gebhart/patrepeval huggingface dataset:
Structures and Mechanisms of Polyketide Synthases (2009)

Nearly a quarter-century ago, the advent of molecular genetic tools in the field of natural product biosynthesis led to the remarkable revelation that the genes responsible for the biosynthesis, regulation, and self-resistance of complex polyketide antibiotics were clustered in the genomes of the bacteria that produced these compounds. This in turn facilitated rapid cloning and sequencing of genes encoding a number of polyketide synthases (PKSs). By now, it is abundantly clear that, notwithstanding extraordinary architectural and biocatalytic diversity, all PKSs are evolutionarily related enzyme assemblies. As such, understanding the molecular logic for the biosynthesis of literally thousands of amazing polyketide natural products made by nature can benefit enormously from detailed investigations into a few "model systems". For nearly the past two decades, our laboratory has focused its efforts on two such PKSs. One of them synthesizes two polyketides in approximately equal ratios, SEK4 and SEK4b, and both shunt products from the pathway that leads to the biosynthesis of the pigmented antibiotic actinorhodin. The other synthesizes 6-deoxyerythronolide B, the first isolable intermediate in the biosynthetic pathway for the widely used antibacterial agent erythromycin. Our present-day knowledge of the structures and mechanisms of these two PKSs is summarized here.
Dual Pathways to Tubular Morphogenesis of Vascular Endothelial Cells by Human Glioma Cells: Vascular Endothelial Growth Factor/Basic Fibroblast Growth Factor and Interleukin‐8 (1995)

In this study, we examined whether human glioma cells are angiogenic in a model using human microvascular endothelial cells, and also which factor is responsible for the glioma-dependent angiogenesis. Tubular morphogenesis in type I collagen gel by human microvascular endothelial cells was stimulated in the presence of 10 and 100 ng/ml of vascular endothelial growth factor (VEGF), 10 ng/ml basic fibroblast growth factor (bFGF) and 10 ng/ml of interleukin-8 (IL-8). Tube formation of the microvascular endothelial cells was assayed in the glioma cell lines IN157 and IN301, co-cultured using the double chamber method. IN301 cells had much higher levels of VEGF, bFGF and transforming growth factor-beta mRNA than IN157 cells, whereas the two had similar levels of transforming growth factor-alpha mRNA. By contrast, IN157 cells had much higher levels of IL-8 mRNA than IN301 cells. IN301-dependent tubular morphogenesis was inhibited by anti-VEGF or anti-bFGF antibody, and the inhibition was almost complete when anti-VEGF and anti-bFGF antibodies were present. On the other hand, IN157-dependent tubular morphogenesis was inhibited by anti-IL-8 antibody, but not by anti-VEGF or anti-bFGF antibodies. These findings demonstrated dual paracrine controls of tumor angiogenesis by human glioma cells. One is mediated through VEGF and/or bFGF, and the other, through IL-8.
Mid-Infrared Opto-nanofluidic Slot-Waveguide for Label-free On-Chip Chemical Sensing (2014)

A mid-infrared sensor for label-free on-chip chemical detection was developed using an engineered nanofluidic channel consisting of a Si-liquid-Si slot-structure. A sensitivity with 75 times improvement was achieved compared to conventional evanescent-wave sensing.
Address equation multiplexing for real-time signal processing applications (2002)

This paper describes several sharing techniques, tuned to hardware address generation for large memories in real-time signal processing systems. These strategies are oriented to minimize the area overhead introduced by the use of application-specific address generation units. The objective is to explore at the system level, when the signal processing application is being defined, the trade-offs involved in alternative algorithmic specifications. This will allow one to arrive faster at area efficient specifications as input for the actual address hardware generation stage. The principles are demonstrated on a realistic test-vehicle for which very promising results have been achieved.
Maximizing the Retention of Antigen Specific Lymphocyte Function after Cryopreservation (2004)

s for the 19th Annual Scientific Meeting of the International Society for Biological Therapy of Cancer, San Francisco, California, November 4-7, 2004: Immune Monitoring
Enabling technologies for 3D System on Chip (SoC) integration and examples of 3D integrated structures (2007)

3D Integration of patterned semiconductors circuits or/and integrated sensors requires some knowledge of vertical circuits stacking architecture and available technologies to realise expected by this integration performances. 3D architectures have emerged as serious contender in the challenge of functionality and potentiality increasing. Innovative circuit design, new advanced substrates, improved thin layer materials, new integration processes and technical approaches elaborated in last generation tools have grandly contributed in emerging various forms of 3D integration and packaging. In the context of More Moore and More than Moore considerations, the road maps place the vertical circuits stacking and associated post processing of stacked elements as a very serious opportunity for new generation of ICs. Furthermore, the mixing of advanced ICs with integrated passives, image sensors, mechanical and optical micro and nano-systems etc., based on a 3D architecture have been developed during the last years. That contributes in emerging of new generation of System on Chip (SoC) with new or increased functionalities. Some of them are on the merge of commercialisation and many continued advancements and improvements are expected in the near future. In most applications cases of 3-D integration, successive staking requires the patterned wafers or dies which have already a complex integrated structures, furthermore these structures are often fragile and sensitive to the conditions of complementary processing. Therefore, before 3D integration a selection of adapted process will be done and carefully checked for its technological compatibilities. We propose to examine the advanced methods of patterned wafer or die vertical integration and discuss its compatibility approaches for 3D integration processing. Some examples of demonstrators achieved at LETI will illustrate the patterned structures transfer, with original performances or improved characteristics thanks to 3D architecture and integration processes. Advanced front-end and back-end architecture will be discussed regarding the 3D-integration challenging requirements: ICs density increasing, interconnections distance reduction, new above IC functions development, multiple functions in smart integrated hetero-structures and systems... The wafer level integration concept will be illustrated by : the double gate MOS architecture (BDGMOS), the completely integrated (front and back-end) circuits aligned transfer and deep via achievement for chips interconnection, the innovative concept of capacitive interconnections for chip-to-chip communication, the multiple transferred circuits for above IC application. Furthermore the recent developments in die-to-wafer bonding will be reported, illustrating heterogeneous structure integration for optoelectronic devices.
Demonstration of Advanced EMI Models for Live-Site UXO Discrimination at Former Camp Butner, North Carolina (2012)

Abstract : This demonstration is designed to illustrate the discrimination performance at a challenging livesite of a suite of advanced electromagnetic induction (EMI) modeling approaches developed to go beyond the simple dipole model in accuracy and predictive ability. The core of the suite consists of the orthonormalized volume magnetic source (ONVMS) model for target characterization, a target-counting pre-processing procedure based on joint diagonalization (JD), and an implementation of the differential evolution (DE) algorithm for nonlinear optimization used to locate targets. The study used cued data sets collected at Camp Butner in North Carolina using two next-generation EMI sensors, the Geometrics MetalMapper (MM) and the Timedomain Electro-Magnetic Towed Array Detection System (TEMTADS) developed by the NRL and G&G Sciences. The site was contaminated with fuzes and a mix of 37-mm and 105-mm munitions. Each data set was inverted with the purpose of estimating the number of targets producing each anomaly and the parameters associated with each target, both extrinsic its orientation, location and depth and intrinsic its total volume magnetic source amplitude (ONVMS), which depends on its size, shape and material properties. The inverted intrinsic parameters were then used to classify the targets, and in the end we generated sensor-specific dig-lists for each EMI instrument and submitted them to the Institute of Defense Analyses (IDA) for independent scoring.
A note on native level 1 BLAS in Java (1997)

In this research note, we explore the potential of extending the Java Application Programming Interface with some mathematical primitives to improve the performance of certain operations in Java programs while maintaining portability. In particular, we show that providing straightforward native implementations of primitives from Level 1 BLAS can already improve the performance substantially. On multi-processors, combining this native Level 1 BLAS with the multi-threading mechanism of Java may even provide a simple and portable way to obtain a Java program that runs faster than compiled serial C code. © 1997 John Wiley & Sons, Ltd.
Short-term Morbidity and Mortality Associated With Correction of Thoracolumbar Fixed Sagittal Plane Deformity (2010)

The short-term complication rate for treatment of FSPD is 29.4%. The complication rate was significantly higher in patients undergoing osteotomies, and more aggressive osteotomies were associated with progressively higher complication rates.
On the Role of the CMC Binder for Si Negative Composite Electrodes (2010)

Abstract not Available.
Faculty Opinions recommendation of A single gene produces mitochondrial, cytoplasmic, and peroxisomal NADP-dependent isocitrate dehydrogenase in Aspergillus nidulans. (2001)

NADP-dependent isocitrate dehydrogenase enzymes catalyze the decarboxylation of isocitrate to 2-oxoglutarate accompanied by the production of NADPH. In mammals two different genes encode mitochondrial and cytoplasmic/peroxisomal located enzymes, whereas in Saccharomyces cerevisiae three separate genes specify compartment specific enzymes. We have identified a single gene, idpA, in the filamentous fungus Aspergillus nidulans that specifies a protein with a high degree of identity to mammalian and S. cerevisiae enzymes. Northern blot analysis and reverse transcription-polymerase chain reaction revealed the presence of two idpA transcripts and two transcription start points were identified by sequencing cDNA clones and by 5'-rapid amplification of cDNA ends. The shorter transcript was found to be inducible by acetate and by fatty acids while the longer transcript was present in higher amounts during growth in glucose containing media. The longer transcript is predicted to encode a polypeptide containing an N-terminal mitochondrial targeting sequence as well as a C-terminal tripeptide (ARL) as a potential peroxisomal targeting signal. The shorter transcript is predicted to encode a polypeptide lacking the mitochondrial targeting signal but retaining the C-terminal sequence. Immunoblotting using antibody raised against S. cerevisiae Idp1p detected two polypeptides consistent with these predictions. The functions of the predicted targeting sequences were confirmed by microscopic analysis of transformants containing fluorescent protein fusion constructs. Using anti-Idp1p antibodies, protein localization to mitochondria and peroxisomes was observed during growth on glucose whereas cytoplasmic and peroxisomal localization was found upon acetate or fatty acid induction. Therefore, we have established that by the use of two transcription start points a single gene is sufficient to specify localization of NADP-dependent isocitrate dehydrogenase to three different cellular compartments in A. nidulans. PMID: 11483612
The anti-aging factor GDF11 has both direct and indirect effects on mouse neural stem cells (P5.089) (2017)

Determine the direct and indirect effects of the anti-aging factor GDF11 on neural stem cells and endothelial cells.
Analysis of UAV Corridors in Cellular Networks (2023)

In this article, we introduce a new mathematical framework for the analysis and design of UAV corridors in cellular networks, while considering a realistic network deployment, antenna radiation pattern, and propagation channel model. By leveraging quantization theory, we optimize the electrical tilts of existing ground cellular base stations to maximize the coverage of both legacy ground users and UAVs flying along specified aerial routes. Our practical case study shows that the optimized network results in a cell partitioning that significantly differs from the usual hexagonal pattern, and that it can successfully guarantee coverage all over the UAV corridors without degrading the perceived signal strength on the ground.
Rheumatoid arthritis synovial fluid macrophages express decreased tumor necrosis factor–related apoptosis‐inducing ligand R2 and increased decoy receptor tumor necrosis factor–related apoptosis‐inducing ligand R3 (2003)

TRAIL R1 and R2, which are required for signal transmission by TRAIL, were not detected on RA SF lymphocytes, macrophages, or synovial fibroblasts. These observations do not support a potential therapeutic role for TRAIL in RA.
100 MHz, 85% efficient integrated AlGaAs/GaAs supply modulator for RF power amplifier modules (2013)

A 100 MHz DC-DC converter for RF power amplifier modules employing polar modulation is presented. A resonant low side gate driver and phase shedding/segmentation in the output stage are used for light load efficiency improvement. The proposed two-phases four-segments flip chip DC-DC converter is implemented in 0.5 μm AlGaAs/GaAs p-HEMT technology and occupies 2.5×2 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> for the two segments. An efficiency improvement of 5% is achieved at 4.5 V to 1 V conversion using the resonant low side gate driver. The peak efficiency at 4.5 V/3.3 V and 2 A output current is 85% with the peak value maintained as the load current changes from 0.2 A to 2.8 A under phase shedding/segmentation.
Piezoelectric-assisted removal of a benign fibrous histiocytoma of the mandible: An innovative technique for prevention of dentoalveolar nerve injury (2011)

In this article, we present our experience with a piezoelectric-assisted surgical device by resection of a benign fibrous histiocytoma of the mandible.A 41 year-old male was admitted to our hospital because of slowly progressive right buccal swelling. After further radiographic diagnosis surgical removal of the yellowish-white mass was performed. Histologic analysis showed proliferating histiocytic cells with foamy, granular cytoplasm and no signs of malignancy. The tumor was positive for CD68 and vimentin in immunohistochemical staining. Therefore the tumor was diagnosed as primary benign fibrous histiocytoma. This work provides a new treatment device for benign mandibular tumour disease. By using a novel piezoelectric-assisted cutting device, protection of the dentoalveolar nerve could be achieved.
Random vector functional link neural network for short-term wind power ramp forecasting (2015)

Wind is a clean and renewable energy source with huge potential in power generation. However, due to the intermittent nature of the wind, the power generated by wind farms is uctuating and often has large ramps, which are harmful to the power grid. This paper presents algorithms to forecast the ramps in the wind power generation. The importance and challenges of accurate wind power ramp forecasting are addressed. Wind power ramp and power ramp rate are defined in this paper. A random vector functional link neural network (RVFLNN) is employed to forecast the wind power ramp and the ramp rate. The RVFLNN applied to wind power forecasting based on regression has comparable performance as the benchmark methods: Artificial neural network (ANN), random forests (RF) and support vector machine (SVM) but RVFLNN with classification approach has better performance than the other three benchmark methods. The computation time of training and testing is also in favor of RVFLNN. Possible future research directions are also identified.
Integrated Silicon Microfluidic Cooling of a High-Power Overclocked CPU for Efficient Thermal Management (2022)

The stagnation of Dennard scaling along with the move towards heterogeneous 2.5D and 3D ICs is increasing the thermal design power (TDP) envelopes of general-purpose CPUs. With conventional cooling approaches such as air-cooling and cold plates, it is challenging to meet these increased requirements. Moreover, these increasing cooling requirements necessitate larger thermal management overheads in datacenter settings. All these trends point towards the need for a more aggressive and efficient cooling solutions. Monolithic microfluidic cooling, where silicon micropin-fins or microchannels are etched directly into the backside of the functional silicon, has shown great potential in this regard. In this work, we use micropin-fins etched directly on the back of an Intel Core i7-8700K CPU and overclocked it to dissipate up to 215W of power while being cooled by room temperature de-ionized (DI) water. We demonstrate up to 44.4% reduction in junction-to-inlet thermal resistance while using only 0.3&#x00D7; of volumetric coolant flow per Watt of power dissipated in the CPU compared to a conventional cold-plate. Furthermore, we demonstrate higher sustained core frequencies even when being cooled with elevated inlet temperatures, showing the potential for more efficient datacenter operations without the need for expensive and energy intensive refrigeration loops. The scalability towards heterogeneous 2.5D and 3D devices is also discussed. These results point towards a more scalable, efficient cooling solution, which can unlock higher power, more efficient compute systems, while minimizing the environmental impacts by reducing the thermal management overheads.
How Data-Warehousing Can Benefit the Whole Agency: A Case Study of a Recent Deployment at the Chattanooga Area Regional Transit Authority (2009)

In 2004, the Chattanooga Area Regional Transit Authority (CARTA) completed the initial deployment of a Data Warehouse that consolidated all CARTA operational data into a single location and provided the agency with tools to generate reports and maintain this consolidated data. CARTA has continued to integrate data into the Data Warehouse over time and has used that integrated data to automate many of its monthly and annual reporting processes. The agency has also had several occasions to perform ad hoc analyses of that data to support specific decision-making. This paper describes the CARTA Data Warehouse and some of the benefits that the agency has experienced to date.
Power Factor Correction Using Magnetic Energy Recovery Current Switches (2005)

In this paper, we propose a Magnetic Energy Recovery Switch (MERS). The switch consists of four MOSFET elements and one capacitor. A power factor improvement is automatically possible regardless of the impedance and power frequency of the load by synchronized switching of MERS with a power supply. MERS itself generates voltage and compensates for the inductance voltage unlike a conventional series capacitor, so that another dc power supply is not needed. An experiment was carried out to demonstrate the automatic correction of the power factor. We can also expect energy saving of electromachies such as an electric motor by the power factor correction with MERS.
Protocol for in vitro analysis of pro-inflammatory and metabolic functions of cultured primary murine astrocytes (2021)

Robust protocols are required to investigate <i>in vitro</i> the molecular mechanisms that control astrocyte metabolism and pro-inflammatory activities. In the present protocol, we describe step by step the isolation and culture of primary murine astrocytes from neonatal brains, followed by their genetic manipulation with siRNA. We further describe cytokine activation of the cultured astrocytes for the analysis of their pro-inflammatory responses, and the oxygen consumption analysis to assess their metabolic function. For complete details on the use and execution of this protocol, please refer to Chao et al. (2019), Clark et al. (2021), and Rothhammer et al. (2018).
Visualization and simulation of the transfer process of index‐matched silica microparticle inks for gravure printing (2016)

A combined experimental and computational study of the transfer of transparent index‐matched silica‐particle inks between two flat plates is presented for gravure printing applications. The influence of printing speed and initial ink droplet size on the ability to accurately transfer ink during the printing process is explored systematically. Smooth interface volume of fluid simulations show the same trends as the ink transfer observed in experiments over a wide range of printing speeds and for inks having different silica particle loadings. Our calculations indicate that for ink droplets with characteristic dimensions in the vicinity of 10 μm, which are of particular interest for gravure printing applications, ink transfer improves significantly due to the diminishing effect of gravity, and the increased importance of capillary forces at small length scales. © 2016 American Institute of Chemical Engineers AIChE J , 63: 1419–1429, 2017
DynaMaR: Dynamic Prompt with Mask Token Representation (2022)

Recent research has shown that large language models pretrained using unsupervised approaches can achieve significant performance improvement on many downstream tasks. Typically when adapting these language models to downstream tasks, like a classification or regression task, we employ a fine-tuning paradigm in which the sentence representation from the language model is input to a task-specific head; the model is then fine-tuned end-to-end. However, with the emergence of models like GPT-3, prompt-based fine-tuning has been proven to be a successful approach for few-shot tasks. Inspired by this work, we study discrete prompt technologies in practice. There are two issues that arise with the standard prompt approach. First, it can overfit on the prompt template. Second, it requires manual effort to formulate the downstream task as a language model problem. In this paper, we propose an improvement to prompt-based fine-tuning that addresses these two issues. We refer to our approach as DynaMaR -- Dynamic Prompt with Mask Token Representation. Results show that DynaMaR can achieve an average improvement of 10% in few-shot settings and improvement of 3.7% in data-rich settings over the standard fine-tuning approach on four e-commerce applications.
Supplementary Tables 1-5 from The Development of a Selective Cyclin-Dependent Kinase Inhibitor That Shows Antitumor Activity (2023)

Supplementary Tables 1-5 from The Development of a Selective Cyclin-Dependent Kinase Inhibitor That Shows Antitumor Activity