gebhart/patrepeval huggingface dataset:
Luciferase fragment complementation imaging in preclinical cancer studies (2014)

The luciferase fragment complementation assay (LFCA) enables molecular events to be non-invasively imaged in live cells in vitro and in vivo in a comparatively cheap and safe manner. It is a development of previous enzyme complementation assays in which reporter genes are split into two, individually enzymatically inactive, fragments that are able to complement one another upon interaction. This complementation can be used to externally visualize cellular activities. In recent years, the number of studies which have used LFCAs to probe questions relevant to cancer have increased, and this review summarizes the most significant and interesting of these. In particular, it focuses on work conducted on the epidermal growth factor, nuclear and chemokine receptor families, and intracellular signaling pathways, including IP3, cAMP, Akt, cMyc, NRF2 and Rho GTPases. LFCAs which have been developed to image DNA methylation and detect RNA transcripts are also discussed.
p‐Hydroxyphenylpyruvate dioxygenase inhibitor‐resistant plants (2005)

The enzyme p-hydroxyphenylpyruvate dioxygenase (HPPD) catalyzes the formation of homogentisic acid, the aromatic precursor of plastoquinone and vitamin E. HPPD is the specific target of several herbicide families: isoxazoles, triketones and pyroxazoles. Its inhibition results in the depletion of the plant plastoquinone and vitamin E pools, leading to bleaching symptoms. These herbicides are very potent for the selective pre- and in some cases post-emergence control of a wide range of broadleaf and grass weeds in maize and rice. Their herbicidal potential raised interest in the development of highly resistant transgenic crops. This goal was first achieved by over-expression of a bacterial HPPD in crop plants, and an increased level of resistance was obtained by using a mutant enzyme. A second strategy based on bypassing HPPD in the production of homogentisate was then developed. Recently, a third strategy of resistance based on the increase of p-hydroxyphenylpyruvate substrate flux has been developed. This was achieved by the introduction of the yeast prephenate dehydrogenase gene (PDH) into transgenic plants already overexpressing HPPD. In addition to a high level of herbicide resistance, a massive accumulation of vitamin E, mainly tocotrienols, was observed in leaves of the transgenic HPPD-PDH plants.
Experimental and numerical modeling of mixing and settling in continuous metal production (1994)

Metal is now produced from ore in novel single reactors. These converters provide substantial improvement in fuel efficiency and much better pollution control than common practice. The reactors are operated essentially in a horizontal mode to permit staging of fuel and oxygen potential in the bath along the reactor by utilizing bottom-blowing of oxygen and fuel through injectors directly into the liquid bath. The submerged injectors must create sufficient turbulence to provide excellent heat and mass transfer between gas and liquid in the bath, but this turbulence must be localized to provide zones for separation of metal and slag between the active turbulent mixing and chemical reaction zones. For the design and refinement of these processes it is important to know the behavior of gas and liquids in the plume created by submerged gas injection, the nature of liquid entrainment into the plume, the extent of the mixing zone and the effect of baffles on the confinement of said mixing zone. Experimental and numerical work was conducted to study stirring of single liquid reactors and mixing and settling in a bath of a two liquid reactor stirred by submerged gas injection.
A ZVS-PWM interleaved boost DC/DC converter (2013)

A novel zero-voltage-switching pulse-width-modulation (ZVS-PWM) interleaved boost dc/dc converter is proposed in this paper. The proposed converter combines the conventional pulse-width-modulation technique, soft commutation technique to promote the circuit performance. The proposed converter uses two boost dc/dc converters with interleaved operation to increase the output power and reduce the input ripple current and output ripple voltage. Comparison with conventional interleaved boost dc/dc converter, the proposed converter has not additional voltage stress on main switches. A ZVS-PWM auxiliary circuit is configured in the presented dc/dc converter to provide the ZVS function on main switches and auxiliary switches and improve the problem of switching losses and EMI. A prototype has been implemented in laboratory to verify circuit theory.
Semiconductor Devices a Simulation Approach (1997)

1. Introduction. I. BASICS. 2. Fundamentals of Electromagnetism and its Numerical Analysis. 3. Transport Phenomena and Their Numerical Analysis. II. SEMICONDUCTOR SIMULATION. 4. The Semiconductor Equations. 5. Numerical Solution of PDEs. 6. The SGFramework. III. SEMICONDUCTOR DEVICES. 7. PN Junction Diodes. 8. Bipolar Junction Transistors. 9. Junction Field-Effect Transistors. 10. Metal-Oxide-Semiconductor Structures. 11. Power Semiconductor Devices. IV. ADVANCED TOPICS. 12. Mixed-Mode Simulations. 13. Kinetic Transport Models. 14. Related Work. 15. The SGFramework User's Manual.
Improving Statistical Machine Translation Efficiency by Triangulation. (2008)

In current phrase-based Statistical Machine Translation systems, more training data is generally better than less. However, a larger data set eventually introduces a larger model that enlarges the search space for the decoder, and consequently requires more time and more resources to translate. This paper describes an attempt to reduce the model size by filtering out the less probable entries based on testing correlation using additional training data in an intermediate third language. The central idea behind the approach is triangulation, the process of incorporating multilingual knowledge in a single system, which eventually utilizes parallel corpora available in more than two languages. We conducted experiments using Europarl corpus to evaluate our approach. The reduction of the model size can be up to 70 % while the translation quality is being preserved. 1.
Pneumonia Prevention to Decrease Mortality in Intensive Care Unit: A Systematic Review and Meta-analysis (2014)

Selective digestive decontamination with systemic antimicrobial therapy reduced mortality and should be considered in critically ill patients at high risk for death.
Method for Recirculation of Signals in the Problem of Observation of a Point Object above a Metal Surface (2019)

Application of ultrawideband centimeter-wavelength signals using recirculation of signals in spatial recirculation loops (emitter–target–element of the receiving antenna–emitter) is analyzed in the problem of localization of the position of a point object above a reflecting metal surface. Determination of the coordinates of object above a metal surface is based on the calculation of a generalized correlation integral in the spectral domain for frequency transmission coefficients of the recirculation loops over all receiving elements with allowance for coordinates of a true object, its mirror reflection, and reference point in space. The results of sounding in the presence and absence of the recirculation are compared.
Development of a real-world sensor-aided target acquisition model based on human visual performance with a Landolt C (2013)

With the growing number of image-producing sensors in different spectral bands it is often desirable to provide the operational community with an estimation of the level of target acquisition/recognition performance that could be expected for specific scenarios using these sensors. Many target acquisition/recognition models have been developed over the decades to try and predict expected human performance under various conditions. Many of these are relatively complicated and often concentrate on specific aspects, such as search strategies, atmospherics, or sensor parameters while ignoring other factors. This paper describes the development of a simple, high-level target acquisition/recognition model for predicting human performance for a particular class of operationally relevant, time-based scenarios involving sensor-aided viewing. Assumptions and relevant factors considered in developing the model are discussed and the model, in different forms, is presented. Fundamentally, the model is based on previously-collected human visual performance data using images of the Landolt C acuity target recorded using a short-wave infrared sensor, the Johnny Johnson target recognition criteria, and basic scenario parameters. Limited real-world testing of the model has been accomplished.
Evolutionary patchwork of an insecticidal toxin shared between plant-associated pseudomonads and the insect pathogens Photorhabdus and Xenorhabdus (2015)

Our findings suggest that multiple independent evolutionary events led to formation of at least three versions of the Mcf/Fit toxin highlighting the dynamic nature of insect toxin evolution.
Oxidative Kinetic Self-Sorting of a Dynamic Imine Library (2010)

Dynamic libraries of [n × n] imine components spontaneously simplify during a slow oxidation reaction to produce only n discrete products. The selectivity of this self-sorting process is a consequence of different oxidation rates for various imines, while the dynamic nature of the library enables self-sorting to proceed with high efficiency.
Financial information, physical proximity and COVID: The experience of Asian sell-side equity research analysts (2022)

The need for physical proximity and face-to-face communication in financial information flows is contested. But the movement restrictions imposed across Asia during the COVID-19 pandemic, together with the elevated information needs as financial markets became stressed, provided the unique circumstances for a natural experiment to test the extent to which physical interaction is important in the origination and distribution of financial information. Drawing upon 70 interviews undertaken across Asia during 2021, primarily with sell-side analysts who act as information intermediaries in the financial ecosystem, this article provides evidence that physical proximity and face-to-face communication remains highly valued, particularly when accessing information embedded in informal local networks and originated through reciprocal client relationships. Analysts physically restricted from contacts at corporates and within their associated operating environments, reported a degradation of knowledge, especially versus more proximate competitors. The enforced physical separation also weakened previously strong social and reciprocal relationships with clients, even those co-located in the same city. Although these trends may be gradual and incremental rather than dramatic, they are persistent and self-reinforcing, and demonstrate the continued benefits of proximity and face-to-face interaction, with longer-term implications for financial geographies.
Efficient discovery of functional and approximate dependencies using partitions (2002)

Discovery of functional dependencies from relations has been identified as an important database analysis technique. We present a new approach for finding functional dependencies from large databases, based on partitioning the set of rows with respect to their attribute values. The use of partitions makes the discovery of approximate functional dependencies easy and efficient, and the erroneous or exceptional rows can be identified easily. Experiments show that the new algorithm is efficient in practice. For benchmark databases the running times are improved by several orders of magnitude over previously published results. The algorithm is also applicable to much larger datasets than the previous methods.
Quantitative Magnetization Transfer Imaging Using Non-Balanced SSFP (2009)

Similar to balanced steady-state free precession (bSSFP), the signal of non-balanced SSFP (nb-SSFP, such as SSFP-FID or SSFP-echo) depends on magnetization transfer (MT) in tissues. Based on a binary spin-bath model, an extended SSFP signal equation is presented which takes MT effects into account. Using this new SSFP signal equation, quantitative MT imaging (qMTI) is demonstrated ex-vivo and in-vivo. High correlation with literature values is observed and furthermore, this method benefits from short acquisition times, high signal-to-noise ratios and off-resonance insensitivity.
Leucine Carboxyl Methyltransferase 1 (LCMT-1) Methylates Protein Phosphatase 4 (PP4) and Protein Phosphatase 6 (PP6) and Differentially Regulates the Stable Formation of Different PP4 Holoenzymes (2016)

The protein phosphatase 2A (PP2A) subfamily of phosphatases, PP2A, PP4, and PP6, are multifunctional serine/threonine protein phosphatases involved in many cellular processes. Carboxyl methylation of the PP2A catalytic subunit (PP2Ac) C-terminal leucine is regulated by the opposing activities of leucine carboxyl methyltransferase 1 (LCMT-1) and protein phosphatase methylesterase 1 (PME-1) and regulates PP2A holoenzyme formation. The site of methylation on PP2Ac is conserved in the catalytic subunits of PP4 and PP6, and PP4 is also methylated on that site, but the identities of the methyltransferase enzyme for PP4 are not known. Whether PP6 is methylated is also not known. Here we use antibodies specific for the unmethylated phosphatases to show that PP6 is carboxyl-methylated and that LCMT-1 is the major methyltransferase for PP2A, PP4, and PP6 in mouse embryonic fibroblasts (MEFs). Analysis of PP2A and PP4 complexes by blue native polyacrylamide gel electrophoresis (BN-PAGE) indicates that PP4 holoenzyme complexes, like those of PP2A, are differentially regulated by LCMT-1, with the PP4 regulatory subunit 1 (PP4R1)-containing PP4 complex being the most dramatically affected by the LCMT-1 loss. MEFs derived from LCMT-1 knock-out mouse embryos have reduced levels of PP2A B regulatory subunit and PP4R1 relative to control MEFs, indicating that LCMT-1 is important for maintaining normal levels of these subunits. Finally, LCMT-1 homozygous knock-out MEFs exhibited hyperphosphorylation of HDAC3, a reported target of the methylation-dependent PP4R1-PP4c complex. Collectively, our data suggest that LCMT-1 coordinately regulates the carboxyl methylation of PP2A-related phosphatases and, consequently, their holoenzyme assembly and function.
Optical properties of reflective bistable twisted nematic liquid crystal display (2000)

A model of a reflective bistable twisted nematic liquid crystal display was studied by detailed numerical simulation. The optimized modes of a 5 μm reflective bistable twisted nematic liquid crystal were determined by the parameter space method. We have shown that large wavelength dispersion in the reflection coefficient of such displays cause the optimal mode to have a small value of dΔn, around 0.2 μm. By using a quarter-wave plate compensation film the optimized modes can have a dΔn value of around 0.4 μm. Numerical simulations show a wide viewing angle of up to ±60° for both types of reflective bistable twisted nematic liquid crystal display.
Predicting prognosis in patients with acute myeloid leukemia: The role of next-generation sequencing and mutational profiling. (2014)

7068 Background: Although cytogenetics-based prognostication systems are well described in acute myeloid leukemia (AML), Patel et al. (NEJM 2012) recently used data from patients <60 years enrolled in a randomized controlled trial to create a new integrated prognostic (IP) schema using mutations in 9 genes. Our objective was to assess whether the IP schema was relevant in clinical practice. Methods: Our study consisted of 2 cohorts of patients with de novo AML, each from single large academic institutions. We included 181 patients from the Hospital of the University of Pennsylvania and 188 patients from Washington University (The Cancer Genome Atlas) for whom clinical, cytogenetic and genetic data were available. We evaluated survival outcomes among 4 mutational profiles defined by Patel et al. in the IP schema. Results: Clinical characteristics and outcomes were similar in both cohorts (n=369 overall, n=217 age <60), so they were combined for further analysis. Median age was 57 years with 59% <60 years. Patients <60 years with intermediate-risk cytogenetics (n=137) were classified as having favorable, intermediate or unfavorable mutational profiles (see table). In patients >60 years, long-term survival was poor for patients with all 4 mutational profiles and was not further evaluated for this study. Conclusions: The IP schema identifies mutational profiles that have differential survival in younger patients with intermediate-risk cytogenetics. Our findings validate Patel et al.’s IP schema in patients <60 years for some but not all mutational profiles. Performing next-generation sequencing at diagnosis may inform patient management and be cost-effective if gene panels include validated mutations and their use is tailored to patient age. Integrated prognostic (IP) assessment of patients <60 years with intermediate-risk cytogenetics. Mutational profile Prognosis n 3-year overall survival p-value FLT3-ITD negative with mutant NPM1 and IDH1/2 Favorable 13 55% 0.004 FLT3-ITD negative with mutant TET2, MLL-PTD, ASXL1 or PHF6 Unfavorable 32 45% 0.994 FLT3-ITD positive with trisomy 8 or mutant TET2, MLL-PTD or DNMT3A Unfavorable 30 17% 0.039 All others Intermediate 62 35% Reference
The Biliary Manometric Perfusion Test and Clinical Trial—Long-term Predictive Value of Success after Treatment of Bile Duct Strictures: Ten-year Experience (1998)

Patients who initially pass either the biliary manometric perfusion test or clinical trial have a significantly increased probability of patency versus those who fail; however, patients who fail either test and who then receive definitive additional treatment have a similar probability of patency as those who initially pass. Although the log rank test demonstrated the Kaplan-Meier survival curves from the biliary manometric perfusion test and clinical trial not to be significantly different in any of the three groups (ie, passing, failing, re-treated), the biliary manometric perfusion test is recommended over the clinical trial because of its simplicity, immediate results, and predicted cost savings.
An improvement in the pointer coding of LZ77 data compression method (1996)

Abstract There are essentially two approaches in the Ziv‐Lempel code to be used in the data compression. They have already been proposed also as the improvements of the Ziv‐Lempel code, which can be considered as combinations of the two methods. This paper shows that by executing the combination, not only are advantages produced, but also the structure of the Ziv‐Lempel code is derived which realizes a more efficient coding. A precise data compression method is proposed based on the derived structure. the proposed method corresponds to an improvement of the LZ77 method. As the pointer information for the substrings for the coding the parameter corresponding to the length of the substring is encoded first, in contrast to most of the past methods. Then, utilizing the result, the coding method for the position of the reference substring is adjusted selectively. the proposed method is one method with the highest compession ability among the modifications of the Ziv‐Lempel code.
A Facile Microwave Assisted Synthesis, Characterization and Antibacterial Activity of 5-Phenyl-1,3,4-Oxadiazole Derivatives for Chemotherapeutic Use (2014)

This paper deals with an efficient synthesis of some 2-amino-5-substituted phenyl-1,3,4-oxadiazoles by using both conventional and microwave methods for chemotherapeutic use. The obtained results confirmed that, microwave assisted technique is efficient, eco-friendly, and inexpensive method which not only gives higher yield but also reduces the reaction time significantly. The structural elucidation of the prepared compounds was carried out by the aid of IR, 1H NMR, UV-Vis and mass spectral analyses. Compounds Sa-Sf showed antimicrobial activities against Escherichia coli, Serratia marcescens, Salmonella enterica and Proteus vulgaris (Gram-negative bacteria) and Bacillus subtilis and Staphylococcus aureus (Gram-positive bacteria) at low concentrations (10–1000 µg/mL). Keywords: Microwave assisted synthesis, oxadiazoles, characterization, antibacterial activity. Read more →
Dealing with indetermination in biochemical networks (2017)

A main aspect in computational modelling of biological sys- tems is the determination of model structure and model pa- rameters. Due to economical and technical reasons, only part of these details are well characterized, while the rest are unknown. To deal with this difficulty, many reverse en-
Data from Therapeutically Active RIG-I Agonist Induces Immunogenic Tumor Cell Killing in Breast Cancers (2023)

&lt;div&gt;Abstract&lt;p&gt;Cancer immunotherapies that remove checkpoint restraints on adaptive immunity are gaining clinical momentum but have not achieved widespread success in breast cancers, a tumor type considered poorly immunogenic and which harbors a decreased presence of tumor-infiltrating lymphocytes. Approaches that activate innate immunity in breast cancer cells and the tumor microenvironment are of increasing interest, based on their ability to induce immunogenic tumor cell death, type I IFNs, and lymphocyte-recruiting chemokines. In agreement with reports in other cancers, we observe loss, downregulation, or mutation of the innate viral nucleotide sensor retinoic acid-inducible gene I (RIG-I/&lt;i&gt;DDX58&lt;/i&gt;) in only 1% of clinical breast cancers, suggesting potentially widespread applicability for therapeutic RIG-I agonists that activate innate immunity. This was tested using an engineered RIG-I agonist in a breast cancer cell panel representing each of three major clinical breast cancer subtypes. Treatment with RIG-I agonist resulted in upregulation and mitochondrial localization of RIG-I and activation of proinflammatory transcription factors STAT1 and NF-κB. RIG-I agonist triggered the extrinsic apoptosis pathway and pyroptosis, a highly immunogenic form of cell death in breast cancer cells. RIG-I agonist also induced expression of lymphocyte-recruiting chemokines and type I IFN, confirming that cell death and cytokine modulation occur in a tumor cell–intrinsic manner. Importantly, RIG-I activation in breast tumors increased tumor lymphocytes and decreased tumor growth and metastasis. Overall, these findings demonstrate successful therapeutic delivery of a synthetic RIG-I agonist to induce tumor cell killing and to modulate the tumor microenvironment &lt;i&gt;in vivo&lt;/i&gt;.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Significance:&lt;/b&gt; These findings describe the first in vivo delivery of RIG-I mimetics to tumors, demonstrating a potent immunogenic and therapeutic effect in the context of otherwise poorly immunogenic breast cancers. &lt;i&gt;Cancer Res; 78(21); 6183–95. ©2018 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
[Design and Implementation of Remote Firmware Update System Based on IAP Technology]. (2019)

This paper introduces a network remote firmware update system based on IAP technology, which aims to solve the problems of low efficiency and high cost in the traditional upgraded medical device firmware (lower computer program) mode, and to improve the portability of the lower computer program upgrade maintenance. In order to better cope with market changes, customer needs, and solve software failures in medical devices, it is necessary to update and upgrade medical device software in a timely manner. Through the IAP technology and Internet communication technology of STM32 platform, this solution can complete the update of all instrument firmware in a short time, which not only saves a lot of travel expenses, mailing costs and labor costs, but also greatly shortens the update time.