gebhart/patrepeval huggingface dataset:
Structural and Functional Consequences of Three Cancer-Associated Mutations of the Oncogenic Phosphatase SHP2 (2016)

The proto-oncogene PTPN11 encodes a cytoplasmic protein tyrosine phosphatase, SHP2, which is required for normal development and sustained activation of the Ras-MAPK signaling pathway. Germline mutations in SHP2 cause developmental disorders, and somatic mutations have been identified in childhood and adult cancers and drive leukemia in mice. Despite our knowledge of the PTPN11 variations associated with pathology, the structural and functional consequences of many disease-associated mutants remain poorly understood. Here, we combine X-ray crystallography, small-angle X-ray scattering, and biochemistry to elucidate structural and mechanistic features of three cancer-associated SHP2 variants harboring single point mutations within the N-SH2:PTP interdomain autoinhibitory interface. Our findings directly compare the impact of each mutation on autoinhibition of the phosphatase and advance the development of structure-guided and mutation-specific SHP2 therapies.
HIV Protease Inhibitors (1996)

The protease encoded by the human immunodeficiency virus (HIV protease) mediates the maturation of newly formed HIV particles through proteolytic processing of the gag and gag-pol gene products. Because of its essential role in the HIV replication cycle, this enzyme represents a logical target for the treatment of HIV infection. The intimate knowledge of the function and three-dimensional structure of HIV protease has prompted numerous approaches to the rational design of inhibitors. Despite rapid advances in the design of potent and specific inhibitors, the identification of clinically viable agents has proven challenging, the greatest obstacle being the problem of poor pharmacodynamic properties. Nonetheless, clinical trials of agents with substantially improved pharmacological properties Ii.ave demonstrated that protease inhibitors can produce a dramatic antiviral effect in vivo. In this chapter, recent approaches to HIV protease inhibitor design, with a particular focus on advances in the preclinical pharmacokinetic properties, are reviewed.
Reticle inspection using an image filter method (2003)

This paper reports a technique of reticle inspection incorporating the use of an image filter. In this technique, optical intensity distribution is calculated by optical simulation of electron beam lithography (EB) data or an image file obtained from a SEM photograph to evaluate the printability of defects on a reticle. When an image file is compared with the EB data, the image file has differences at the rounded corners as well as at the areas with defects because the image file is obtained from the reticle pattern. To reduce the differences, an image filter (or reticle filter), which simulates the pattern creation process on a reticle, was applied to the EB data. The simulated EB data is defined as the non-defect reference pattern. The optical intensity and critical dimension (CD) were then obtained. Image files of defects were obtained from the SEM photographs of reticle patterns having various sizes of defects. By applying optical simulation to patterns obtained from the image files, the optical intensity and CD were calculated and compared with those of the reference pattern, and the differences are evaluated. The evaluation results showed that optical intensity and CD changes fluctuate regardless of the size or type of defect. Correlation was confirmed between the differences in optical intensity and the CD changes in the defect area. It was thus concluded that defect printability can be evaluated by the differences in optical intensity obtained from image files.
Synthesis of Nanometer-Sized Sodalite Without Adding Organic Additives (2008)

Aggregates (80 nm) of sodalite nanocrystals with crystallite sizes ranging from 20 to 40 nm have been synthesized from a sodium aluminosilicate solution at low temperature, without adding any organic additives, while paying attention to the key factors for the synthesis of nanosized zeolite crystals. The physical properties of nanosized sodalite crystals were characterized by X-ray diffraction, scanning electron microscopy, high-resolution transmission electron microscopy, 29Si solid-state magic-angle spinning (MAS) NMR, and N2 adsorption. As expected, the external surface area of nanosized sodalite crystals is significantly increased compared with that of microsized sodalite crystals. The size of synthesized sodalite crystals can be controlled from 20 nm to 10 microm. It is found that the preparation of a homogeneous aluminosilicate solution followed by the formation of an aluminosilicate hard gel by adjusting the initial composition, for example, SiO2/Al2O3 and Na2O/H2O ratios, is critical for synthesis.
A 45-ns 16-Mbit DRAM with triple-well structure (1989)

A 16-Mbit DRAM fabricated with a 0.6- mu m triple-well CMOS technology on an n-substrate is described. The fast RAS access time of 45 ns has been achieved by the use of a triple-well structure, an optimized chip architecture, and a decoded word-line bootstrap driver. An advanced trench capacitor cell of area 4.8 mu m/sup 2/ is realized by introducing a quarter-pitched memory array arrangement. A three-way voltage-down conversion system enhances RAM performance as well as reliability. The RAM measures 7.87*17.4 mm/sup 2/.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Electrical and mechanical behavior of carbon black–filled poly(vinyl acetate) latex–based composites (2001)

Abstract The electrical and mechanical behaviors of carbon black‐filled. Poly(vinyl acetate) latex‐based polymer composites were examined. These composites were found to exhibit percolation thresholds in electrical conductivity near 2 vol% carbon black due to their segregated microstructures. Storage modulus and ultimate tensile strength (UTS) both exhibited discontinuities at 10 vol% carbon black, corresponding to a critical pigment volume concentration. Drying composites at 60°C rather than room temperature produced a higher percolation threshold and better mechanical properties at carbon black loadings above 10 vol% carbon black. A figure of merit was proposed to assess the balance of electrical conductivity, storage modulus and UTS. The figure of merit exhibited a peak value at 10 vol% for composites dried at room temperature and was shifted to higher carbon black concentrations when composites were dried at 60°C.
A speech processor providing fricative and low-frequency periodicity information for single channel cochlear prosthesis (2005)

Single channel cochlear prostheses have been shown to be effective as aids to lipreading. Due to the small range of the pulse repetition rate available for electrical stimulation, these devices usually do not provide clues regarding certain fricative sounds characterized by high-frequency noise bursts. A speech processor for presenting the information corresponding to these noise bursts along with the low-frequency periodicity (voicing and intonation) information has been developed and tested on two patients. Results indicate that the high-frequency fricative noise burst information can be presented without any adverse effect on the reception of voicing and place information.
Pre‐stack stratigraphic inversion in a deep offshore turbiditic environment (2005)

Seismic data is a prime source of information on reservoir heterogeneity between wells. In the past few years, the use of pre‐stack inversion techniques has become more widespread, due to improvements in seismic data quality and in computer science. Apart from acoustic impedances, pre‐stack inversion allows the extraction of shear impedances from seismic pre‐stack amplitudes. When the quality of the inversion is good enough, the joint use of these parameters can then improve a lot the characterization of reservoir properties such as facies, porosity… Moreover, inversion is known to work as a multi‐channel amplitude filter, removing various types of noise from seismic data, and thus, increasing its spatial resolution. In this paper, we will describe the various steps of inversion in a deep offshore turbidite case‐study: • well‐to‐seismic calibration; • control of the wavelet lateral variations; • geological a priori model building; • pre‐stack seismic inversion; • quality control of the results.
Supplementary Figures and Tables from Sym015: A Highly Efficacious Antibody Mixture against <i>MET</i>-Amplified Tumors (2023)

&lt;p&gt;Suppl. Figure 1 In vivo efficacy of Sym015 treatment at various dose levels in the EBC-1 xenograft model. Suppl. Figure 2 In vivo efficacy of Sym015 and unbalanced mixtures of the two constituent antibodies Hu9006 and Hu9338, applied at 10 mg/kg or 50 mg/kg doses in the EBC-1 xenograft model. Suppl. Figure 3 In vivo efficacy of Sym015 treatment in the H596 CDX model, which harbors a MET exon 14 deletion without MET gene amplification. Suppl. Figure 4 2 Map of clinically relevant mutations, obtained from the Cancer Cell Line Encyclopedia(31), in 64 cell lines. Suppl. Table S1 List of the 64 cell lines used in the study with information on tissue of origin, supplier, and growth medium used for propagation. Suppl. Table S2 Yellow columns: FISH scores for CDX and PDX models, denoting the average number of MET and CEP7 signals per cell, the MET/CEP7 ratio, and the percentage of tumor cells amplified. Suppl. Table S3 Prediction of human pharmacokinetics based on one-species allometric scaling(33).&lt;/p&gt;
A Multistage Resonant DC–DC Converter for Step-Up Applications (2021)

Resonant switched capacitor converters are a viable option for high-efficiency dc-dc converters. This article proposes a generic multistage resonant switched capacitor converter (MSR-SCC) for step-up applications. This article studies the performance of the MSR-SCC using a systematic approach both above and below the resonant frequency, which results in zero-voltage switching and zero-current switching, respectively. It also proposes a control algorithm to regulate the output voltage of the converter in both operating conditions. To validate the proposed analysis and control algorithms, an MSR-SCC is simulated and experimentally implemented with GaN switching devices, which enable converter operation at lower conduction losses and higher switching frequencies.
Exploiting Prunability for Person Re-identification (2020)

Abstract Recent years have witnessed a substantial increase in the deep learning (DL) architectures proposed for visual recognition tasks like person re-identification, where individuals must be recognized over multiple distributed cameras. Although these architectures have greatly improved the state-of-the-art accuracy, the computational complexity of the CNNs commonly used for feature extraction remains an issue, hindering their deployment on platforms with limited resources, or in applications with real-time constraints. There is an obvious advantage to accelerating and compressing DL models without significantly decreasing their accuracy. However, the source (pruning) domain differs from operational (target) domains, and the domain shift between image data captured with different non-overlapping camera viewpoints leads to lower recognition accuracy. In this paper, we investigate the prunability of these architectures under different design scenarios. This paper first revisits pruning techniques that are suitable for reducing the computational complexity of deep CNN networks applied to person re-identification. Then, these techniques are analysed according to their pruning criteria and strategy, and according to different scenarios for exploiting pruningmethods to ne-tuning networks to target domains. Experimental results obtained using DL models with ResNet feature extractors, and multiple benchmarks re-identification datasets, indicate that pruning can considerably reduce network complexity while maintaining a high level of accuracy. In scenarios where pruning is performed with large pre-training or ne-tuning datasets, the number of FLOPS required by ResNet architectures is reduced by half, while maintaining a comparable rank-1 accuracy (within 1% of the original model). Pruning while training a larger CNNs can also provide a significantly better performance than ne-tuning smaller ones.
Figure S3 from The <i>MCT4</i> Gene: A Novel, Potential Target for Therapy of Advanced Prostate Cancer (2023)

&lt;p&gt;Treatment of nude mice with MCT4 ASO did not cause host toxicity as measured by animal weights. A) Animal weights were monitored throughout the duration of the in vivo study, and treatment with MCT4 ASOs did not significantly affect the average animal weight of each group. B) The individual animal weights also remained stable throughout the treatment period.&lt;/p&gt;
Analysis of Human V-erbA Related EAR-3 Gene Expression between Transitional Cell Carcinoma and Normal Tissue in Bladder Cancer (2007)

Purpose&#13;\nThe prognosis of bladder cancer is related to tumor grade and stage. Because these pathological changes are preceded by molecular alterations, new molecular markers are needed in early diagnosis. New target molecular biomarkers can be differentially expressed genes (DEGs) between normal and cancer tissues. We tried to find a new DEG and demonstrated that it may be related to the development of the bladder cancer.&#13;\n&#13;\nMaterials and Methods&#13;\nCancer tissues were obtained from 39 patients with urothelial cell carcinoma, treated by transurethral resection of tumor (TURB) since 2002. Normal bladder tissues were obtained from the same patients during TURB. We compared the mRNA profiles between normal and cancer tissues using annealing control primer (ACP)-based Genefishing�꽓 PCR to identify the DEGs in normal and cancer tissues of one same patient. To validate the result of ACP-based GeneFishing�꽓 PCR, reverse transcription-polymerase chain reaction (RT-PCR) was performed on those of 39 patients.&#13;\n&#13;\nResults&#13;\nAccording to the result of ACP-based Genefishing�꽓 PCR, EAR-3 gene was only present or markedly upregulated in normal tissue, compared with cancer tissues. The expression pattern that EAR-3 gene was downregulated in cancer tissues, irrespective of the clinicopathologic parameters was confirmed by RT-PCR in 39 patients.&#13;\n&#13;\nConclusions&#13;\nEAR-3 gene was downregulated in cancer tissues, irrespective of clinicopathologic parameters, compared with normal tissues in the bladder of the same patient. Therefore, we suggested that EAR-3 gene may be also play a role in bladder cancer development.
Adaptive Disturbance Cancellation for Indirect Drive Robots Using Joint Sensing Information (2009)

Harmonic drives are widely used in robotics and precision positioning systems because of their unique properties such as near-zero backlash, and high speed reduction ratio. However, they possess a periodic positioning error known as the transmission error and it causes vibrations on the output shaft of the gear. In this paper, an adaptive compensation scheme for the transmission error in indirect drive robots is proposed. To enhance the performance and to avoid deteriorating the transient response, two modifications are introduced to the basic compensation structure. The load side acceleration information is adopted in real-time control to measure and to reject the load side oscillations. Also, it is used in the adaptation laws to generate the compensation signal that cancels the vibrations on the load side. Experimental results show the effectiveness of the proposed schemes and the improvement in load side performance.
Code Reverse Engineering Problem for Identification Codes (2012)

At ITW'10, Bringer suggested to strengthen their previous identification protocol where the security depends on computational assumptions (related to the Polynomial Reconstruction problem) by extending the Code Reverse Engineering (CRE) problem to identification codes. We formalize this new problem and we extend security results by Tillich on this very problem. This enables us to prove the security of this protocol using information theoretical arguments.
Congenital limb deficiencies with vascular etiology: Possible association with maternal thrombophilia (2016)

Congenital limb deficiency defects (LDDs) are etiologically heterogeneous. Acquired causes include amniotic bands, teratogens exposure, and chorionic villus sampling before 10 weeks' gestation and intrinsic causes include single-gene disorders and chromosome abnormalities. However, a substantial number of cases, especially terminal transverse deficiency defects, occur without an obvious cause and are ascribed to vascular disruption events. Some studies have found an association between maternal thrombophilia and congenital LDDs. We investigated this association through a review of all prenatally identified LDDs at a major tertiary care center in Toronto, Canada over a 12-year period. Our results showed a higher prevalence of thrombophilias among women with a pregnancy affected with an LDD when compared to the general population [χ<sup>2</sup> (3) = 54.63, P < 0.01]. Our research was strengthened by the inclusion of affected pregnancies regardless of outcome, and strict criteria to avoid including LDDs with a non-vascular etiology. Most LDDs were identified during the routine 18-20 week anatomy ultrasound, but some were discovered as early as 13 weeks' gestation. We found an excess of left-sided defects among terminal transverse but not longitudinal deficiencies; additionally, all diagnoses of maternal thrombophilia occurred in the terminal transverse group. Our results support thrombophilia screening in all women with a prenatally diagnosed fetal LDD as well as careful evaluation of the fetal extremities during prenatal ultrasounds in women with a known thrombophilia. © 2016 Wiley Periodicals, Inc.
A neural network based method for predicting PCB glass weave induced skew (2016)

This paper proposes the use of a neural network based tool to predict the skew factor of PCB laminate differential channel designs. A multitude of differential stripline design scenarios are 3D modelled, each with a different expected within differential pair skew factor. The modelled data is used to train a neural network. The neural network is tested using an unseen set of design data in order to evaluate the goodness of its predictions. Preliminary results show this machine learned technique to be a viable way to predict PCB glass weave skew without the need to resort to intensive 3D modelling. This method has potential to shorten design cycles and simplify analysis while still achieving good simulation accuracy.
Soft-decision list decoding of Reed-Muller codes with linear complexity (2011)

Let a binary Reed-Muller code RM(s;m) of length n be used on a memoryless channel with an input alphabet ±1 and a real-valued output ℝ. Given a received vector y in ℝ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</sub> ; we define its generalized distance T to any codeword c as the sum Σ|y <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">j|</sub> taken over all positions j, in which vectors y, c have opposite signs. We then consider the list ℒ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</sub> of codewords located within distance T from the received vector y and estimate the size L <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</sub> of this list using the generalized Johnson bound. For any RM code RM(s,m) of fixed order s, the algorithm is proposed that performs list decoding beyond the error-correcting radius with linear complexity in length n and retrieves the code list ℒ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</sub> with complexity of order nsL <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</sub> for any decoding radius T within the generalized Johnson bound.
Data from Quantitative Detection of Promoter Hypermethylation of Multiple Genes in the Tumor, Urine, and Serum DNA of Patients with Renal Cancer (2023)

&lt;div&gt;Abstract&lt;p&gt;Aberrant promoter hypermethylation of several known or putative tumor suppressor genes occurs frequently during the pathogenesis of human cancers and is a promising marker for cancer detection. We investigated the feasibility of detecting aberrant DNA methylation in the urine and serum samples of renal cancer patients. We examined the tumor and the matched urine and serum DNA for aberrant methylation of nine gene promoters (CDH1, APC, MGMT, RASSF1A, GSTP1, p16, RAR-β2, and ARF) from 17 patients with primary kidney cancer by quantitative fluorogenic real-time PCR. An additional 9 urine samples (total, 26) and 1 serum sample (total, 18) also were tested from renal cancer patients. Urine from 91 patients without genitourinary cancer and serum from 30 age-matched noncancer individuals were used as controls. Promoter hypermethylation of at least two of the genes studied was detected in 16 (94%) of 17 primary tumors. Aberrant methylation in urine and serum DNA generally was accompanied by methylation in the matched tumor samples. Urine samples from 91 control subjects without evidence of genitourinary cancer revealed no methylation of the &lt;i&gt;MGMT&lt;/i&gt;, &lt;i&gt;GSTP1&lt;/i&gt;, &lt;i&gt;p16&lt;/i&gt;, and &lt;i&gt;ARF&lt;/i&gt; genes, whereas methylation of &lt;i&gt;RAR-β2&lt;/i&gt;, &lt;i&gt;RASSF1A&lt;/i&gt;, &lt;i&gt;CDH1&lt;/i&gt;, &lt;i&gt;APC&lt;/i&gt;, and &lt;i&gt;TIMP3&lt;/i&gt; was detected at low levels in a few control subjects. Overall, 23 (88%) of 26 urine samples and 12 (67%) of 18 serum samples from cancer patients were methylation positive for at least one of the genes tested. By combination of urine or serum analysis of renal cancer patients, hypermethylation was detected in 16 of 17 patients (94% sensitivity) with high specificity. Our findings suggest that promoter hypermethylation in urine or serum can be detected in the majority of renal cancer patients. This noninvasive high-throughput approach needs to be evaluated in large studies to assess its value in the early detection and surveillance of renal cancer.&lt;/p&gt;&lt;/div&gt;
Variable camshaft timing engine control (2000)

Retarding camshaft timing in an engine equipped with a dual equal camshaft timing phaser reduces the unburned hydrocarbons (HC) and oxides of nitrogen (NO/sub x/) emitted to the exhaust system. Apart from this positive effect to feedgas emissions, camshaft timing can cause large air-to-fuel ratio excursions if not coordinated with the fuel command. Large air-to-fuel ratio excursions can reduce the catalytic converter efficiency and effectively cancel the benefits of camshaft timing. The interaction between the camshaft timing and the air-to-fuel ratio results in an inherent tradeoff between reducing feedgas emissions and maintaining high catalytic converter efficiency. By designing and analyzing a decentralized and a multivariable controller, we describe the design limitation associated with the decentralized controller architecture and we demonstrate the mechanism by which the multivariable controller alleviates the limitation.