gebhart/patrepeval huggingface dataset:
User-driven dynamic traffic prioritization for home networks (2012)

Network contention in a multi-user home setting can degrade performance for all participants. To maximize user experience, we propose that traffic be prioritized based on the specific activity of the user: the more a user interacts with an application and its associated traffic flows, the higher the priority that the application's traffic should receive. We introduce a client-side application that resides on the user's machine that monitors user activity and interaction with the application. This application sends information to the home router about user activity associated with different traffic flows; the home router then prioritizes traffic for flows that correspond to interactive traffic over those that are not. Finally, we introduce a protocol that allows the router and application to communicate. We show that the collective system improves the user experience for interactive applications by providing better performance for traffic associated with applications that a user is interacting with directly.
Sentinel scheduling for VLIW and superscalar processors (1992)

Speculative execution is an important source of parallelism for VLIW and superscalar processors. A serious challenge with compiler-controlled speculative execution is to accurately detect and report all program execution errors at the time of occurrence. In this paper, a set of architectural features and compile-time scheduling support referred to as sentinel scheduling is introduced. Sentinel scheduling provides an effective framework for compiler-controlled speculative execution that accurately detects and reports all exceptions. Sentinel scheduling also supports speculative execution of store instructions by providing a store buffer which allows probationary entries. Experimental results show that sentinel scheduling is highly effective for a wide range of VLIW and superscalar processors.
Complementary DNA cloning for galactosyltransferase associated with tumor and determination of antigenic epitopes recognized by specific monoclonal antibodies. (1992)

The galactosyltransferase associated with tumor (GAT) was the name given to the isoenzyme that tends to polymerize resulting in slower moving in a nondenaturing polyacrylamide gel electrophoresis than normal (beta 1-4)galactosyltransferase (normal GalT). A complementary DNA (cDNA) library was constructed from a human ovarian cancer cell line, RMG-I, which secreted an amount of GAT into the culture supernatant and screened with monoclonal antibodies (MAbs) against GAT and normal GalT. One of six cDNA clones, UG86-1, encoded an epitope recognized by a GAT-specific MAb, 8513. Recombinant proteins expressed by UG86-1 in Escherichia coli also had antigenic epitopes recognized by the other MAbs against normal GalT. The 229-base pair nucleotide sequence encoded by UG86-1 was identical to the stem region sequence of HGT832 which encodes a full-length cDNA of human GalT. Using recombinant proteins directed by deletion mutant cDNAs, the antigenic epitopes recognized by each MAb were determined. The epitope of MAb8628, which reacts to both the GAT and normal GalT, was localized to the COOH-terminal side of proteolytic cleavage site where the membrane-bound form enzyme is cleaved to be converted to soluble forms, while MAb8513 epitope was at the NH2-terminal side from this cleavage site between the COOH-terminal end of the membrane-binding domain and the cleavage site. These results demonstrate that GAT is produced by aberrant proteolytic cleavage at the different site, closer to the membrane-binding domain, from the normal GalT.
Amniotic membrane and adipose-derived stem cell co-culture system enhances bone regeneration in a rat periodontal defect model (2015)

Periodontal disease is a chronic inflammatory process that potentially leads to alveolar bone destruction and tooth loss. Tissue engineering combined with stem cell therapy is a potential effective treatment for periodontal bone loss. Amniotic membrane (AM) is a potential scaffold enriched with multiple growth factors. It has the effects of anti-inflammation, antiangiogenesis, and immunosuppression. Herein, we used adipose-derived stem cells (ADSCs) and an AM co-cultured system to study bone regeneration in a rat periodontal defect model in vivo. Human ADSCs were isolated from the infrapatellar fat pad, and characterized by flow cytometry, reverse transcription-polymerase chain reaction, and multipotent differentiation assays. The co-culture system was applied in the periodontal two-wall osseous defect in a rat model, and computed tomography was used to measure the effect. Human ADSCs isolated from the infrapatellar fat pad showed spindle-like morphology. Flow cytometry results demonstrated that ADSCs expressed a high level of CD90 and CD105, but not CD31, CD34, and CD45. ADSCs strongly expressed stemness genes, including SOX2, OCT4, NANOG, and KLF4 on different passages. Furthermore, ADSCs were able to differentiate into osteogenic, chondrogenic, and adipogenic cells. In the periodontal osseous defect rat model, ADSCs and the AM co-culture system significantly increased bone regeneration. This study provides the basis for using ADSCs with an AM co-culture system as stem cell therapy and scaffold transplantation in clinical periodontology.
<title>Polymeric helices with submicron dimensions for MEMS devices (Invited Paper)</title> (2005)

Polymer helices with submicron dimensions have been fabricated from a variety of isotropic and liquid crystalline polymers with storage moduli ranging from 38MPa to 1.9GPa (measured at 1Hz, room temperature). These helices are made using a double templating process, in which a thin film comprised of independent helical structures deposited using glancing angle deposition (GLAD) acts as the master. In our process the 'positive' structure of the master is copied into a polymer 'negative', which then itself acts as a template for the final film of polymer helices. Liquid crystalline polymers are of particular interest for use in MEMS because highly ordered liquid crystalline polymers can be actuated by exposing them to a stimulus (such as heat) that causes a decrease in order, leading to a reversible, macroscopic change in shape. The phase behavior, optical properties, and mechanical properties of planar aligned monoacrylate liquid crystalline polymers with varying crosslinker content are investigated, in order to determine the composition that will yield the largest deformations upon heating. We find that films with the lowest crosslinker content investigated (2.5%) undergo the largest reduction in birefringence as they are heated, corresponding to a loss in order. However, we also observe that the films with the highest crosslinker content investigated (10%) undergo the largest physical deformation upon heating. SEM images illustrating the deformation of liquid crystalline polymer helices as they are heated are also presented.
Acid-catalyzed alkylation and cyclialkylation of the cymenes with isobutylene and related olefins (1971)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAcid-catalyzed alkylation and cyclialkylation of the cymenes with isobutylene and related olefinsEdmund J. Eisenbraun, D. E. Boone, Pat W. . Flanagan, and R. D. GrigsbyCite this: J. Org. Chem. 1971, 36, 15, 2042–2048Publication Date (Print):July 1, 1971Publication History Published online1 May 2002Published inissue 1 July 1971https://pubs.acs.org/doi/10.1021/jo00814a002https://doi.org/10.1021/jo00814a002research-articleACS PublicationsRequest reuse permissionsArticle Views157Altmetric-Citations1LEARN 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
Development of Crash Warning Interface Metrics (CWIM) (2013)

Based on the findings of a recent field study, Nodine (2011) reported that 88% of forward collision warning (FCW) system alerts in that study were accurate when the lead vehicle was moving. Similarly, 86% of lane departure warning (LDW) alerts activated accurately when the vehicle departed its lane without signaling. However, safety benefits are only realized when the system is both accurate in identifying a crash imminent situation and when the warning presented to the driver elicits a timely and appropriate response (braking or steering). The National Highway Traffic Safety Administration (NHTSA) is conducting studies under the Crash Warning Interface Metrics (CWIM) program to develop valid and sensitive “distracted driver” protocols for the evaluation of the driver vehicle interfaces (DVIs) of FCW and LDW systems on test tracks and in driving simulators as well as examining potential safety-related effects of consistent DVIs for these warning systems. CWIM focuses on distracted drivers because distraction-affected crashes represent a substantial crash risk, including 9% of the fatal crashes and 18% of injury crashes that occurred in 2010 (NHTSA, 2012). The DVI consists of the displays of the warning system, including the warning itself and associated system status displays. Although controls and settings are available for some systems, their usability and effectiveness are outside of the scope of the CWIM program. In this paper, the authors review some of the prominent results and methodological issues encountered in studies conducted under the CWIM program and describe how they are addressed in the work that is currently underway.
The Evolving Profile of the Signature Amino Acid Residues in HIV-1 Subtype C Tat (2015)

Using several HIV-1 tat exon 1 amino acid sequences available from public databases and additional sequences derived from a southern Indian clinical cohort, we compared the profile of the signature amino acid residues (SAR) between two different time periods, 1986-2004 and 2005-2014. The analysis identified eight positions as signature residues in subtype C Tat and demonstrated a changing pattern at four of these positions between the two periods. At three locations (histidine 29, serine 57, and proline 60), there appears to be a nonuniform negative selection against the SAR. The negative selection appears to be severe, especially against histidine 29 (p < .0001) and moderate against proline 60 (p < .0001). The negative selection against serine 57 is statistically insignificant and appears to have begun recently. At position 63, the frequency of signature residue glutamic acid increased over the past decade, although the difference was not significant. Importantly, at the three locations where the negative selection is in progress, the substitute amino acids are the generic residues present in most of the other HIV-1 subtypes. Our data demonstrate that viral evolution can subject specific amino acid residues to subtle and progressive selection pressures without affecting the prevalence of other amino acid residues.
Dark Electric Conductivity (2023)

These recommendations are specifically for polymers and polymer systems showing a significant response to an electromagnetic field or one of its components (electric field or magnetic field), i.e., for electromagnetic-field-responsive polymer materials. The structures, processes, phenomena and quantities relating to this interdisciplinary field of materials science and technology are herein defined. Definitions are unambiguously explained and harmonized for wide acceptance by the chemistry, physics, polymer and materials science communities. A survey of typical electromagnetic-field-responsive polymers is included.
Rapid screening for sickle cell disease by polymerase chain reaction-high resolution melting analysis (2014)

Each year, ~300,000 individuals with sickle cell disease (SCD), a hemoglobinopathy caused by β-globin gene mutation, are born, and >75% of those are in Africa. The present study examined 511 individuals on the island of Bioko (Equatorial Guinea) and attempted to establish a method for rapid sickle cell disease screening. Following DNA extraction and polymerase chain reaction (PCR) amplification, high resolution melting (HRM) analysis was used to assess the specificity of fluorescence signals of the PCR products and to differentiate various genotypes of these products. The analytical results of HRM were validated using DNA sequencing. By HRM analysis, 80 out of 511 samples were classified as hemoglobin S (Hb S) heterozygotes, while 431 out of 511 samples were classified as wild-type. No mutant homozygote was identified. DNA sequencing indicated that within the 431 wild-type samples as indicated by HRM analysis, one case was actually a Hb S heterozygote and another case was a rare hemoglobin S-C genotype (sickle-hemoglobin C disease). One out of 80 suspected Hb S heterozygotes as indicated by HRM was confirmed as wild-type by DNA sequencing and the results of residual 508 cases were consistent for HRM analysis and sequencing. In conclusion, HRM analysis is a simple, high-efficiency approach for Hb S screening and is useful for early diagnosis of SCD and particularly suitable for application in the African area.
Influence of exciton ionization on recombination dynamics inIn0.53Ga0.47As/InP quantum wells (1993)

We have investigated the carrier dynamics in ${\mathrm{In}}_{0.53}$${\mathrm{Ga}}_{0.47}$As/InP quantum wells with various well widths as a function of temperature and carrier density using time-resolved photoluminescence spectroscopy. At low temperatures (T50 K), we find pure excitonic recombination. At elevated temperatures, two radiative recombination paths are present, and the proportion of free-carrier recombination to excitonic recombination increases as the temperature is raised. We observe a nonlinear increase of the radiative lifetime caused by thermal ionization of excitons. Exciton binding energies in the range between 9 and 15 meV and majority carrier concentrations of about 1.2\ifmmode\times\else\texttimes\fi{}${10}^{10}$ ${\mathrm{cm}}^{\mathrm{\ensuremath{-}}2}$ are deduced from the ratio between the high and low injection lifetimes. The exciton binding energy increases with decreasing well thicknesses, in good agreement with theoretical predictions.
Predicting Viscosity-Shear Relationships of VI Improved Lubricants (1994)

&lt;div class="htmlview paragraph"&gt;The majority of crankcase lubricants are now formulated to contain polymeric additives to improve the viscosity temperature properties to provide a better lubricating film in the various bearing systems in an internal combustion engine. These VI (viscosity index) improved lubricants are non-Newtonian under the high shear conditions that exist in most automotive bearing systems. The conditions of interest range from starting the engine at temperatures of as low as -40°C to operating the engine at normal operating conditions including bearing temperatures of 150°C or higher. This paper presents a method for predicting the viscosity shear relationship for a series of SAE multigrade engine oils as a function of temperature and shear stress. The method is demonstrated using three types of polymeric VI improvers currently used in SAE multigrade engine oils. The polymer types include olefin copolymers (OCP), polymethacrylates (PMA), and styrene-isoprene copolymers (SI).&lt;/div&gt;
Antibiotic-Loaded Chitosan Hydrogel with Superior Dual Functions: Antibacterial Efficacy and Osteoblastic Cell Responses (2014)

It is critical for the clinical success to take the biological function into consideration when integrating the antibacterial function into the implanted biomaterials. To this aim, we prepared gentamycin sulfate (GS)-loaded carboxymethyl-chitosan (CM-chitosan) hydrogel cross-linked by genipin. The prepared hydrogels not only achieved superb inhibition on bacteria growth and biofilm formation of Staphylococcus aureus but also significantly enhanced the adhesion, proliferation, and differentiation of MC3T3-E1 cells. The observed dual functions were likely based on the intrinsic property of the positive charged chitosan-based hydrogel, which could be modified to selectively disrupt the bacteria wall/membrane and promote cell adhesion and proliferation, as suggested by the membrane permeability study. The genipin concentration played an important role in controlling the degradation time of the chitosan hydrogel and the MC3T3-E1 cell responses. The loading of GS not only significantly increased the antibacterial efficiency but also was beneficial for the osteoblastic cell responses. Overall, the biocompatibility of the prepared chitosan-GS hydrogel could be tuned with both the genipin and GS concentrations, which control the available positive charged sites of chitosan. The results demonstrated that chitosan-GS hydrogel is an effective and simple approach to achieving combined antibacterial efficacy and excellent osteoblastic cell responses, which has great potential in orthopedic applications.
L-arginine metabolism in early-onset and late-onset pre-eclamptic pregnancies (2013)

Parameters of l-arginine metabolism do not discriminate the early-onset from late-onset pre-eclampsia. Our study provided indirect evidences for the redirection of l-arginine-NOS to the l-arginine-arginase pathway.
Investigating the Conditionally Essential Role of Human METAP1 (2022)

CRISPR‐based forward genetic screens make it possible to systematically identify genes required for survival and growth in human cells, and therefore provide a powerful approach to characterize protein function and uncover targetable vulnerabilities in human cancer cells. Notably, it has become appreciated that gene essentiality can be context‐dependent, as CRISPR‐based loss‐of‐function screens across hundreds of human cancer cell lines have uncovered cell‐essential genes that can vary with cell‐intrinsic characteristics such as genotype and lineage. Importantly, environmental factors also influence cell physiology. However, there has been little consideration into how nutrient availability might impact gene essentiality, and most CRISPR‐based screens of human cells are performed in vitro using culture media that poorly recapitulate nutrient conditions in the body. To test the hypothesis that medium composition influences gene essentiality, our lab recently performed genome‐wide CRISPR screens of human blood cancer cell lines in traditional versus Human Plasma‐Like Medium (HPLM), a physiologic medium that we previously developed to more closely reflect the metabolic composition of human blood. Among the strongest HPLM‐essential hits identified from our screen results is METAP1 , which encodes one of two human enzymes (METAP1 and METAP2) that can catalyze the cleavage of N‐terminal methionine from nascent polypeptides. Interestingly, these two METAPs are co‐expressed across most human cell lines, are each localized to the cytosol, and also share seemingly similar substrate preferences. However, our screen results indicate that endogenous METAP2 cannot complement the loss of METAP1 in HPLM‐cultured cells, suggesting that METAP1 serves a non‐redundant and context‐dependent cell‐essential role. Therefore, we hypothesize that identifying the gene‐nutrient interaction that underlies conditional METAP1 essentiality will provide key insights into this unforeseen role. Importantly, we have engineered METAP1 ‐knockout cells and, in turn, confirmed the conditional CRISPR phenotype for METAP1 by performing relative growth assays. Therefore, we are now poised to identify the gene‐nutrient interaction and will proceed to use tools in biochemistry, metabolomics, and molecular biology to explore the context‐dependent role of METAP1 in proliferating human cells.
Hydroxylation of Steroids by a Microbial Substrate-Promiscuous P450 Cytochrome (CYP105D7): Key Arginine Residues for Rational Design (2019)

Our previous study showed that CYP105D7, a substrate-promiscuous P450, catalyzes the hydroxylation of 1-deoxypentalenic acid, diclofenac, naringenin, and compactin. In this study, 14 steroid compounds were screened using recombinant <i>Escherichia coli</i> cells harboring genes encoding CYP105D7 and redox partners (Pdx/Pdr, RhFRED, and FdxH/FprD), and the screening identified steroid A-ring 2β- and D-ring 16β-hydroxylation activity. Wild-type CYP105D7 was able to catalyze the hydroxylation of five steroids (testosterone, progesterone, 4-androstene-3,17-dione, adrenosterone, and cortisone) with low (<10%) conversion rates. Structure-guided site-directed mutagenesis of arginine residues around the substrate entrance and active site showed that the R70A and R190A single mutants and an R70A/R190A double mutant exhibited greatly enhanced conversion rates for steroid hydroxylation. For the conversion of testosterone in particular, the R70A/R190A mutant's <i>k</i><sub>cat</sub>/<i>K<sub>m</sub></i> values increased 1.35-fold and the <i>in vivo</i> conversion rates increased significantly by almost 9-fold with high regio- and stereoselectivity. Molecular docking analysis revealed that when Arg70 and Arg190 were replaced with alanine, the volume of the substrate access and binding pocket increased 1.08-fold, which might facilitate improvement of the hydroxylation efficiency of steroids.<b>IMPORTANCE</b> Cytochrome P450 monooxygenases (P450s) are able to introduce oxygen atoms into nonreactive hydrocarbon compounds under mild conditions, thereby offering significant advantages compared to chemical catalysts. Promiscuous P450s with broad substrate specificity and reaction diversity have significant potential for applications in various fields, including synthetic biology. The study of the function, molecular mechanisms, and rational engineering of substrate-promiscuous P450s from microbial sources is important to fulfill this potential. Here, we present a microbial substrate-promiscuous P450, CYP105D7, which can catalyze hydroxylation of steroids. The loss of the bulky side chains of Arg70 and Arg190 in the active site and substrate entrance resulted in an up to 9-fold increase in the substrate conversion rate. These findings will support future rational and semirational engineering of P450s for applications as biocatalysts.
Extending ASSERT for HW/SW Co-Design (2011)

Advances in single-cell and -nucleus transcriptomics have enabled generation of increasingly large-scale datasets from hundreds of subjects and millions of cells. These studies promise to give unprecedented insight into the cell type specific biology of human disease. Yet performing differential expression analyses across subjects remains difficult due to challenges in statistical modeling of these complex studies and scaling analyses to large datasets. Our open-source R package dreamlet (DiseaseNeurogenomics.github.io/dreamlet) uses a pseudobulk approach based on precision-weighted linear mixed models to identify genes differentially expressed with traits across subjects for each cell cluster. Designed for data from large cohorts, dreamlet is substantially faster and uses less memory than existing workflows, while supporting complex statistical models and controlling the false positive rate. We demonstrate computational and statistical performance on published datasets, and a novel dataset of 1.4M single nuclei from postmortem brains of 150 Alzheimer's disease cases and 149 controls.