gebhart/patrepeval huggingface dataset:
A fully integrated triple-band CMOS power amplifier for WCDMA mobile handsets (2012)

The recent rapid spread of smart-phone use has resulted in a strong demand for a multi-band RF part with reduced size and power consumption. In the creation of an ideal RF system-on-a-chip, the biggest challenge is to realize a fully integrated PA in CMOS. In conventional PAs in compound semiconductor technologies, face-up wire-bond assembly with off-chip matching components is typically used, but flip-chip packaging is more suitable for slim mobile phones in which low-profile components are desired as well as for future integration with an RF transceiver in which the same packaging scheme is widely used. The PA for GSM [1] was insufficient for our target, so we needed to greatly improve the linearity in order to comply with the W-CDMA standard, which has better frequency-usage efficiency. Conventional CMOS PAs only support a single band [2,3] or are for WLAN [4] where the output power level is low (typically about 20dBm). In this paper, we present a fully-integrated triple-band linear CMOS PA for W-CDMA. Its flip-chip package is just 3.5×4×0.7mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> , and the average current consumption is less than 20mA.
Recognition and manipulation of branched DNA by the RusA Holliday junction resolvase of Escherichia coli (1998)

Homologous recombination is a fundamental cellular process that shapes and reshapes the genomes of all organisms and promotes repair of damaged DNA. A key step in this process is the resolution of Holliday junctions formed by homologous DNA pairing and strand exchange. In Escherichia coli , a Holliday junction is processed into recombinant products by the concerted activities of the RuvA and RuvB proteins, which together drive branch migration, and RuvC endonuclease, which resolves the structure. In the absence of RuvABC, recombination can be promoted by increasing the expression of the RusA endonuclease, a Holliday junction resolvase encoded by a cryptic prophage gene. Here, we describe the DNA binding properties of RusA. We found that RusA was highly selective for branched molecules and formed complexes with these structures even in the presence of a large excess of linear duplex DNA. However, it does bind weakly to linear duplex DNA. Under conditions where there was no detectable binding to duplex DNA, RusA formed a highly structured complex with a synthetic Holliday junction that was remarkably stable and insensitive to divalent metal ions. The duplex arms were found to adopt a specific alignment within this complex that approximated to a tetrahedral conformation of the junction.
The impact of continuous multicolumn chromatography on biomanufacturing efficiency (2013)

Over the past few years, the capacity bottleneck in biomanufacturing has shifted from the upstream process to the purification process. In particular, capture chromatography steps have become a limiting factor in facility throughput. This is a direct result of the discrepancy between expression levels, which have increased by a factor of ten, and the capacity of biochromatography media, which has at best doubled. Continuous countercurrent multicolumn chromatography is a promising approach to deal with the capacity bottleneck, particularly if designed in a single-use format. BioSMB™ technology is a disposable bioprocess technology that allows standard capture chromatography steps, such as Protein A capture, to be executed with much less installed chromatographic media using a multicolumn chromatography process. This allows an economically favorable, single-use option where none has previously been available. Various case studies have demonstrated the advantages of this technology for various separations. I...
The DNA Exonucleases of Escherichia coli (2011)

DNA exonucleases, enzymes that hydrolyze phosphodiester bonds in DNA from a free end, play important cellular roles in DNA repair, genetic recombination and mutation avoidance in all organisms. This article reviews the structure, biochemistry, and biological functions of the 17 exonucleases currently identified in the bacterium Escherichia coli. These include the exonucleases associated with DNA polymerases I (polA), II (polB), and III (dnaQ/mutD); Exonucleases I (xonA/sbcB), III (xthA), IV, VII (xseAB), IX (xni/xgdG), and X (exoX); the RecBCD, RecJ, and RecE exonucleases; SbcCD endo/exonucleases; the DNA exonuclease activities of RNase T (rnt) and Endonuclease IV (nfo); and TatD. These enzymes are diverse in terms of substrate specificity and biochemical properties and have specialized biological roles. Most of these enzymes fall into structural families with characteristic sequence motifs, and members of many of these families can be found in all domains of life.
Phase I/II study of niraparib plus pembrolizumab in patients with triple-negative breast cancer or recurrent ovarian cancer (KEYNOTE-162). (2016)

TPS5599 Background: Homologous recombination defects are common in triple-negative breast cancer and high-grade serous ovarian cancer. Both niraparib, a highly selective inhibitor of PARP1/2, and pembrolizumab, a monoclonal antibody that blocks binding of the immune checkpoint receptor programmed death-1 (PD-1) to its ligands (PD-L1/2) and alleviates negative regulation of immune responses to cancer cells, have demonstrated single-agent antitumor activity in patients with breast or ovarian cancer. Combinations of PARP inhibitors with immune checkpoint inhibitors have shown synergistic effects in preclinical tumor models, suggesting that co-treatment with these drugs may improve clinical efficacy compared with monotherapy. This multicenter, open-label phase 1/2 study is evaluating niraparib plus pembrolizumab in metastatic triple-negative breast cancer and advanced ovarian cancer. Methods: Eligible patients have triple-negative breast cancer and ≤ 3 lines of prior chemotherapy ( ≤ 2 lines for the phase 2 portion) in the metastatic setting or recurrent, platinum-resistant ovarian cancer and ≤ 4 lines of prior chemotherapy ( ≤ 3 lines for the phase 2 portion) for advanced disease. Patients must have measurable lesions per RECIST v1.1 and no prior treatment with a PARP inhibitor or an anti-PD-1 or anti-PD-L1/2 agent. The phase 1 portion is enrolling ≈18 patients to identify the recommended phase 2 dose (RP2D) and schedule of niraparib (starting dose: 200 mg orally once daily) combined with pembrolizumab (200 mg IV on day 1 of 21-day cycles). The phase 2 portion will enroll patients with triple-negative breast cancer or ovarian cancer (≈48 of each) to receive the RP2D and schedule of niraparib plus pembrolizumab. Tumors will be assessed per RECIST v1.1 and immune-related RECIST (irRECIST), a modified version to assess responses to immunotherapies. The primary endpoint of the phase 2 portion is objective response rate (ORR) per RECIST v1.1. Secondary endpoints are ORR per irRECIST; duration of response, disease control rate, and progression-free survival per RECIST and irRECIST; and overall survival. Niraparib pharmacokinetics and biomarkers will be investigated. Clinical trial information: NCT02657889.
The molecular determinants of the efficiency of green fluorescent protein mutants. (2000)

The Green Fluorescent Protein (GFP) is a spontaneously fluorescent polypeptide of 27 kD from the jellyfish Aequorea victoria that absorbs UV-blue light and emits in the green region of the spectrum. GFP has been successfully expressed both in bacteria and in eukaryotic cells and is widely used to monitor the localization of tagged proteins in living cells. Since wtGFP performs inefficiently in different cellular contexts, efforts have been devoted to the improvement of GFP expression levels and/or fluorescence. We will here review the basic characteristics of wt and mutated GFP, in particular their protein expression vs fluorescent properties. Emphasis will be given to unexpected consequences of mutations of the GFP gene, i.e. on transcription and translation rates and on protein folding in different cell types, and to how these critically reflect on the use of GFP in different cellular environments.
CCAAT displacement protein/ cut homolog recruits G9a histone lysine methyltransferase to repress transcription (2004)

CCAAT displacement protein/cut homolog (CDP/cut) is a highly conserved homeodomain protein that contains three cut repeat sequences. CDP/cut is a transcriptional factor for many diverse cellular and viral genes that are involved in most cellular processes, including differentiation, development, and proliferation. Here, we report that CDP/cut interacts with a histone lysine methyltransferase (HKMT), G9a, in vivo and in vitro. The deletion of the cut repeats within CDP/cut abrogates the interaction with G9a. The transcriptional repressor function of CDP/cut is mediated through HKMT activity of G9a associated with CDP/cut. We show that the recruitment of G9a to the human p21(waf1/cdi1) promoter is contingent on the interaction with CDP/cut, and CDP/cut is directly associated with an increase in the methylation in vivo of Lys-9 in histone H3 within the CDP/cut-regulatory region of the p21(waf1/cdi1) promoter. The endogenous level of p21(waf1/cdi1) expression is repressed through CDP/cut and mediated by HKMT activity of G9a. Furthermore, we report the identification of G9a as a component of CDP/cut complex. G9a colocalizes with CDP/cut in the nucleus. These results indicate that G9a functions as a transcriptional corepressor in association with a CDP/cut complex. These studies now reveal the interaction of G9a with a sequence-specific transcription factor that regulates gene repression through CDP/cut.
The importance of first-phase insulin secretion: implications for the therapy of type 2 diabetes mellitus (2001)

Type 2 diabetes is a heterogeneous disorder characterized by defects in insulin secretion and action. Insulin resistance is a key feature of type 2 diabetes. However, insulin resistance alone does not appear to be sufficient to cause diabetes. Longitudinal studies have shown that the development of overt hyperglycemia is associated with a decline in beta-cell secretion. In patients with impaired glucose tolerance or in the early stages of type 2 diabetes, first-phase insulin release is almost invariably lost despite the enhancement of second-phase secretion. Both animal and human studies support the critical physiologic role of the first-phase of insulin secretion in the maintenance of postmeal glucose homeostasis. This effect is primarily mediated at the level of the liver, allowing prompt inhibition of endogenous glucose production (EGP) and thereby restraining the mealtime rise in plasma glucose. In type 2 diabetes, the loss of the early surge of insulin release is a precocious and quite common defect that plays a pathogenic role in postmeal hyperglycemia and one that may require specific therapeutic intervention. This becomes even more apparent if the negative impact of prandial glucose spikes is taken into consideration. Epidemiological evidence exists to indicate that 2-h postload plasma glucose levels are strongly associated with all-cause and cardiovascular mortality relative risk. Indeed the acute elevation of plasma glucose concentration triggers an array of tissue responses that may contribute to the development of diabetic complications. Considering that type 2 diabetes begins with meal-related hyperglycemia in many patients, it becomes apparent that normalization of postmeal plasma glucose levels should be the target for rational therapy and the goal in the early stages of the disease. If a primary goal of diabetes therapy is control of postmeal glucose excursion, then the regulation of glucose absorption from the gut and entry into the circulation is an important mechanism to consider. The restoration of the rapid increase in plasma insulin concentration may be quite an efficient therapeutic approach.
The Role of X-Ray Computed Tomography in Core Analysis (2003)

Abstract Over the past several decades, x-ray computed tomography (CT) has gained acceptance as a routine core analysis tool. Its use for in-situ saturation determination, for example, has made it the method of choice for steady state relative permeability testing. The main objective of this paper is to provide a repository of information on CT scanning for core analysis, and to group the many earlier studies into reservoir engineering categories for convenient reference by others in the future. The review is prefaced with the introduction of a conceptual model (Cloud Model) for representing the influences of major factors on reservoir NPV, and a discussion of the value of CT for core analysis. The literature review is followed by an update of emerging CT technology (microscanning), and presentation of a new method for 3-phase saturation determination using combined CT and NMR.
Misincorporation during DNA synthesis, analyzed by gel electrophoresis (1984)

A method has been developed for simultaneous comparison of the propensity of a DNA polymerase to misincorporate at different points on a natural template-primer. In this method elongation of a [5'-32P] primer, annealed to a bacteriophage template strand, is carried out in the presence of only three dNTPs (highly purified by HPLC). Under these conditions the rate of primer elongation (monitored by gel electrophoresis/autoradiography) is limited by the rate of misincorporation at template positions complementary to the missing dNTP. Variations in the rate of elongation (revealed by autoradiographic banding patterns) reflect variations in the propensity for misincorporation at different positions along the template. The effect on primer elongation produced by addition of a chemically modified dNTP to 'minus' reactions reveals the mispairing potential of the modified nucleotide during DNA synthesis. By use of this electrophoretic assay of misincorporation we have demonstrated that the fidelity of E. coli DNA polymerase I varies greatly at different positions along a natural template, and that BrdUTP and IodUTP can be incorporated in place of dCTP during chain elongation catalyzed by this enzyme.
Substrate properties of C′‐methyl UTP derivatives in T7 RNA polymerase reactions. Evidence for N‐type NTP conformation (1997)

The number of synthetic UTP analogues containing methyl groups in different positions of the ribose moiety were tested as substrates for T7 RNA polymerase (T7 RNAP). Two of these compounds (containing substituents in the 5' position) were shown to be weak substrates of T7 RNAP. 3'Me-UTP was neither substrate nor inhibitor of T7 RNAP while 2'Me-UTP was shown to terminate RNA chain synthesis. Conformational analysis of the analogues and parent nucleotide using the force-field method indicates that the allowed conformation of UTP during its incorporation into the growing RNA chain by T7 RNAP is limited to the chi angle range of 192-256 degrees of N-type conformation.
pH-Dependent Solubility and Permeability Criteria for Provisional Biopharmaceutics Classification (BCS and BDDCS) in Early Drug Discovery (2012)

The Biopharmaceutics Classification System (BCS) is a scientific framework that provides a basis for predicting the oral absorption of drugs. These concepts have been extended in the Biopharmaceutics Drug Disposition Classification System (BDDCS) to explain the potential mechanism of drug clearance and understand the effects of uptake and efflux transporters on absorption, distribution, metabolism, and elimination. The objective of present work is to establish criteria for provisional biopharmaceutics classification using pH-dependent passive permeability and aqueous solubility data generated from high throughput screening methodologies in drug discovery settings. The apparent permeability across monolayers of clonal cell line of Madin-Darby canine kidney cells, selected for low endogenous efflux transporter expression, was measured for a set of 105 drugs, with known BCS and BDDCS class. The permeability at apical pH 6.5 for acidic drugs and at pH 7.4 for nonacidic drugs showed a good correlation with the fraction absorbed in human (Fa). Receiver operating characteristic (ROC) curve analysis was utilized to define the permeability class boundary. At permeability ≥ 5 × 10(-6) cm/s, the accuracy of predicting Fa of ≥ 0.90 was 87%. Also, this cutoff showed more than 80% sensitivity and specificity in predicting the literature permeability classes (BCS), and the metabolism classes (BDDCS). The equilibrium solubility of a subset of 49 drugs was measured in pH 1.2 medium, pH 6.5 phosphate buffer, and in FaSSIF medium (pH 6.5). Although dose was not considered, good concordance of the measured solubility with BCS and BDDCS solubility class was achieved, when solubility at pH 1.2 was used for acidic compounds and FaSSIF solubility was used for basic, neutral, and zwitterionic compounds. Using a cutoff of 200 μg/mL, the data set suggested a 93% sensitivity and 86% specificity in predicting both the BCS and BDDCS solubility classes. In conclusion, this study identified pH-dependent permeability and solubility criteria that can be used to assign provisional biopharmaceutics class at early stage of the drug discovery process. Additionally, such a classification system will enable discovery scientists to assess the potential limiting factors to oral absorption, as well as help predict the drug disposition mechanisms and potential drug-drug interactions.
Multi-Objective / Multidisciplinary Design Optimisation of Blended Wing Body UAV via Advanced Evolutionary Algorithms (2007)

Improvement of wing aerodynamic efficiency is one of the common challenges in Unmanned (Combat) Aerial Vehicles (UCAV) to provide a short distance take-off, long endurance that leads to lower fuel consumption. In addition, the stealth function is one of the essential requirements to complete diverse missions and the survivability of UAVs. This paper explores the application of a robust Evolutionary Algorithm (EA) for aerofoil sections and wing planform design and optimisation for the improvement of aerodynamic performance and the reduction of Radar Cross Section (RCS). The method is based on a canonical evolution strategy and incorporates the concepts of hierarchical topology, parallel computing and asynchronous evaluation. Results obtained from the optimisation show that utilising the designing transonic wing aerofoil sections and planform in combination with Evolutionary techniques improve the aerodynamic efficiency and this produced a set of shock-free aerofoils and achieved the supercritical aero-diamond wings. Results also indicate that the method is efficient and produces optimal and non-dominated solutions.
Evaluation of scheduling techniques on a SPARC-based VLIW testbed (1997)

The performance of Very Long Instruction Word (VLIW) microprocessors depends on the close cooperation between the compiler and the architecture. This paper evaluates a set of important compilation techniques and related architectural features for VLIW machines. The evaluation is performed on a SPARC-based VLIW testbed where gcc-generated optimized SPARC code is scheduled into high-performance VLIW code. As a base scheduling compiler, we experiment with three core scheduling techniques including enhanced pipeline scheduling, all-path speculation, and renaming. We analyze the characteristics of the useful and useless ALUs in each cycle to see how many of those ALUs execute non-speculative operations, speculative operations, and copies, respectively. Then, we evaluate the following compilation techniques: software pipelining, loop unrolling, non-greedy enhanced pipeline scheduling, profile-based all-path speculation, trace-based speculation, renaming, restricted speculative loads, and memory disambiguation. Since we experiment on a uniform testbed based on a detailed analysis of ALUs, our evaluation provides an useful insight on the performance impact of these techniques.
Inhibition of Histone Deacetylase Activates Side Population Cells in Kidney and Partially Reverses Chronic Renal Injury (2007)

Bone morphogenic protein (BMP)-7 is expressed in the adult kidney and reverses chronic renal injury when given exogenously. Here, we report that a histone deacetylase inhibitor, trichostatin A (TSA), attenuates chronic renal injury, in part, by augmenting the expression of BMP-7 in kidney side population (SP) cells. We induced accelerated nephrotoxic serum nephritis (NTN) in C57BL/6 mice and treated them with TSA for 3 weeks. Compared with vehicle-treated NTN mice, treatment with TSA prevented the progression of proteinuria, glomerulosclerosis, interstitial fibrosis, and loss of kidney SP cells. Basal gene expression of renoprotective factors such as BMP-7, vascular endothelial growth factor, and hepatocyte growth factor was significantly higher in kidney SP cells as compared with non-SP cells. Treatment with TSA significantly upregulated the expression of BMP-7 in SP cells but not in non-SP cells. Moreover, initiation of treatment with TSA after 3 weeks of NTN (for 3 weeks, until 6 weeks) partially but significantly reversed renal dysfunction. Our results indicate an important role of SP cells in the kidney as one of the possible generator cells of BMP-7 and TSA as a stimulator of the cells in reversing chronic renal disease. Disclosure of potential conflicts of interest is found at the end of this article.
Identification of a human neuroectodermal tumor antigen (OFA-I-2) as ganglioside GD2. (1982)

Two monospecific human antibodies (anti-OFA-I-1 and anti-OFA-I-2) produced in vitro by lymphoblast cell lines originating from melanoma patients have been shown previously to recognize cell surface antigens (OFA-I-1 and OFA-I-2) on human tumors and fetal brain: OFA-I-1 is expressed on a variety of human tumors, while OFA-I-2 has been detected only on tumors of neuroectodermal origin. Evidence presented in this report suggests that the two antigens expressed by a cultured human melanoma cell line (M14) are chemically distinct and that OFA-I-2 is a cell surface glycolipid, ganglioside GD2: GalNAc beta 1 leads to 4 NeuAc alpha 2 leads to 8NeuAc alpha 2 leads to 3 Gal beta 1 leads to 4Glc-ceramide.
Accurate Image Based Localization by Applying SFM and Coordinate System Registration (2016)

Finding accurate positions of mobile devices based on visual information involves searching for query-matching images in a very large dataset, typically containing millions of images. Although the main problem is designing a reliable image retrieval engine, accurate localization also depends on a good fusion algorithm between the GPS data (geo-tags) of each query-matching image and the query image. This paper proposes a new method for reliable estimation of the actual query camera position (geo-tag) by applying structure from motion (SFM) with bundle adjustment for sparse 3D camera position reconstruction, and a linear rigid transformation between two different 3D Cartesian coordinate systems. The experimental results on more than 170 query images show the proposed algorithm returns accurate results for a high percentage of the samples. The error range of the estimated query geo-tag is compared with other related research and indicates an average error less than 5 meters that improves on some of the published works.