gebhart/patrepeval huggingface dataset:
Kinome-Wide RNAi Screen Implicates at Least 5 Host Hepatocyte Kinases in Plasmodium Sporozoite Infection (2008)

Plasmodium sporozoites, the causative agent of malaria, are injected into their vertebrate host through the bite of an infected Anopheles mosquito, homing to the liver where they invade hepatocytes to proliferate and develop into merozoites that, upon reaching the bloodstream, give rise to the clinical phase of infection. To investigate how host cell signal transduction pathways affect hepatocyte infection, we used RNAi to systematically test the entire kinome and associated genes in human Huh7 hepatoma cells for their potential roles during infection by P. berghei sporozoites. The three-phase screen covered 727 genes, which were tested with a total of 2,307 individual siRNAs using an automated microscopy assay to quantify infection rates and qRT-PCR to assess silencing levels. Five protein kinases thereby emerged as top hits, all of which caused significant reductions in infection when silenced by RNAi. Follow-up validation experiments on one of these hits, PKCsigma (PKCzeta), confirmed the physiological relevance of our findings by reproducing the inhibitory effect on P. berghei infection in adult mice treated systemically with liposome-formulated PKCsigma-targeting siRNAs. Additional cell-based analyses using a pseudo-substrate inhibitor of PKCsigma added further RNAi-independent support, indicating a role for host PKCsigma on the invasion of hepatocytes by sporozoites. This study represents the first comprehensive, functional genomics-driven identification of novel host factors involved in Plasmodium sporozoite infection.
The Catalytic Enantioselective Total Synthesis of (+)‐Liphagal (2011)

Ring a ding: The meroterpenoid natural product (+)-liphagal has been synthesized enantioselectively in 19 steps from commercially available materials. The trans-homodecalin system was achieved by ring expansion followed by stereoselective hydrogenation.
A novel approach to investigating frictional electrification and charge decay on woven textile fabrics treated with ionic antistatic and hydrophilic surface finishes (2018)

The results of a study of charge generation and decay for range of woven fabrics from ring spun cotton yarns, ring spun polyester yarns, and flat continuous filament polyester yarns treated with topical finishes are reported. The topical finishes include commercially available ionic antistatic finishes, one commercially available hydrophilic finish, and a new experimental moisture management finish. The fabrics were rubbed against surface of steel and Polytetrafluoroethylene (PTFE; Teflon®) and their frictional electrification and charge dissipation were monitored. It is shown that fabrics from cotton have a more rapid inherent charge decay than fabrics from polyester. Ionic antistatic finishes are shown to be effective in reducing charge generation and promoting charge decay and this is particularly true for the fabrics made from filament polyester. When commercially available and experimental hydrophilic finishes were applied on fabrics made from filament polyester, less charge was generated and the generated charge decayed quickly compared to the control untreated fabrics. In an attempt to understand the mechanism of charge decay, two probes were used with one placed on the top of the rubbed area and the other placed some distance from the rubbed area. It was found that the generated charge migrated from the rubbed areas to other parts of the sample. This behavior is more pronounced for fabrics treated with hydrophilic and moisture management finishes, which cause the charge to decay exponentially.
Synthesis of new trimeric lignin model compounds containing 5-5' and beta-O-4' substructures, and their characterization by 1D and 2D NMR Techniques (2000)

Trimeric lignin model compounds containing biphenyl (5-5') and beta-aryl ether (beta-O-4') were synthesized from dehydrodivanillin derivatives and alpha-bromo acetovanillone derivatives via Williamson's reaction. The ¹H and 13C NMR characteristics of the resulting trimers were studied using corresponding ¹H and 13C NMR spectra as well as homo- and heteronuclear 2D NMR techniques. The results are discussed in terms of signal assignment and conformation of the molecules.
Light-assisted drying (LAD) for anhydrous preservation of biologics: processing sample volumes comparable to a therapeutic dose (2022)

Cold-chain storage can be challenging and expensive for the transportation and storage of biologics, especially in low-resource settings. Recent research has demonstrated that anhydrous preservation in a trehalose amorphous solid matrix offers an alternative to freeze drying for the preservation of biologics. We have previously described a new processing technique, light assisted drying (LAD), to create trehalose preservation matrices of small volume (40 &mu;L) samples. LAD uses illumination by near-infrared laser light to selectively heat water and speed dehydration. In this study we apply the LAD technique to large volume samples (250 &mu;L) that are more comparable to therapeutic doses.
Molecular Solids as Ligands in Organometallic Chemistry: [CpTi6Na7F19·2.5thf] (Cp* C5Me5) and [CpTi4Mg2F12·7thf], Links Between Ionic Solids and Organometallic Compounds (1994)

Central NaF and MgF 2 frameworks are present in the title compounds obtained from the reaction of [Cp * TiF 3 ] (Cp  C 5 Me 5 ) with elemental sodium and magnesium, respectively. In these reactions Ti IV is reduced to Ti III . The Cp * Ti units function as organometallics shields around the cagelike core and are responsible for the high solubility of the compounds.
Special considerations in breast cancer risk and survival (1999)

Experimental and clinical evidence suggests that breast neoplasia appears to be a hormone-dependent process that may also be influenced by dietary factors in many women. Conflicting reports on the relationship between exogenous hormones and the development, progression, and recurrence of breast cancer are critically examined in this report. The absolute breast cancer risk associated with either hormone replacement therapy or oral contraceptive use has not been clearly defined. Data from some large prospective studies have actually documented lower mortality rates for women taking hormone replacement compared with those for women who did not have hormone replacement therapy. In this regard, age, duration of use, and preexisting breast cancer risk factors must be taken into account. Although the results of two major prospective clinical trials addressing the role of timing of surgery within the menstrual cycle are forthcoming, the majority of studies have found no consistent association between timing of surgery and breast cancer survival. Recently reported prospective randomized data showing that selective-estrogen-receptor-modulators can act as effective chemoprevention agents in women at increased risk for breast cancer development are presented. Finally, information regarding the effect of dietary manipulation on breast cancer risk and survival is reviewed. J. Surg. Oncol. 1999;71:250–260. © 1999 Wiley-Liss, Inc.
Harnessing Solar Power: Novel Strategies for Rational Design of Photocatalysts and Photovoltaic Materials (2015)

Abstract : The goal of this effort was to develop the spectroscopic infrastructure to be able to probe non- Born-Oppenheimer couplings near conical intersections in the condensed phase. This effort required 2D electronic spectroscopy to be extended to broader bandwidth, higher sensitivity and improved resolution of coherent dynamics to detect phase. We invented a new approach to 2D spectroscopy to address these issues: Gradient-Assisted Photon Echo Spectroscopy (GRAPES). This approach allowed improved bandwidth due to purely reflective optics, improved sensitivity due to elimination of laser power fluctuations in the indirect domain, and improved phase resolution. We applied this spectroscopy to a range of synthetic and natural photosynthetic light harvesting systems to examine the system-bath coupling (electronic-vibrational couplings) using coherences as a detailed probe of the environment.
Design and implementation of a fine-grained software inspection tool (2003)

Although software inspection has led to improvements in software quality, many software systems continue to be deployed with unacceptable numbers of errors, even when software inspection is part of the development process. The difficulty of manually verifying that the software under inspection conforms to the rules is partly to blame. We describe the design and implementation of a tool designed to help alleviate this problem. The tool provides mechanisms for fine-grained inspection of software by exposing the results of sophisticated whole-program static analysis to the inspector. The tool computes many static-semantic representations of the program, including an accurate call graph and dependence graph. A whole-program pointer analysis is used to make sure that the representation is precise with respect to aliases induced by pointer usage. Views on the dependence graph and related representations are supported. Queries on the dependence graph allow an inspector to answer detailed questions about the semantics of the program. Facilities for openness and extensibility permit the tool to be integrated with many software development processes. The main challenge of the approach is to provide facilities to navigate and manage the enormous complexity of the dependence graph.
Protein kinase C enhances myosin light-chain kinase effects on force development and ATPase activity in rat single skinned cardiac cells (1992)

Many neurohormones alter the force of cardiac contraction by variations in the intracellular Ca2+ concentration. alpha 1-Adrenergic and muscarinic stimulations, rather, modify the sensitivity of contractile proteins to Ca(2+)-calmodulin-myosin light-chain kinase (MLCK) complex induces a large increase in Ca2+ sensitivity (0.14 pCa unit) of these easily accessible myofilaments. This increase is further enhanced by up to 0.19 pCa unit when protein kinase C (PKC) is added together with MLCK. Similarly, the Ca2+ ATPase activity of skinned cells in suspension is increased in the presence of MLCK and further in the presence of both kinases. 32P-labelling and SDS/PAGE show that these changes are associated with light-chain 2 (LC2) phosphorylation together with phosphorylation of troponin I and troponin T when PKC is added. Although to a smaller extent than in smooth muscle, phosphorylation of cardiac myosin LC2 may be involved in the modulation of heart contractility.
Combination of lentivector immunization and low‐dose chemotherapy or PD‐1/PD‐L1 blocking primes self‐reactive T cells and induces anti‐tumor immunity (2011)

In the last two decades, anti-cancer vaccines have yielded disappointing clinical results despite the fact that high numbers of self/tumor-specific T cells can be elicited in immunized patients. Understanding the reasons behind this lack of efficacy is critical in order to design better treatment regimes. Recombinant lentivectors (rLVs) have been successfully used to induce antigen-specific T cells to foreign or mutated tumor antigens. Here, we show that rLV expressing a murine nonmutated self/tumor antigen efficiently primes large numbers of self/tumor-specific CD8(+) T cells. In spite of the large number of tumor-specific T cells, however, no anti-tumor activity could be measured in a therapeutic setting, in mice vaccinated with rLV. Accumulating evidence shows that, in the presence of malignancies, inhibition of T-cell activity may predominate overstimulation. Analysis of tumor-infiltrating lymphocytes revealed that specific anti-tumor CD8(+) T cells fail to produce cytokines and express high levels of inhibitory receptors such as programmed death (PD)-1. Association of active immunization with chemotherapy or antibodies that block inhibitory pathways often leads to better anti-tumor effects. We show here that combining rLV vaccination with either cyclophosphamide or PD-1 and PD-L1 blocking antibodies enhances rLV vaccination efficacy and improves anti-tumor immunity.
Improved in vivo measurement of alternative oxidase respiration in field‐collected pine roots (2018)

Cellular respiration via the alternative oxidase pathway (AOP) leads to a considerable loss in efficiency. Compared to the cytochrome pathway (COP), AOP produces 0-50% as much ATP per carbon (C) respired. Relative partitioning between the pathways can be measured in vivo based on their differing isotopic discriminations against <sup>18</sup> O in O<sub>2</sub> . Starting from published methods, we have refined and tested a new protocol to improve measurement precision and efficiency. The refinements detect an effect of tissue water content (P < 0.0001), which we have removed, and yield precise discrimination endpoints in the presence of pathway-specific respiratory inhibitors [CN<sup>-</sup> and salicylhydroxamic acid (SHAM)], which improves estimates of AOP/COP partitioning. Fresh roots of Pinus sylvestris were sealed in vials with a CO<sub>2</sub> trap. The air was replaced to ensure identical starting conditions. Headspace air was repeatedly sampled and isotopically analyzed using isotope-ratio mass spectrometry. The method allows high-precision measurement of the discrimination against <sup>18</sup> O in O<sub>2</sub> because of repeated measurements of the same incubation vial. COP and AOP respiration discriminated against <sup>18</sup> O by 15.1 ± 0.3‰ and 23.8 ± 0.4‰, respectively. AOP contributed to root respiration by 23 ± 0.2% of the total in an unfertilized stand. In a second, nitrogen-fertilized, stand AOP contribution was only 14 ± 0.2% of the total. These results suggest the improved method can be used to assess the relative importance of COP and AOP activities in ecosystems, potentially yielding information on the role of each pathway for the carbon use efficiency of organisms.
NV-SRAM: a nonvolatile SRAM with backup ferroelectric capacitors (2001)

This paper demonstrates new circuit technologies that enable a 0.25-/spl mu/m ASIC SRAM macro to be nonvolatile with only a 17% cell-area overhead. New capacitor-on-metal/via-stacked-plug process technologies permit a nonvolatile SRAM (NV-SRAM) cell to consist of a six-transistor ASIC SRAM cell and two backup ferroelectric capacitors stacked over the SRAM portion. READ and WRITE operations in this NV-SRAM cell are very similar to those of a standard SRAM, and this NV-SRAM shares almost all the circuit properties of a standard SRAM. Because each memory cell can perform STORE and RECALL individually, both can execute massive-parallel operations. A V/sub dd//2 plate-line architecture makes READ/WRITE fatigue negligible. A 512-byte test chip was successfully fabricated to show compatibility with ASIC technologies.
Effect of VEGF and minoxidil on the production of arachidonic acid metabolites by cultured hair, dermal papilla cells (1996)

The aims of this study were to investigate : (1) the production of all arachidonic acid metabolites in hair dermal, papilla cells (DPC) and (2) the effects of minoxidil and vascular endothelial growth factor (VEGF) on this production. Eicosanoid synthesis was evaluated in culture medium after incorporation of tritiated arachidonic acid into DPC membrane phospholipids. Compared to controls, exposure of DPC to 1 μM 12-O-tetradecanoyl phorbol 13-acetate did not stimulate arachidonic acid metabolism, however exposure to calcium ionophore A23187, produced large amounts of eicosanoids, consisting mainly of 273% PG6KF 1α , 176% of PGE 2 and 68% LTB 4 . A good correlation was found with ELISA and radioassay techniques for total synthesis of major metabolites. The ELISA technique was also used to investigate the effects of minoxidil and VEGF on DPC production of three arachidonic acid metabolites : prostaglandins 6KF 1α , E 2 and leukotriene B 4 , before and after stimulation with A23187. High concentrations of VEGF induced an activation of the production of these metabolites, and a low concentration of minoxidil (12 μM) inhibited PG6KF 1α production but stimulated that of PGE 2 and LTB 4 . These data confirm the implication of VEGF and minoxidil in the modulation of eicosanoid production by hair, dermal papilla cells.
Metabolites associate with kidney function decline and incident chronic kidney disease in the general population (2013)

Baseline serum concentrations of spermidine and two metabolite ratios were associated with kidney function change over subsequent years in the general population. In separate analyses, baseline serum metabolites were able to predict incident CKD to a similar but not better extent than selected clinical parameters. Our longitudinal findings provide a basis for targeted studies of certain metabolic pathways, e.g. tryptophan metabolism, and their relation to kidney function decline.
Radiation and Actinomycin D Mortality Studies: Circadian Variations in Lethality Due to Independent Effects of Either Agent (1973)

SummaryC57BL/6 mice were exposed to either ionizing radiation or actinomycin at the peak and nadir of jejunal crypt cell mitotic activity. Animals exposed at the peak were more sensitive than animals exposed at the nadir. Conversely, animals treated with actinomycin D were slightly more sensitive at the nadir. These observations suggest that studies of the combined lethal effects of ionizing radiation and actinomycin D may be complicated by the change in sensitivity of normal tissues to either treatment under the influence of a circadian variable.
The Theory of Transactional Memory (2009)

Transactional memory (TM) is a promising paradigm for concurrent programming. This paper is an overview of our recent work on defining a theory of TM. We first present a correctness condition of a TM, ensured by most existing TM implementations. Then, we describe two progress properties that characterize the two main classes of TM implementations: obstruction-free and lock-based TMs. We use these properties to establish several results on the inherent power and limitations of TMs.
S131011 Study on laser processing of Carbon Fiber Reinforced Plastic : Effect of cooling water on heat-affected zone (2012)

Laser processing is the necessary technology for the high speed cutting about materials. However, there are heat-affected zone at the cut surface, and it causes the reduction of the material strength. In this study, the cutting characteristics of carbon fiber reinforced plastic (CFRP) with nanosecond pulsed Nd:YAG laser beam are investigated. The effect of cooling water on the heat-affected zone at the cut surface is evaluated. The eliminated volume of CFRP in water environment was smaller than that in air environment due to the thermal expansion by water. However, the cut-off of the CFRP with a thickness of 1 [mm] was achieved without any heat-affected zone at the cutting surface although the input energy to the CFRP was larger than the air environment.
Semantically Smooth Knowledge Graph Embedding (2015)

Shu Guo, Quan Wang, Bin Wang, Lihong Wang, Li Guo. Proceedings of the 53rd Annual Meeting of the Association for Computational Linguistics and the 7th International Joint Conference on Natural Language Processing (Volume 1: Long Papers). 2015.
Epidemiologic studies utilizing surveys: accounting for the sampling design. (1991)

Which particular aspects of the sampling design to use in the analysis of complex survey data and how to use them depend on certain features of the design. We give some guidelines for when to use the sample clustering and sample weights in the analysis.
Trans-hepatic cannulation: a novel approach for placement of a pediatric percutaneous ventricular assist device. (2006)

Pediatric ventricular assist device (VAD) use is increasing. The TandemHeart PTVA system is a percutaneous VAD used in adults. Pediatric use is limited by cannula size. Trans-hepatic left atrial (LA) cannulation offers the possibility of shorter, larger-diameter cannulae, but specific requirements for cannula size and flow characteristics need to be developed. We evaluated the feasibility of trans-hepatic cannulation based on patient measurements and bench-top modeling. Two hundred patients admitted to the University of Michigan Pediatric CICU were evaluated. Patients over 14 years and dextrocardiac patients were excluded. The distance from the skin between the 10th and 11th ribs at the mid-axillary line to the left-heart border was measured on x-ray. LA size was measured on echocardiogram. From these measurements, prototype cannulae were fabricated. Benchtop testing of developed cannulae was performed with a pump speed of 8500 RPM and fluid viscosity of 4.0 cP at physiologic atrial and arterial pressures. Inlet pressure and deliverable flows were measured. The proposed design delivered sufficient flow with negative pressures low enough to avoid hemolysis. Trans-hepatic LA cannulation for percutaneous VAD placement is feasible. The shorter distance to the LA and larger hepatic vein size allows design of pediatric-appropriate cannulae with adequate flow rates.
CCCXII.—A modification of the Gabriel synthesis of amines (1926)

The first page of this article is displayed as the abstract.
Energy management optimisation using a combined Long Short-Term Memory recurrent neural network – Particle Swarm Optimisation model (2021)

Energy load forecasting is essential to effectively optimise the use of energy for the purpose of smart grid operation. In this work, a focus is placed on Short-Term Load Forecasts (STLF) using measured heat pump data from the UK utilising the Long Short-Term Memory (LSTM) method. A load forecasting program is developed to forecast the electricity consumption of heat pumps based on historical data. LSTM is compared to Backpropagation Neural Network (BPNN), Seasonal Autoregressive Integrated Moving Average (SARIMA), Random Forest (RF) and Holt-Winters Exponential Smoothing (ES). The best average Mean Absolute Percent Error (MAPE) of 1.59% is achieved for the test data set by LSTM, which outperforms other models compared and a number of models presented in papers in the literature. By conducting the Wilcoxon signed-rank test, it is proven that the prediction accuracy improvement of LSTM compared to other models is statistically significant with the exception when comparing with RF with the training data. The impact of data aggregation resolution to forecast accuracy is investigated. The proposed LSTM model performs best on 1-h resolution data compared with other resolution time periods. The results of the LSTM model are integrated with Home Energy Management Systems (HEMS). The electricity costs of the HEMS are compared when using forecasted and measured heat pump data respectively. The results indicate an average percentage difference of 2.06% between the predicted and the actual electricity cost of HEMS for the test data. Furthermore, this paper presents a combined neural network and Particle Swarm Optimisation (PSO) model to develop an optimised energy management system while proving the effectiveness of the LSTM algorithm.
Individualized scan protocols for CT angiography: an animal study for contrast media or radiation dose optimization (2023)

• Computed tomography angiography protocols could be adapted to individual patient requirements using an automated tube voltage selection system combined with adjusted contrast media injection. • Using an adapted automated tube voltage selection system, a contrast media dose reduction (-26%) or radiation dose reduction (-30%) could be possible.