gebhart/patrepeval huggingface dataset:
Smartphone-Based SARS-CoV-2 and Variants Detection System using Colorimetric DNAzyme Reaction Triggered by Loop-Mediated Isothermal Amplification (LAMP) with Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) (2022)

Coronavirus disease (COVID-19) has affected people for over two years. Moreover, the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants has raised concerns regarding its accurate diagnosis. Here, we report a colorimetric DNAzyme reaction triggered by loop-mediated isothermal amplification (LAMP) with clustered regularly interspaced short palindromic repeats (CRISPR), referred to as DAMPR assay for detecting SARS-CoV-2 and variants genes with attomolar sensitivity within an hour. The CRISPR-associated protein 9 (Cas9) system eliminated false-positive signals of LAMP products, improving the accuracy of DAMPR assay. Further, we fabricated a portable DAMPR assay system using a three-dimensional printing technique and developed a machine learning (ML)-based smartphone application to routinely check diagnostic results of SARS-CoV-2 and variants. Among blind tests of 136 clinical samples, the proposed system successfully diagnosed COVID-19 patients with a clinical sensitivity and specificity of 100% each. More importantly, the D614G (variant-common), T478K (delta-specific), and A67V (omicron-specific) mutations of the SARS-CoV-2 S gene were detected selectively, enabling the diagnosis of 70 SARS-CoV-2 delta or omicron variant patients. The DAMPR assay system is expected to be employed for on-site, rapid, accurate detection of SARS-CoV-2 and its variants gene and employed in the diagnosis of various infectious diseases.
Incorporating the Effects of Variable Wall Properties in Large-Scale Deformable Models of the Cardiovascular System (2007)

Numerical simulation of blood flow in arteries has important applications in disciplines such as surgical planning, medical device design, and disease research. However, there are many challenges involved in accurately characterizing the motion of blood within the arterial system. First, computational models can require finite element meshes with several million degrees of freedom. Furthermore, surgical planning applications require solving these problems as quickly as possible. Second, the boundary conditions must faithfully represent the flow and pressure characteristics of the vascular trees external to the computational model. These conditions must also be consistent with the intrinsic wave propagation phenomena within the model. Third, the fluid-solid interactions between blood, vessel wall and surrounding tissues and organs need to be modeled. In order to represent the pulsation of blood within arteries, one must consider the variations in arterial compliance (especially significant when dealing with large models), points of attachment of the vessels to the surrounding organs, etc. Prior vascular fluid-structure interaction models have considered uniform vessel wall properties and a zero pressure reference state.
Synthesis of Fused Sulfonamide (1,1‐Dioxoisothiazole)substituted 1,5‐Diarylpyrazoles as Cyclooxygenase Inhibitors. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Low‐frequency electromagnetic field effects on functional groups in human skin keratinocytes cells revealed by IR‐SNOM (2008)

Human HaCaT cells, exposed for 24 h to a 1 mT (rms) 50 Hz sinusoidal magnetic field in a temperature-regulated solenoid, suffer detectable changes in their biochemical properties and shapes. By using infrared wavelength-selective scanning near-field optical microscopy, we observed changes in the distribution of the inner chemical functional groups and in the cell morphology with a resolution of 80-100 nm.
GaInN‐based LED structures on selectively grown semi‐polar crystal facets (2010)

Abstract In conventional nitride‐based light emitting diodes, huge internal electric fields lead to a reduced overlap of electron and hole wave functions in the active GaInN quantum wells as a consequence of the piezoelectricity of these polar materials. In order to minimize these internal fields while still maintaining the well‐established c‐direction as main epitaxial growth direction for high‐quality low‐defect‐density layers, we have investigated semi‐polar LED structures on the side‐facets of triangular GaN stripes grown by selective area epitaxy. The reduced internal electric field could be confirmed by several spectroscopic methods. We found a strongly facet dependent growth mechanism leading to very flat surfaces on $\{ 1\bar {1}01\}$ facets as opposed to their $\{ 11\bar {2}2\}$ counterparts. An increased indium uptake on semipolar $\{ 1\bar {1}01\}$ facets as compared to conventional c‐plane layers helped to shift the LED emission to longer wave lengths beyond 500 nm in the green spectral range despite the significantly reduced field‐dependent Stark shift.
Exploration of the effect of 2,6-(t-Bu)2-4-Me-C6H2OH (BHT) in chain shuttling polymerization (2013)

The interactions of a sterically hindered phenol [2,6-(t-Bu)2-4-Me-C6H2OH] (BHT) with the scavenger MAO (AlR3) and ZnR2 during Hf/Zr-based chain shuttling polymerization in a semi-batch reactor have been investigated. NMR model studies indicated preferential binding of BHT to aluminum under these conditions. Subsequently, reproducible polymerization runs gave rise to copolymers that were thoroughly characterized by HT-SEC, HT-HPLC, DSC, thermal fractionation (SSA), 13C NMR, density measurements, CRYSTAF and optical microscopy to unravel their complex microstructures. The obtained materials differ from a simple solution blend of materials, separately produced by single catalysts, but also from multi-block copolymers as obtained by DOW's continuous process, although a blocky structure can be rationalized.
Temporal Changes in a Natural Population of Copepods (1989)

Adaptation was measured in a natural population of the estuarine copepod, Eurytemora affinis (Poppe). Significant changes occurred between generations in tolerance to elevated temperature and in body size, in both sexes, and in reproductive traits in females. If these changes were genetic, they did not result in different heritabilities for the traits and genetic variation was maintained in the population. However, genetic correlations between temperature tolerance and brood size in females showed significant changes between generations, lending support to two models for the maintenance of genetic variance. Linkage disequilibrium is discussed as an alternative explanation for the observed genetic changes that took place and for decreased hatchability of broods. Evidence for decreased hatchability, measured as proportion hatch, suggests summer diapause in this species.
Oscillatory Blowing: A Tool to Delay Boundary-Layer Separation (1993)

The effects of oscillatory blowing as a means of delaying separation are discussed. Experiments were carried out on a follow, flapped NACA 01115 airfoil equipped with a two-dimensional slot over the hinge of the flap. The flap extended over 25% of the chord and was detected at angles as high as 40 deg. The steady blowing momentum coefficients could be varied independently of the amplitudes and frequencies of the superimposed oscillations. The modulated blowing was a major factor in improving the performance of the airfoil at much lower energy inputs than was hitherto known. Optimum benefits in performance were obtained at reduced frequencies, based on the flap chord, of an order of unity. Significant increase in lift as well as cancellation of form drag were observed
Slugging (2016)

This Glossary of Terms Related to Pharmaceutics is needed by practitioners in the field of pharmaceutics as this field fulfills an important and crucial role, different from the roles of other scientific disciplines involved in the drugmaking process. The glossary contains 168 definitions used in pharmaceutics. These are related to various aspects of this discipline, such as: (1) physicochemical characterization of pharmaceutical preparations and the active ingredients they contain; (2) unit operations used in the practice of pharmaceutics; (3) terms related to the various dosage forms; (4) terms related to the various modes and routes of drug delivery; (5) terms used in pharmacokinetics and biopharmaceutics in general; and additional miscellaneous terms. The field of pharmaceutics itself is of a multidisciplinary nature as its practitioners come from a variety of disciplines, such as chemistry or various biological sciences, thus a glossary containing authoritative definitions would be useful for them. The terms used in pharmaceutics are rarely covered by existing glossaries, and in the cases they are, their definitions are often inappropriate for the field of pharmaceutics and require new or modified definitions to better fit the new context.
Performance of the light emitting diodes versus conventional light sources in the UV light cured formulations (2007)

Abstract UV light emitting diodes (LED) are compared with conventional light sources for curing acrylate formulations. Both polymerization rates and the properties of the resulting coatings were examined. UV LEDs are acceptable alternatives to conventional light sources for a variety of applications. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci 2007
Achieving Class-Based QoS for Transactional Workloads (2006)

Transaction processing systems lie at the core of modern e-commerce applications such as on-line retail stores, banks and airline reservation systems. The economic success of these applications depends on the ability to achieve high user satisfaction, since a single mouse-click is all that it takes a frustrated user to switch to a competitor. Given that system resources are limited and demands are varying, it is difficult to provide optimal performance to all users at all times. However, often transactions can be divided into different classes based on how important they are to the online retailer. For example, transactions initiated by a "big spending" client are more important than transactions from a client that only browses the site. A natural goal then is to ensure short delays for the class of important transactions, while for the less important transactions longer delays are acceptable.
Kinetic studies and active site-binding properties of glutathione S-transferase using spin-labeled glutathione, a product analogue. (1984)

Kinetic and binding studies with substrates, products, and a spin-labeled product analogue of glutathione (sl-glutathione) have been used to characterize the kinetic mechanism and properties of the catalytic site of the homodimer YaYa of glutathione S-transferase. Product inhibition studies and inhibition by sl-glutathione indicate the random addition of substrates. The kinetically determined dissociation constant for the product S-(2,4-dinitrophenyl)glutathione is approximately 7 microM. A newly described spin-labeled product analogue, S-[[(2,2,5,5,-tetramethyl-1-oxy-3-pyrrolidinyl)-carbamoyl]methyl] glutathione (sl-glutathione), acts as a competitive inhibitor with respect to both substrates (glutathione and 1-Cl-2,4-dinitrobenzene) with a kinetically determined dissociation constant of approximately 40 microM. Analysis of the glutathione S-transferase X sl-glutathione complex by EPR gives a rigid limit spectrum indicative of highly immobilized spin label. Kinetic and EPR results support the proposal that sl-glutathione binds as a bisubstrate or product analogue by occupying both the glutathione and hydrophobic substrate sites. Binding studies of sl-glutathione by EPR give a dissociation constant of 28 microM and a single binding site per homodimer. Displacement of sl-glutathione by substrates and product have been used to directly determine enzyme-ligand dissociation constants. Dissociation constants of 2.1 mM, 17 microM, and 25 microM were obtained for glutathione, 1-Cl-2,4-dinitrobenzene and S-(2,4-dinitrophenyl)glutathione when enzyme was added to a mixture of sl-glutathione and the competing ligand. The dissociation constants for glutathione and 1-Cl-2,4-dinitrobenzene but not for S-(2,4-dinitrophenyl) glutathione were dependent on the order of addition, consistent with the existence of several kinetically stable conformations for the enzyme. The sl-glutathione described here may provide a useful analogue for similar studies with other glutathione S-transferases or other enzymes which bind glutathione.
Problem C (2020)

Logic "re"-simulation can be defined as gate level simulation where the input waveforms at every primary input and pseudo-primary input (such as register/RAM outputs) are known. Such waveforms could come from the unit's RTL simulation trace or Automatic Test Pattern Generation (ATPG) vectors. This type of simulation is useful in doing functional verification on gate level netlists and power analysis, since we can take the known trace on all primary and pseudo-primary inputs, re-simulate the trace using propagation of signals through timing-aware gate-level combinational logic, and verify that results at the primary and pseudo-primary outputs match the reference RTL simulation results. However, gate level simulation is usually much slower than RTL simulation. Thus, there is motivation for faster solutions. In this contest, we ask contestants to use Graphic Processing Units (GPUs) to speedup the re-simulation task.
Viper (2012)

The reliability of future processors is threatened by decreasing transistor robustness. Current architectures focus on delivering high performance at low cost; lifetime device reliability is a secondary concern. As the rate of permanent hardware faults increases, robustness will become a first class constraint for even low-cost systems. Current research into reliable architectures has focused on ad-hoc solutions to improve designs without altering their centralized control logic. Unfortunately, this centralized control presents a single point of failure, which limits long-term robustness. To address this issue, we introduce Viper, an architecture built from a redundant collection of fine-grained hardware components. Instructions are perceived as customers that require a sequence of services in order to properly execute. The hardware components vie to perform what services they can, dynamically forming virtual pipelines that avoid defective hardware. This is done using distributed control logic, which avoids a single point of failure by construction. Viper can tolerate a high number of permanent faults due to its inherent redundancy. As fault counts increase, its performance degrades more gracefully than traditional centralized-logic architectures. We estimate that fault rates higher than one permanent faults per 12 million transistors, on average, cause the throughput of a classic CMP design to fall below that of a Viper design of similar size.
ChemInform Abstract: A MILD, RAPID, AND CONVENIENT ESTERIFICATION OF α‐KETO ACIDS (1981)

Abstract Zur Veresterung von α‐Keto‐carbonsäuren (I) werden diese mit Chlorkohlensäureestern (II) bei niedrigen Temperaturen in Gegenwart von Triethylamin umgesetzt.
Transverse Wakefield of Waveguide Damped Structures and Beam Dynamics [Dissertation] (1995)

In the design of new high energy particle colliders with higher luminosity one is naturally led to consider multi-bunch operation. However, the passage of a leading bunch through an accelerator cavity generates a wakefield that may have a deleterious effect on the motion of the subsequent bunches. Therefore, the suppression of the wake field is an essential requirement for beam stability. One solution to this problem, which has been studied extensively, is to drain the wakefield energy out of the cavity by means of waveguides coupled with the cavity and fed into matched terminations. Waveguide dimensions are chosen to yield a cutoff frequency well above the frequency of the accelerating mode so that the latter is undamped. This paper presents a thorough investigation of the wakefield for this configuration.
Interconnects for All-Spin Logic Using Automotion of Domain Walls (2015)

In this paper, an interconnect scheme based on automotion of domain walls (DWs) for all-spin logic (ASL) has been proposed. The proposed interconnect is analyzed using a comprehensive numerical model including an equivalent circuit for ASL operations, the 1-D Landau-Lifshitz-Gilbert equation for DW creation, reflection, and disappearance at the boundaries. Analytical expressions for DW transport along the wire are also presented. From the model, it is found that the reflection of the DW can be eliminated using a material with a high Gilbert damping coefficient at the end, the energy dissipation can be independent of the interconnect length, and DW displacement and energy dissipation can be further improved using a material with a low damping factor and saturation magnetization. Furthermore, the interconnect reliability is also studied by applying the thermal random noise analysis on the dynamics of DWs, and it is found that thermal fluctuations can have a significant impact on the interconnect performance; thus, the interconnect with a low Gilbert damping factor is desired to suppress the thermal noise effects.
Modulation of Prohormone Convertase 1/3 Properties Using Site-Directed Mutagenesis (2010)

Prohormone convertase (PC)1/3 and PC2 cleave active peptide hormones and neuropeptides from precursor proteins. Compared with PC2, recombinant PC1/3 exhibits a very low specific activity against both small fluorogenic peptides and recombinant precursors, even though the catalytic domains in mouse PC1/3 and PC2 share 56% amino acid sequence identity. In this report, we have designed PC2-specific mutations into the catalytic domain of PC1/3 in order to investigate the molecular contributions of these sequences to PC1/3-specific properties. The exchange of residues RQG(314) with the SY sequence present in the same location within PC2 paradoxically shifted the pH optimum of PC1/3 upward into the neutral range; other mutations in the catalytic domain had no effect. Although none of the full-length PC1/3 mutants examined exhibited increased specific activity, the 66-kDa form of the RQG(314)SY mutant was two to four times more active than the 66-kDa form of wild-type PC1/3. However, stable transfection of RQG(314)SY into PC12 cells did not result in greater activity against the endogenous substrate proneurotensin, implying unknown cellular controls of PC1/3 activity. Mutation of GIVTDA(243-248) to QPFMTDI, a molecular determinant of 7B2 binding, resulted in increased zymogen expression but no propeptide cleavage or secretion, suggesting that this mutant is trapped in the endoplasmic reticulum due to an inability to cleave its own propeptide. We conclude that many convertase-specific properties are attributable less to convertase-specific catalytic cleft residues than to convertase-specific domain interactions.
Investigation of the Adrenergic and Opioid Binding Affinities, Metabolic Stability, Plasma Protein Binding Properties, and Functional Effects of Selected Indole-Based Kratom Alkaloids (2019)

Selected indole-based kratom alkaloids were evaluated for their opioid and adrenergic receptor binding and functional effects, in vivo antinociceptive effects, plasma protein binding, and metabolic stability. Mitragynine, the major alkaloid in <i>Mitragyna speciosa</i> (kratom), had higher affinity at opioid receptors than at adrenergic receptors while the vice versa was observed for corynantheidine. The observed polypharmacology of kratom alkaloids may support its utilization to treat opioid use disorder and withdrawal.
Bulk Conductivity and Defect Chemistry of Acceptor‐Doped Strontium Titanate in the Quenched State (1991)

The grain bulk conductivity of acceptor‐doped SrTiO 3 ceramics was investigated by the impedance analysis method after quenching from high‐temperature equilibria. The influence of the oxygen partial pressure during equilibration, P Eq O2 , is described in terms of a defect model for titanates. From a comparison between the experimental results and the predictions of this model, a predominant ionic conductivity is concluded for a wide P Eq O2 range (approximately 10 −11 to 10 5 Pa). The influence of the ionization energy of the acceptors and of possible defect association is discussed.
Laser Material Processing Inspired by Digitally-Scripted Genotype Sequencing (2013)

Precise real time modulation of the laser energy flux during material processing enables the regulation of specific chemical/physical properties on a highly localized scale. The presentation focuses on a control-system architecture and its implementation that delivers well defined photon exposures at the proper location and time.
Generation of nonclassical field based on a gain-loss feedback mechanism in the cavity-QED microlaser (2004)

We measured the second-order correlation function of the cavity-QED microlaser output and observed a transition from photon bunching to antibunching as the intracavity number of atoms increased. The observed correlation times and sub- and super-Poissonian photon statistics were well explained by gain-loss feedback or enhanced/reduced restoring actions against momentary photon number fluctuations.
FOXO3-dependent suppression of PD-L1 promotes anticancer immune responses via activation of natural killer cells. (2022)

Boosting anticancer immunity by blocking immune checkpoints such as the programmed death-1 (PD-1) or its ligand (PD-L1) is a breakthrough anticancer therapy. However, many cancer patients do not respond well to immune checkpoint blockades (ICBs) alone. Here we show that low-dose pharmacological immunoactivators (e.g., SN38, topotecan, sorafenib, etc.) notably downregulate PD-L1 and upregulate FOXO3 expression in various human and murine cancer cell lines. In a mouse tumor model, low-dose SN38 treatment markedly suppresses tumor growth, reduces PD-L1 expression, and enhances FOXO3 expression in primary tumor specimens. SN38 therapy engages the tumor-infiltrating mouse NK1.1/CD49b/NKG2D-positive natural killer (NK) cells to attack tumor cells by inducing mouse IFN-γ and granzyme-B secretion in the tumor microenvironment (TME) <i>in vivo</i>. SN38 treatment also promotes tumor cell apoptosis in the TME. SN38 treatment significantly decreases STAT3-pY705 and IL-6 protein levels; FOXO3 is essential for SN38-mediated PD-L1 downregulation. Collectively, these findings may contribute to future translational or clinical investigations tackling difficult-to-treat cancers with immune-activating medicines or combined with ICB immunotherapy.
On programming parallel computers (1975)

In this paper, I will make some general observations about how computers should be programmed, and how programs should be compiled. I will restrict my attention to programming computers to solve numerical analysis problems, although most of my remarks can be applied to other problem areas as well. My primary concern is for large parallel computers. However, I will show that parallelism is not a major issue, and I will not restrict the discussion to any single type of computer architecture.
ChemInform Abstract: Studies Directed Towards the Synthesis of Taxane Diterpenes: A Remarkable Rearrangement. (1987)

Abstract The dioxanone derivative (I), prepared by known methods, is alkylated to yield the isomeric pentenyl compounds (III).
Large amplitude modulation of high-order harmonic generation from vibrationally excited molecules (2008)

We observe large vibrationally-induced modulations in high order harmonic conversion in N<inf>2</inf>O<inf>4</inf>. We explain this unexpected result as due to the changing electronic structure induced by the vibration, leading to preferential emission at the outer turning point of the vibration