gebhart/patrepeval huggingface dataset:
Isolation and characterization of SARS-CoV-2 from the first US COVID-19 patient (2020)

The etiologic agent of the outbreak of pneumonia in Wuhan China was identified as severe acute respiratory syndrome associated coronavirus 2 (SARS-CoV-2) in January, 2020. The first US patient was diagnosed by the State of Washington and the US Centers for Disease Control and Prevention on January 20, 2020. We isolated virus from nasopharyngeal and oropharyngeal specimens, and characterized the viral sequence, replication properties, and cell culture tropism. We found that the virus replicates to high titer in Vero-CCL81 cells and Vero E6 cells in the absence of trypsin. We also deposited the virus into two virus repositories, making it broadly available to the public health and research communities. We hope that open access to this important reagent will expedite development of medical countermeasures.
Honest Signals (2008)

How understanding the signaling within social networks can change the way we make decisions, work with others, and manage organizations.How can you know when someone is bluffing? Paying attention? Genuinely interested? The answer, writes Alex Pentland in Honest Signals, is that subtle patterns in how we interact with other people reveal our attitudes toward them. These unconscious social signals are not just a back channel or a complement to our conscious language; they form a separate communication network. Biologically based "honest signaling," evolved from ancient primate signaling mechanisms, offers an unmatched window into our intentions, goals, and values. If we understand this ancient channel of communication, Pentland claims, we can accurately predict the outcomes of situations ranging from job interviews to first dates.Pentland, an MIT professor, has used a specially designed digital sensor worn like an ID badge—a "sociometer"—to monitor and analyze the back-and-forth patterns of signaling among groups of people. He and his researchers found that this second channel of communication, revolving not around words but around social relations, profoundly influences major decisions in our lives—even though we are largely unaware of it. Pentland presents the scientific background necessary for understanding this form of communication, applies it to examples of group behavior in real organizations, and shows how by "reading" our social networks we can become more successful at pitching an idea, getting a job, or closing a deal. Using this "network intelligence" theory of social signaling, Pentland describes how we can harness the intelligence of our social network to become better managers, workers, and communicators.
Electrode and Bacterial Survival with Iontophoresis in Synthetic Urine (1992)

Urinary catheters, especially in patients with long-term catheter requirements, frequently are a source of infection. Iontophoresis has been proposed as a method to decrease or eliminate such infections. Several types of material were examined for their potential use as electrodes in an iontophoretic catheter system. Silver, copper and nickel electrodes did kill microorganisms but did not show longevity. Carbon and gold electrodes showed longevity and killing of microorganisms. Gold proved to be somewhat better than carbon in killing Klebsiella pneumoniae in a broth. Few organisms survived iontophoresis. Those few that survived (mainly Klebsiella in broth), when rechallenged by iontophoresis, did not show any striking resistance to iontophoresis. Our data support the proposition that inclusion of electrodes, depending on the electrode type, in a catheter probably will decrease or eliminate a bacterial population in urine and, thus, may help prevent catheter-related infections and their sequelae.
Therapeutic vaccination against HIV: current progress and future possibilities (2005)

Although effective in reducing mortality, current antiretroviral therapy for HIV infection involves complex and expensive drug regimens that are toxic and difficult to take. Eradication of HIV reservoirs is not possible with existing therapies. The concept of therapeutic vaccination has been investigated to increase the potency and breadth of anti-HIV immune responses in order to delay or reduce antiretroviral therapy use. A variety of approaches targeted to both cell- and antibody-mediated immunity have been developed, including whole inactivated HIV-1, protein subunits and synthetic peptides, DNA vaccines and a number of viral vectors expressing HIV-1. These investigations have occurred in the absence of a clear understanding of disease pathogenesis or the correlates of protective immunity. At this time, there is no licensed therapeutic vaccine for any viral disease, including HIV; however, this review will consider recent progress in the field and summarize the challenges faced in the development of a therapeutic HIV vaccine.
Couple-Group Consensus for Multiagent Systems via Time-Dependent Event-Triggered Control (2018)

This paper investigates couple-group consensus problems for multiagent first-order and second-order systems. Several consensus protocols are proposed based on the time-dependent distributed event-triggered control. For the case of no communication delays, the time-dependent event-triggered strategies are applied to couple-group consensus problems. Based on the matrix theory, algebraic conditions for couple-group consensus are established. For the system with communication delays, based on event-triggered strategies, a Lyapunov-Krasovskii functional is constructed to prove the input-to-state stability of the systems. Moreover, Zeno behavior is excluded. Finally, numeral examples are given to illustrate the effectiveness of these results.
Modulation of Bax and mTOR for Cancer Therapeutics (2017)

A rationale exists for pharmacologic manipulation of the serine (S)184 phosphorylation site of the proapoptotic Bcl2 family member Bax as an anticancer strategy. Here, we report the refinement of the Bax agonist SMBA1 to generate CYD-2-11, which has characteristics of a suitable clinical lead compound. CYD-2-11 targeted the structural pocket proximal to S184 in the C-terminal region of Bax, directly activating its proapoptotic activity by inducing a conformational change enabling formation of Bax homooligomers in mitochondrial membranes. In murine models of small-cell and non-small cell lung cancers, including patient-derived xenograft and the genetically engineered mutant KRAS-driven lung cancer models, CYD-2-11 suppressed malignant growth without evident significant toxicity to normal tissues. In lung cancer patients treated with mTOR inhibitor RAD001, we observed enhanced S184 Bax phosphorylation in lung cancer cells and tissues that inactivates the propaoptotic function of Bax, contributing to rapalog resistance. Combined treatment of CYD-2-11 and RAD001 in murine lung cancer models displayed strong synergistic activity and overcame rapalog resistance <i>in vitro</i> and <i>in vivo</i> Taken together, our findings provide preclinical evidence for a pharmacologic combination of Bax activation and mTOR inhibition as a rational strategy to improve lung cancer treatment. <i>Cancer Res; 77(11); 3001-12. ©2017 AACR</i>.
A New Gun in Town: The U Box Is a Ubiquitin Ligase Domain (2002)

Ubiquitin ligases determine protein stability in a highly regulated manner by coordinating the addition of polyubiquitin chains to proteins that are then targeted to the proteasome for degradation. Ubiquitin ligases have generally been separated into two groups--those containing HECT domains and those with RING finger domains. Recently, a third group of ubiquitin ligases has emerged: those containing a U-box domain. Patterson discusses what is known about the few U-box-containing proteins that have been characterized, although the general properties of U-box proteins that distinguish them from other ubiquitin ligases are still a matter of speculation.
Postoperative atrial fibrillation independently predicts prolongation of hospital stay after cardiac surgery. (2005)

Despite baseline characteristics differed between patients with and without postoperative AF, most of the prolongation of hospital stay can be attributed to the rhythm disturbance itself.
Macromol. React. Eng. 1/2012 (2012)

Cover: This work demonstrates that the glass transition temperature of an in situ polymerized carbon nanotube/polyimide (CNT/PI) nanocomposite can vary non-monotonically with the concentration of the reactive CNT added. This is due to its influence on the polycondensation reaction stoichiometry and thus on the molecular weight of the matrix PI polymer. Further details can be found in the article by D. H. Kim, and Y.-Y. Won* on page 45.
Let-7 microRNAs are developmentally regulated in circulating human erythroid cells (2009)

These data suggest that a consistent pattern of up-regulation among let-7 miRNA in circulating erythroid cells occurs in association with hemoglobin switching during the fetal-to-adult developmental transition in humans.
Accumulation of high levels of methotrexate polyglutamates in lymphoblasts from children with hyperdiploid (greater than 50 chromosomes) B-lineage acute lymphoblastic leukemia: a Pediatric Oncology Group study (1992)

Abstract Hyperdiploidy (greater than 50 chromosomes, or a DNA index greater than 1.16) confers a favorable prognosis in B-lineage acute lymphoblastic leukemia of childhood. Children with B-lineage acute lymphoblastic leukemia whose lymphoblasts at diagnosis accumulate high levels of methotrexate (MTX) and MTX polyglutamates (MTXPGs) in vitro experience a better event-free survival than those whose lymphoblasts do not (Blood 76:44, 1990). Lymphoblasts from 13 children with hyperdiploidy (greater than 50 chromosomes) accumulated high levels of MTX-PGs (1,095 and 571 to 2,346 pmol/10(9) cells [median and 25% to 75% intraquartile range]). These levels were higher than those in B-lineage lymphoblasts from 19 children with other aneuploidy (326 and 159 to 775 pmol/10(9) cells) and 15 children with diploidy (393 and 204 to 571 pmol/10(9) cells) (P = .0015). Chromosomal trisomies in hyperdiploid cases were highly nonrandom. Chromosome 9 was not one of the chromosomes involved in trisomies, even though this chromosome contains the gene for folate polyglutamate synthetase, which is the enzyme required for MTXPG synthesis. The correlation between MTXPG level and percentage of S- phase cells was weak, suggesting that increased levels of MTXPGs could not be attributed to elevated proportions of cells in active DNA synthesis. The ability of hyperdiploid lymphoblasts to accumulate high levels of MTXPGs may increase their sensitivity to MTX cytotoxicity, accounting in part for the improved outlook for hyperdiploid patients treated with regimens that emphasize MTX as a primary component of continuation therapy.
Evaluation and development of physical-chemical techniques for the separation of emulsified oil from water (1973)

Various methods for separating emulsified oil from water were surveyed and investigated. A state-of-the-art review of physical-chemical processes for oil-water separation included conventional flotation, precipitate flotation, adsorption, flotation, magnetization, coalescence, chromatography, layer filtration, reverse osmosis, absorption filtration, hydrocyclone treatment, centrifugation, settling, chemical coagulation, evaporation-distillation, freezing, biological oxidation, clarification-flotation, and solvent extraction. Promising physico-chemical processes for oil-water separation include granular C adsorption, powdered C adsorption followed by polyelectrolyte coagulation and final polishing, and powdered C adsorption followed by direct filtration. Greater than 99% oil removal can be achieved with these processes.
Antagonism of Nitric Oxide Toward the Inhibition of Cytochrome<i>c</i>Oxidase by Carbon Monoxide and Cyanide (2008)

The principle mitochondrial target where the respiratory inhibitors CO, CN(-), and NO act in the execution of their acute toxic effects is complex IV of the electron-transport chain, cytochrome c oxidase. However, there is a paucity of studies in the literature regarding the concerted effects of such poisons. Accordingly, the combined inhibitory effects of CO + CN(-), NO + CN(-), and NO + CO on the activity of cytochrome c oxidase preparations are reported. Only in the case of CO + CN(-) do the effects of the two inhibitors seem to be additive as expected. NO appears to be antagonistic toward the effects of the other two inhibitors; that is, the effects of both CO an CN(-) on enzyme activity are ameliorated by NO when present. To further clarify these observations, the ligand substitutions of heme-bound CN(-) by NO in cytochrome c oxidase and hemoglobin have also been briefly investigated. These results suggest that displacement of CN(-) from the ferric hemoproteins by NO is rate-limited by heme reduction-and in the case of the enzyme, the presence of nonligand-binding electron-transfer centers facilitates the reaction. The findings are discussed in relation to the idea that NO does not behave as a classic reversible (by dissociation) inhibitor.
High-mobility amorphous In2O3–10wt%ZnO thin film transistors (2006)

The authors report on the fabrication and characterization of thin film transistors that use sputter deposited amorphous indium zinc oxide both for the channel and source-drain metallizations in a gate-down configuration. The channel and source-drain layers were deposited from a single In2O3–10wt%ZnO ceramic target using dc magnetron sputtering onto an unheated substrate. The carrier densities in the channel (2.1×1017∕cm3) and source/drain regions (3.3×1020∕cm3) were adjusted by changing the reactive oxygen content in the sputter chamber during deposition. The resulting transistors operate as depletion mode n-channel field effect devices with saturation mobility of 20cm2∕Vs and on/off current ratio of 108.
IFN- <i>β</i> <sub>1b</sub> Induces Kynurenine Pathway Metabolism in Human Macrophages: Potential Implications for Multiple Sclerosis Treatment (2001)

Interferon-beta(1b) (IFN-beta(1b)) has limited efficacy in the treatment of relapsing-remitting multiple sclerosis (RRMS). The kynurenine pathway (KP) is chiefly activated by IFN-gamma and IFN-alpha, leading to the production of a variety of neurotoxins. We sought to determine whether IFN-beta(1b) induces the KP in human monocyte-derived macrophages, as one explanation for its limited efficacy. Serial dilutions of IFN-beta(1b) (at concentrations comparable to those found in the sera of IFN-beta(1b)-treated patients) were added to human macrophage cultures. Supernatants were collected at various time points and assayed for the KP end product, quinolinic acid (QUIN). The effect of IFN-beta(1b) on the KP enzymes indoleamine 2,3-dioxygenase (IDO), 3-hydroxyanthranilate dioxygenase (3HAO), and quinolinate phosphoribosyltransferase (QPRTase) mRNA expression was assessed by semiquantitative RT-PCR. IFN-beta(1b) (> or =10 IU/ml) led to increased mRNA expression of both IDO and QUIN production (7901 +/- 715 nM) after 72 h at 50 IU/ml IFN-beta(1b) (p < 0.0001). This study demonstrates that IFN-beta(1b), in pharmacologically relevant concentrations, induces KP metabolism in human macrophages and may be a limiting factor in its efficacy in the treatment of MS. Inhibitors of the KP may be able to augment the efficacy of IFN-beta in MS.
Characterization of the Velocity Skin Effect in the Surface Layer of a Railgun Sliding Contact (2008)

We present a characterization of contact velocity skin effect (VSEC), which is a major velocity- and efficiency-limiting effect at a railgun's sliding contact. Despite enormous contact forces, the armature remains separated from the rail by a thin layer, 4 to 12 A thick. Evidence suggests VSEC is also the primary mechanism responsible for the contact voltage drop. VSEC effects are seen in both electromagnetic launcher (EML) efficiency and breech voltage. We compare theoretical predictions of system efficiency and breech voltage to experimental measurements for both a conventional and an augmented railgun. The characterization of VSEC extends our previous theoretical work in this area and provides new insights into the physics of EML operation, especially with regards to the armature and sliding contact. VSEC is a significant energy loss mechanism and heat source, possibly contributing to contact erosion and transition. We propose a similar VSEC mechanism to explain velocity saturation and efficiency roll-off in plasma and hybrid armature railguns, as well as arc restrike.
Black silicon with high density and high aspect ratio nanowhiskers (2011)

The physical properties of black silicon (b-Si) formed on Si wafers by reactive ion etching in chlorine plasma are reported in an attempt to clarify the formation mechanism and the origin of the observed optical and electrical phenomena, which are promising for a variety of applications. The b-Si consisting of high density and high aspect ratio sub-micron length whiskers or pillars with tip diameters of well under 3 nm exhibits strong photoluminescence (PL) both in the visible and the infrared, which is interpreted in conjunction with defects, confinement effects and near band-edge emission. Structural analysis indicates that the whiskers are all crystalline and encapsulated by a thin Si oxide layer. The infrared vibrational spectrum of Si-O-Si bondings in terms of transverse-optic (TO) and longitudinal-optic (LO) phonons indicates that disorder induced LO-TO optical mode coupling can be an effective tool in assessing the structural quality of the b-Si. The same phonons are likely coupled to electrons in visible region PL transitions. Field emission properties of these nanoscopic features are demonstrated indicating the influence of the tip shape on the emission. Overall properties are discussed in terms of the surface morphology of the nanowhiskers.
Explorations of display interfaces for virtual reality (2002)

Three alternatives to the traditional head mounted virtual reality display are described. One configuration is the Virtual Holographic Workstation, an external stereo CRT viewed by a user wearing head tracking stereo shutter glasses. Another is the Computer Augmented Reality Camcorder, where virtual objects are composited onto live video using six axis tracking information about the location of the video camera. The third system is the Virtual Portal, where an entire room is turned into a high-resolution inclusive display by replacing three walls with floor-to-ceiling rear projection stereo displays. Details of the systems and experiences and limitations in their use are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Design of active semantic middleware system to support incomplete sensor information based on ubiquitous sensor network (2010)

Sensor network technology has evolved and been applied to many fields including environmental monitoring and construction management. Further, it has extended to the context awareness service that perceives circumstances in each applied area. In this paper, the present study analyzes the incompleteness of real-time sensor data in in-network and server middleware to deal with incomplete data arising in relation to USN monitoring service, to transform them into meaningful data used in an application system, and ultimately to design a real-time USN middleware system providing active semantic data service that predicts industrial safety hazards.
Transferable Dialogue Systems and User Simulators (2021)

Bo-Hsiang Tseng, Yinpei Dai, Florian Kreyssig, Bill Byrne. Proceedings of the 59th Annual Meeting of the Association for Computational Linguistics and the 11th International Joint Conference on Natural Language Processing (Volume 1: Long Papers). 2021.
TCFH–NMI: Direct Access to <i>N</i>-Acyl Imidazoliums for Challenging Amide Bond Formations (2018)

Challenging couplings of hindered carboxylic acids with non-nucleophilic amines to form amide bonds can be accomplished in high yields, and in many cases, with complete retention of the adjacent stereogenic centers using the combination of N, N, N', N'-tetramethylchloroformamidinium hexafluorophosphate (TCFH) and N-methylimidazole (NMI). This method allows for in situ generation of highly reactive acyl imidazolium ions, which have been demonstrated to be intermediates in the reaction. The reagent delivers high reactivity similar to acid chlorides with the ease of use of modern uronium reagents.
Application of design of experiments methodology to model the effect of multiple parameters on simultaneous switching noise (2003)

A new methodology is developed for efficiently analyzing simultaneous switching noise (SSN) using design of experiments (DOE) to model the effect of multiple adjustable parameters on SSN responses, such as ground bounce and local supply droop. Each SSN response is fitted to a 2nd order polynomial equation allowing quick calculation of SSN as a function of load capacitance, number of drivers switching, power/ground inductance, power/ground resistance, on-chip de-coupling capacitance, and rise/fall time of the driver input pulse. This method is applied to two separate driver types to demonstrate the approach, and show that certain parameters are more or less significant for one driver, but not the other. Statistical analysis shows that only two of the five responses are unique to SSN. Drivers are characterized using this method, and the analytical expressions provide immediate feedback for making engineering decisions regarding future IC pad-rings and package designs. Results are presented to demonstrate the validity of the proposed methodology and its application for optimizing SSN designs.
Anaerobic naphthalene degradation by Gram-positive, iron-reducing bacteria (2011)

An anaerobic naphthalene-degrading culture (N49) was enriched with ferric iron as electron acceptor. A closed electron balance indicated the total oxidation of naphthalene to CO(2). In all growing cultures, the concentration of the presumed central metabolite of naphthalene degradation, 2-naphthoic acid, increased concomitantly with growth. The first metabolite of anaerobic methylnaphthalene degradation, naphthyl-2-methyl-succinic acid, was not identified in culture supernatants, which does not support a methylation to methylnaphthalene as the initial activation reaction of naphthalene, but rather a carboxylation, as proposed for other naphthalene-degrading cultures. Substrate utilization tests revealed that the culture was able to grow on 1-methyl-naphthalene, 2-methyl-naphthalene, 1-naphthoic acid or 2-naphthoic acid, whereas it did not grow on 1-naphthol, 2-naphthol, anthracene, phenanthrene, indane and indene. Terminal restriction fragment length polymorphism and 16S rRNA gene sequence analyses revealed that the microbial community of the culture was dominated by one bacterial microorganism, which was closely related (99% 16S sequence similarity) to the major organism in the iron-reducing, benzene-degrading enrichment culture BF [ISME J (2007) 1: 643; Int J Syst Evol Microbiol (2010) 60: 686]. The phylogenetic classification supports a new candidate species and genus of Gram-positive spore-forming iron-reducers that can degrade non-substituted aromatic hydrocarbons. It furthermore indicates that Gram-positive microorganisms might also play an important role in anaerobic polycyclic aromatic hydrocarbon-degradation.