direction. In addition, the X-ray rocking curve measurements demonstrated that t -BuPcH 2 possessed highly molecular orientation in the thin film fabricated by bar-coating method.
MALTA: an asynchronous readout CMOS monolithic pixel detector for the ATLAS High-Luminosity upgrade (2019)

The ATLAS collaboration is currently investigating CMOS monolithic pixel sensors for the outermost layer of the upgrade of its Inner Tracker (ITk). For this application, two large scale prototypes featuring small collection electrode have been produced in a radiation-hard process modification of a standard 0.18 μm CMOS imaging technology: the MALTA, with a novel asynchronous readout, and the TJ MONOPIX, based on the well established "column-drain" architecture. The MALTA chip is the first full-scale prototype suitable for the development of a monolithic module for the ITk. It features a fast and low-power front-end, an architecture designed to cope with an hit-rate up to 2 MHz/mm2 without clock distribution over the matrix, hence reducing total power consumption, and LVDS drivers. Laboratory tests confirmed the performance of the asynchronous architecture expected from simulations. Extensive testbeam measurements have proved an average detection efficiency of 96% before irradiation at a threshold of ~230 e− with dispersion of ~36 e− and ENC lower than 10 e−. A non fully functional pixel masking scheme, forces operation at relatively high thresholds, causing inefficiency. A severe degradation of efficiency has been measured after neutron irradiation at a fluence 1 × 1015 1 MeV neq/cm2. Consistent results have been produced with the TJ MONOPIX. A correlation with inefficiency plots and pixel layout has triggered TCAD simulations, ending up to two possible solutions, implemented in a new prototype, the MiniMALTA.
Structure-Based Design of Novel Conformationally Restricted HIV Protease Inhibitors (1999)

In our efforts to discover a new generation of HIV protease inhibitors, which are structurally distinct and have minimal cross resistance to our current clinical candidate, amprenavir (VX-478), we designed a set of potent compounds bearing a novel backbone structure. Structural and modeling analysis of initial leads showed that these inhibitors bind in a strained conformation. We obtained dramatic improvement in binding by relieving the backbone conformational strain of the inhibitor. In this report, we will present our structure-based design approaches as well as the enzymatic results on these novel and highly potent inhibitors.
Characterization of Site-Specific N-Glycopeptide Isoforms of α-1-Acid Glycoprotein from an Interlaboratory Study Using LC–MS/MS (2016)

Glycoprotein conformations are complex and heterogeneous. Currently, site-specific characterization of glycopeptides is a challenge. We sought to establish an efficient method of N-glycoprotein characterization using mass spectrometry (MS). Using alpha-1-acid glycoprotein (AGP) as a model N-glycoprotein, we identified its tryptic N-glycopeptides and examined the data reproducibility in seven laboratories running different LC-MS/MS platforms. We used three test samples and one blind sample to evaluate instrument performance with entire sample preparation workflow. 165 site-specific N-glycopeptides representative of all N-glycosylation sites were identified from AGP 1 and AGP 2 isoforms. The glycopeptide fragmentations by collision-induced dissociation or higher-energy collisional dissociation (HCD) varied based on the MS analyzer. Orbitrap Elite identified the greatest number of AGP N-glycopeptides, followed by Triple TOF and Q-Exactive Plus. Reproducible generation of oxonium ions, glycan-cleaved glycopeptide fragment ions, and peptide backbone fragment ions was essential for successful identification. Laboratory proficiency affected the number of identified N-glycopeptides. The relative quantities of the 10 major N-glycopeptide isoforms of AGP detected in four laboratories were compared to assess reproducibility. Quantitative analysis showed that the coefficient of variation was <25% for all test samples. Our analytical protocol yielded identification and quantification of site-specific N-glycopeptide isoforms of AGP from control and disease plasma sample.
Role of platelets in experimental acute pancreatitis (2010)

Platelets play a crucial role in AP by regulating neutrophil infiltration, most likely mediated by MIP-2 production in the pancreas.
In vitro effects of aceclofenac on cytokines (IL-6, IL-8, LIF) and PGE2 production by human chondrocytes (1997)

peer reviewed
Ring size effects among metal complexes with macrocyclic ligands. The kinetics of aquation of dichlorotetraamine complexes of cobalt(III) involving macrocyclic ligands (1977)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRing size effects among metal complexes with macrocyclic ligands. The kinetics of aquation of dichlorotetraamine complexes of cobalt(III) involving macrocyclic ligandsYann Hung and Daryle H. BuschCite this: J. Am. Chem. Soc. 1977, 99, 15, 4977–4984Publication Date (Print):June 1, 1977Publication History Published online1 May 2002Published inissue 1 June 1977https://pubs.acs.org/doi/10.1021/ja00457a014https://doi.org/10.1021/ja00457a014research-articleACS PublicationsRequest reuse permissionsArticle Views185Altmetric-Citations34LEARN 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 Other access optionsGet e-Alertsclose Get e-Alerts
Memristive effects in oxygenated amorphous carbon nanodevices (2017)

Computing with resistive-switching (memristive) memory devices has shown much recent progress and offers an attractive route to circumvent the von-Neumann bottleneck, i.e. the separation of processing and memory, which limits the performance of conventional computer architectures. Due to their good scalability and nanosecond switching speeds, carbon-based resistive-switching memory devices could play an important role in this respect. However, devices based on elemental carbon, such as tetrahedral amorphous carbon or ta-C, typically suffer from a low cycling endurance. A material that has proven to be capable of combining the advantages of elemental carbon-based memories with simple fabrication methods and good endurance performance for binary memory applications is oxygenated amorphous carbon, or a-CO <sub>x</sub> . Here, we examine the memristive capabilities of nanoscale a-CO <sub>x</sub> devices, in particular their ability to provide the multilevel and accumulation properties that underpin computing type applications. We show the successful operation of nanoscale a-CO <sub>x</sub> memory cells for both the storage of multilevel states (here 3-level) and for the provision of an arithmetic accumulator. We implement a base-16, or hexadecimal, accumulator and show how such a device can carry out hexadecimal arithmetic and simultaneously store the computed result in the self-same a-CO <sub>x</sub> cell, all using fast (sub-10 ns) and low-energy (sub-pJ) input pulses.
Gene expression differences between PAXgene and Tempus blood RNA tubes are highly reproducible between independent samples and biobanks (2017)

Most transcripts are affected by the choice of sampling system, but these effects are highly reproducible between independent samples. We propose that by running a control experiment with samples on both systems in parallel with biologically relevant samples, researchers may adjust for technical differences between the sampling systems.
Structural changes on reheating plasma-sprayed alumina. (1968)

Structural changes on reheating plasma sprayed alumina free standing shapes, noting polymorphic transformations effect on porosity and pore size distribution
NIS02-6: A Game for Ad Hoc Network Connectivity in the Presence of Malicious Users (2006)

Ad hoc network users are resource constrained: Before transmitting data, they have to take into account the energy expenditure involved. Even if a user is, in principle, willing to spend energy to improve network connectivity, his actual decision will be heavily influenced by the decisions of his neighboring users, since they act as relay nodes for him. Moreover, some of the neighbors may not be as benign as he is; in fact, they could be outright malicious. We are abstracting the tradeoff between spending energy and increasing connectivity by modeling the interaction of a user with his one-hop neighbors in a game theoretic fashion. Two types of users exist: Good users willingly trade energy for connectivity, but only if they expect their neighbors to do the same; Bad users try to destroy connectivity, but also lure the Good users to waste energy. Within our model for user behavior and sophistication, we explore outcomes that can arise in this graphical game.
K-ras Oncogene Mutations in Osteoclast-like Giant Cell Tumors of the Pancreas and Liver (1998)

Osteoclast-like giant cell tumors (OCGTs) of the pancreas and liver are enigmatic tumors. Despite their striking morphologic resemblance to certain mesenchymal tumors of bone and tendon sheath, it has been suggested that these tumors may, in fact, arise from epithelial precursors. It is also unclear whether the osteoclast-like giant cells in OCGTs are neoplastic or nonneoplastic. We identified OCGTs of the pancreas and liver that were associated with atypical intraductal epithelial proliferations or mucinous cystic neoplasms. To determine the relationship between the noninvasive epithelial proliferations and the infiltrating OCGTs, each individual component was analyzed for mutations at codon 12 of the K-ras oncogene. Four of the five-duct epithelial lesions harbored activating mutations of the K-ras oncogene. In each case, the same K-ras mutation was also present in the mononuclear cells from the paired OCGT. Moreover, these same mutations were detected when the osteoclast-like giant cells were individually microdissected and analyzed. A panel of immunohistochemical stains was performed, and the osteoclast-like giant cells demonstrated macrophage differentiation. These cells were consistently reactive for the monocyte/macrophage marker KP1, but showed absent staining for a panel of epithelial markers. The infiltrating mononuclear cells lacked strong staining for epithelial markers and monocyte/macrophage markers. These findings suggest that OCGTs of the pancreas and liver are undifferentiated carcinomas that arise directly from intraductal epithelial precursors. The finding of K-ras mutations in the osteoclast-like giant cells may reflect their propensity to phagocytize tumor cells.
Endogenous retroviral proteins provide an immunodominant but not requisite antigen in a murine immunotherapy tumor model (2020)

Clinical observations suggest that responses to cancer immunotherapy are correlated with intra-tumoral T cell receptor (TCR) clonality, tumor mutation burden (TMB) and host HLA genotype, highlighting the importance of host T cell recognition of tumor antigens. However, the dynamic interplay between T cell activation state and changes in TCR repertoire in driving the identification of potential immunodominant antigen(s) remains largely unexplored. Here, we performed single-cell RNA-sequencing on CD8<sup>+</sup> tumor-infiltrating T cells (TILs) using the murine colorectal tumor model MC38 to identify unique TCR sequences and validate their tumor reactivity. We found that the majority of clonally expanded TILs are tumor-reactive and their TCR repertoire is unique amongst individual MC38 tumor-bearing mice. Our query identified that multiple expanded TCR clones recognized the retroviral epitope p15E as an immunodominant antigen. In addition, we found that the endogenous retroviral genome encoding for p15E is highly expressed in MC38 tumors, but not in normal tissues, due to epigenetic derepression. Further, we demonstrated that the p15E-specific TILs exhibit an activated phenotype and an increase in frequency upon treatment with anti-41BB and anti-PD-1 combination immunotherapy. Importantly, we showed that although p15E-specific TILs are not required to mount a primary anti-tumor response, they contributed to the development of strong immune memory. Overall our results revealed that endogenous retroviral antigens expressed by tumor cells may represent an important and underappreciated category of tumor antigens that could be readily targeted in the clinic.
Short-read, high-throughput sequencing technology for STR genotyping (2012)

DNA-based methods for human identification principally rely upon genotyping of short tandem repeat (STR) loci. Electrophoretic-based techniques for variable-length classification of STRs are universally utilized, but are limited in that they have relatively low throughput and do not yield nucleotide sequence information. High-throughput sequencing technology may provide a more powerful instrument for human identification, but is not currently validated for forensic casework. Here, we present a systematic method to perform high-throughput genotyping analysis of the Combined DNA Index System (CODIS) STR loci using short-read (150 bp) massively parallel sequencing technology. Open source reference alignment tools were optimized to evaluate PCR-amplified STR loci using a custom designed STR genome reference. Evaluation of this approach demonstrated that the 13 CODIS STR loci and amelogenin (AMEL) locus could be accurately called from individual and mixture samples. Sensitivity analysis showed that as few as 18,500 reads, aligned to an in silico referenced genome, were required to genotype an individual (>99% confidence) for the CODIS loci. The power of this technology was further demonstrated by identification of variant alleles containing single nucleotide polymorphisms (SNPs) and the development of quantitative measurements (reads) for resolving mixed samples.
Adaptive iterative reconstruction (2011)

It is well known that, in CT reconstruction, Maximum A Posteriori (MAP) reconstruction based on a Poisson noise model can be well approximated by Penalized Weighted Least Square (PWLS) minimization based on a data dependent Gaussian noise model. We study minimization of the PWLS objective function using the Gradient Descent (GD) method, and show that if an exact inverse of the forward projector exists, the PWLS GD update equation can be translated into an update equation which entirely operates in the image domain. In case of non-linear regularization and arbitrary noise model this means that a non-linear image filter must exist which solves the optimization problem. In the general case of non-linear regularization and arbitrary noise model, the analytical computation is not trivial and might lead to image filters which are computationally very expensive. We introduce a new iteration scheme in image space, based on a regularization filter with an anisotropic noise model. Basically, this approximates the statistical data weighting and regularization in PWLS reconstruction. If needed, e.g. for compensation of the non-exactness of backprojector, the image-based regularization loop can be preceded by a raw data based loop without regularization and statistical data weighting. We call this combined iterative reconstruction scheme Adaptive Iterative Reconstruction (AIR). It will be shown that in terms of low-contrast visibility, sharpness-to-noise and contrast-to-noise ratio, PWLS and AIR reconstruction are similar to a high degree of accuracy. In clinical images the noise texture of AIR is also superior to the more artificial texture of PWLS.
On representation of simulation time in functional programming style (2018)

Functional programming plays the big role in the modern computer science and its importance is growing. This is not accidential: this approach helps to create better and more reliable software that is easy to reason about (both manually and automatically). However, these techniques are hardly used in the field of tools helping designing and modeling mission-critical systems. In this paper, we are trying to apply some nice techniques of functional programming to create a modeling system, in particular a simulation system for analysis of temporal behavioural properties of mission-critical systems. As a first step, we designed a representation of simulation time in terms of abstractions used in functional programming and tried to study its compositionability properties.
Protonation of norbornadienetricarbonyliron (1967)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTProtonation of norbornadienetricarbonylironDonald R. Falkowski, Donald F. Hunt, C. Peter. Lillya, and Marvin D. RauschCite this: J. Am. Chem. Soc. 1967, 89, 24, 6387–6389Publication Date (Print):November 1, 1967Publication History Published online1 May 2002Published inissue 1 November 1967https://pubs.acs.org/doi/10.1021/ja01000a090https://doi.org/10.1021/ja01000a090research-articleACS PublicationsRequest reuse permissionsArticle Views39Altmetric-Citations17LEARN 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 Other access optionsGet e-Alertsclose Get e-Alerts
Expandable graphite: A fire retardant additive for polyurethane coatings (2003)

Abstract The study investigates the mechanism of fire retardancy induced by expandable graphite in a polyurethane coating. A complementary investigation to the spectroscopic study performed previously confirms that little interaction occurs between the matrix and the additive. X‐ray diffraction study demonstrates that the crystalline structure of the graphite is maintained during the intumescent process. The presence of free radicals in the protective shield is then demonstrated but at low concentration compared with classical intumescent systems, such as for example polyurethane/ammonium polyphosphate. Finally, the physical properties of the char are then investigated. Blowing measurement demonstrates the high degree of expansion of the layer which may partially explain the fire retardant performance of expandable graphite in polyurethane. Surface analyses by optical microscopy and optical profilometry also enable a better understanding of the efficiency of expandable graphite. In the absence of a fire retardant additive the coating displays cracks and holes, providing a pathway for oxygen diffusion as well as heat and mass transfer between the flame and the virgin polymer. Both phenomena are limited when expandable graphite is added to polyurethane. Consequently, fire retardancy of expandable graphite results more from a physical than from a chemical action. Copyright © 2003 John Wiley &amp; Sons, Ltd.
The opportunity and challenge of spin coat based nanoimprint lithography (2017)

Since multi patterning with spacer was introduced in NAND flash memory<sup>1</sup>, multi patterning with spacer has been a promising solution to overcome the resolution limit. However, the increase in process cost of multi patterning with spacer must be a serious burden to device manufacturers as half pitch of patterns gets smaller.<sup>2, 3</sup> Even though Nano Imprint Lithography (NIL) has been considered as one of strong candidates to avoid cost issue of multi patterning with spacer, there are still negative viewpoints; template damage induced from particles between template and wafer, overlay degradation induced from shear force between template and wafer, and throughput loss induced from dispensing and spreading resist droplet. Jet and Flash Imprint Lithography (J-FIL<sup>4, 5, 6</sup>) has contributed to throughput improvement, but still has these above problems. J-FIL consists of 5 steps; dispense of resist droplets on wafer, imprinting template on wafer, filling the gap between template and wafer with resist, UV curing, and separation of template from wafer. If dispensing resist droplets by inkjet is replaced with coating resist at spin coater, additional progress in NIL can be achieved. Template damage from particle can be suppressed by thick resist which is spin-coated at spin coater and covers most of particles on wafer, shear force between template and wafer can be minimized with thick resist, and finally additional throughput enhancement can be achieved by skipping dispense of resist droplets on wafer. On the other hand, spin-coat-based NIL has side effect such as pattern collapse which comes from high separation energy of resist. It is expected that pattern collapse can be improved by the development of resist with low separation energy.