gebhart/patrepeval huggingface dataset:
Depurinating Acylfulvene−DNA Adducts:  Characterizing Cellular Chemical Reactions of a Selective Antitumor Agent (2007)

Acylfulvenes (AFs) are a class of semisynthetic agents with high toxicity toward certain tumor cells, and for one analogue, hydroxymethylacylfulvene (HMAF), clinical trials are in progress. DNA alkylation by AFs, mediated by bioreductive activation, is believed to contribute to cytotoxicity, but the structures and chemical properties of corresponding DNA adducts are unknown. This study provides the first structural characterization of AF-specific DNA adducts. In the presence of a reductive enzyme, alkenal/one oxidoreductase (AOR), AF selectively alkylates dAdo and dGuo in reactions with a monomeric nucleoside, as well as in reactions with naked or cellular DNA, with 3-alkyl-dAdo as the apparently most abundant AF-DNA adduct. Characterization of this adduct was facilitated by independent chemical synthesis of the corresponding 3-alkyl-Ade adduct. In addition, in naked or cellular DNA, evidence was obtained for the formation of an additional type of adduct resulting from direct conjugate addition of Ade to AF followed by hydrolytic cyclopropane ring-opening, indicating the potential for a competing reaction pathway involving direct DNA alkylation. The major AF-dAdo and AF-dGuo adducts are unstable under physiologically relevant conditions and depurinate to release an alkylated nucleobase in a process that has a half-life of 8.5 h for 3-alkyladenine and less than approximately 2 h for dGuo adducts. DNA alkylation further leads to single-stranded DNA cleavage, occurring exclusively at dGuo and dAdo sites, in a nonsequence-specific manner. In AF-treated cells that were transfected with either AOR or control vectors, the DNA adducts identified match those from in vitro studies. Moreover, a positive correlation was observed between DNA adduct levels and cell sensitivity to AF. The potential contributing roles of AOR-mediated bioactivation and adduct stability to the cytotoxicity of AF are discussed.
A New Sub-topics Clustering Method Based on Semi-supervised Learing (2012)

Sub-topic clustering is a crucial step in multi-document summarization. The traditional k-means clustering method is not effective for topic clustering because the number of clusters k must be given in advance. This paper describes a new method for sub-topic clustering based on semi-supervised learning: the method firstly partition the set of sentences into disjoint subsets, each of which contained sentences covering exactly one topic, and labels the sentences which have high scores in the topic, then use the method of constrained-k-means to decide the number of topics, and finally get the sub-topic sets by k-Means clustering. This algorithm can dynamically generate the number of k-means clustering, and the experiment result indicates that the accuracy of clustering is improved
Akt phosphorylates and regulates the orphan nuclear receptor Nur77 (2001)

The immediate early gene NUR77 (also called NGFI-B) is required for T cell antigen receptor-mediated cell death and is induced to very high levels in immature thymocytes and T cell hybridomas undergoing apoptosis. The Akt (PKB) kinase is a key player in transduction of anti-apoptotic and proliferative signals in T cells. Because Nur77 has a putative Akt phosphorylation site at Ser-350, and phosphorylation of this residue is critical for the transactivation activity of Nur77, we investigated whether Akt regulates Nur77. Coimmunoprecipitation experiments showed the detection of Nur77 in Akt immune complexes, suggesting that Nur77 and Akt physically interact. We further show that Akt specifically phosphorylates Ser-350 of the Nur77 protein within its DNA-binding domain in vitro and in vivo in 293 and NIH 3T3 cells. Because phosphorylation of Ser-350 of Nur77 is critical for its function as a transcription factor, we examined the effect of Akt on this function. By using luciferase assay experiments, we showed that phosphorylation of Nur77 by Akt decreased the transcriptional activity of Nur77 by 50--85%. Thus, we show that Akt interacts with Nur77 and inactivates Nur77 by phosphorylation at Ser-350 in a phosphatidylinositol 3-kinase-dependent manner, connecting the phosphatidylinositol 3-kinase-dependent Akt pathway and a nuclear receptor pathway.
Biotechnological Approaches to Improving Nitrogen Use Efficiency in Plants: Alanine Aminotransferase as a Case Study (2011)

This chapter contains sections titled: Abstract Introduction References
High sample rate array architectures for median filters (1994)

Presents high sample rate semi-systolic array architectures for computing 1D and 2D nonrecursive and recursive median filters. A high sample rate is obtained by pipelining the computations in each processor. Although the nonrecursive filters are pipelined by placing latches in the feedforward paths, the recursive filters are restructured to create additional delays in the feedback paths, and then pipelined using the delays as latches.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Association between angiotensin II type 1 receptor polymorphisms and the occurrence of nonalcoholic fatty liver disease (2009)

This is the first report to demonstrate the genetic variations in ATGR1 that may influence the risk of NAFLD and liver fibrosis in NAFLD.
Efficient encoding of speech LSP parameters using the discrete cosine transformation (2003)

The intraframe and interframe correlation properties are used to develop two efficient encoding algorithms for speech line spectrum pair (LSP) parameters. The first algorithm (2-D DCT), which requires relatively large coding delays, is based on two-dimensional (time and frequency) discrete cosine transform coding techniques; the second algorithm (DCT-DPCM), which does not need any coding delay, uses one-dimensional discrete cosine transform in the frequency domain and DPCM (differential pulse-code modulation) in the time domain. The performances of these systems for different bit rates and delays are studied, and appropriate comparisons are made. It is shown that an average spectral distortion of approximately 1 dB/sup 2/ can be achieved with 21 and 25 bits/frame using the 2-D DCT and DCT-DPCM schemes, respectively. This is a noticeable improvement over the previously reported bit rates of 32 bits/frame and above.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Anatomy of Motor Learning. I. Frontal Cortex and Attention to Action (1997)

We used positron emission tomography to study new learning and automatic performance in normal volunteers. Subjects learned sequences of eight finger movements by trial and error. In a previous experiment we showed that the prefrontal cortex was activated during new learning but not during during automatic performance. The aim of the present experiment was to see what areas could be reactivated if the subjects performed the prelearned sequence but were required to pay attention to what they were doing. Scans were carried out under four conditions. In the first the subjects performed a prelearned sequence of eight key presses; this sequence was learned before scanning and was practiced until it had become overlearned, so that the subjects were able to perform it automatically. In the second condition the subjects learned a new sequence during scanning. In a third condition the subjects performed the prelearned sequence, but they were required to attend to what they were doing; they were instructed to think about the next movement. The fourth condition was a baseline condition. As in the earlier study, the dorsal prefrontal cortex and anterior cingulate area 32 were activated during new learning, but not during automatic performance. The left dorsal prefrontal cortex and the right anterior cingulate cortex were reactivated when subjects paid attention to the performance of the prelearned sequence compared with automatic performance of the same task. It is suggested that the critical feature was that the subjects were required to attend to the preparation of their responses. However, the dorsal prefrontal cortex and the anterior cingulate cortex were activated more when the subjects learned a new sequence than they were when subjects simply paid attention to a prelearned sequence. New learning differs from the attention condition in that the subjects generated moves, monitored the outcomes, and remembered the responses that had been successful. All these are nonroutine operations to which the subjects must attend. Further analysis is needed to specify which are the nonroutine operations that require the involvement of the dorsal prefrontal and anterior cingulate cortex.
Active stabilisation of an HVDC distribution system with multiple constant power loads (2008)

The active stabilisation of an HVDC distribution system with multiple constant power loads is presented. Each constant power load comprises a separate motor drive including the torque and speed control functions. By adding a simple admittance compensating controller to the current control loop of the constant power loads, the loads, and therefore the HVDC distribution system, are stabilised. Small-signal analysis techniques are used to form a basis for the design of the active stabilising controllers. Root locus plots are used to examine the system poles as the active and passive damping parameters are adjusted. First, a single motor drive and input filter is examined, then the source output filter is included and finally a second motor drive and input filter is added. The performance of the final design is verified through detailed Saber simulations of the HVDC distribution system.
Salicylic acid‐inducible binding of a tobacco nuclear protein to a 10 bp sequence which is highly conserved amongst stress‐inducible genes (1993)

A 10 bp sequence motif (TCATCTTCTT) which is repeated several times in the 5' non-transcribed region of a barley beta-1,3-glucanase gene is also present in the non-translated regions of over 30 different plant genes which are known to be induced by one or more forms of stress. Gel retardation assays and South-western blotting experiments provide evidence that the motif is the binding site for a tobacco nuclear protein with an apparent molecular weight of 40 kDa. Binding activity is increased when nuclear extracts from salicylic acid-treated plants are analysed compared with extracts from control plants, indicating that the protein itself is either induced or modified under conditions of stress. These observations suggest roles for the 10 bp motif and its binding protein as cis- and trans-acting regulators of gene expression during response to stress.
Yeast Two-Hybrid, a Powerful Tool for Systems Biology (2009)

A key property of complex biological systems is the presence of interaction networks formed by its different components, primarily proteins. These are crucial for all levels of cellular function, including architecture, metabolism and signalling, as well as the availability of cellular energy. Very stable, but also rather transient and dynamic protein-protein interactions generate new system properties at the level of multiprotein complexes, cellular compartments or the entire cell. Thus, interactomics is expected to largely contribute to emerging fields like systems biology or systems bioenergetics. The more recent technological development of high-throughput methods for interactomics research will dramatically increase our knowledge of protein interaction networks. The two most frequently used methods are yeast two-hybrid (Y2H) screening, a well established genetic in vivo approach, and affinity purification of complexes followed by mass spectrometry analysis, an emerging biochemical in vitro technique. So far, a majority of published interactions have been detected using an Y2H screen. However, with the massive application of this method, also some limitations have become apparent. This review provides an overview on available yeast two-hybrid methods, in particular focusing on more recent approaches. These allow detection of protein interactions in their native environment, as e.g. in the cytosol or bound to a membrane, by using cytosolic signalling cascades or split protein constructs. Strengths and weaknesses of these genetic methods are discussed and some guidelines for verification of detected protein-protein interactions are provided.
Arsenic removal from drinking water using granular ferric hydroxide (2003)

This paper examines the use of granular ferric hydroxide (GFH) to remove both arsenate [As(V)] and arsenite [As(III)] present in drinking water by conducting batch and column studies. The kinetic studies were conducted as a function of pH, and less than 5 mg/l was achieved from an initial concentration of 100 mg/l for both As(III) and As(V) with GFH at a pH of 7.6, which is in the pH range typically encountered in drinking water supplies. In the isotherm studies, the observed data fitted well with both the Freundlich and the Langmuir models. In continuous column tests (five cycles) with tap water using GFH, consistently less than 5 mg/l of arsenic was achieved in the finished water for 38 to 42 hours of column operation, where the influent had a spiked arsenic concentration of 500 mg/l. High bed volumes (1260 and 1140) up to a breakthrough concentration of 5 mg/l were achieved in the column studies. The adsorptive capacities for GFH estimated from the column studies were higher than that of activated alumina reported in the previous studies. Speciation of a natural water sample with arsenic showed the dominance of As(III) species over As(V). Batch and column studies showed that granular ferric hydroxide (GFH) can be effectively used in small water utilities to achieve less than 5 mg As/l in drinking water. Keywords: Adsorption, Drinking water, Arsenic removal, Granular ferric hydroxide, Arsenic speciation (WaterSA: 2003 29(2): 161-170)
Metalorganic vapor-phase epitaxial growth and photoluminescent properties of Zn1−xMgxO(0⩽x⩽0.49) thin films (2001)

High-quality Zn1−xMgxO(0.00⩽x⩽0.49) thin films were epitaxially grown at 500–650 °C on Al2O3(00⋅1) substrates using metalorganic vapor-phase epitaxy. By increasing the Mg content in the films up to 49 at. %, the c-axis constant of the films decreased from 5.21 to 5.14 Å and no significant phase separation was observed as determined by x-ray diffraction measurements. Furthermore, the near-band-edge emission peak position showed blueshifts of 100, 440, and 685 meV at Mg content levels of 9, 29, and 49 at. %, respectively. Photoluminescent properties of the alloy films are also discussed.
Characterization of Differential Gene Expression in Quiescent and Invasive Human Arterial Smooth Muscle Cells (2002)

Proliferation, migration and invasion of smooth muscle cells (SMCs) are essential pathogenic processes in the development of a broad spectrum of cardiovascular disorders, like arteriosclerosis, restenosis after percutaneous transluminal angioplasty and stent implantation as well as transplant vessel disease. As an in vitro model mimicking these processes, the Boyden chamber was employed to characterize the diverging migratory and invasive potentials of proliferating and nonproliferating human arterial SMCs (haSMCs). Using this model, differential gene expression of both phenotypes was analyzed by a cDNA array system (Clontech human cardiovascular array). With these arrays, 558 cardiovascular-associated genes could be compared. Further, gene expression was exactly quantified by real-time RT-PCR. Protein expression was analyzed by ELISA and Western blotting. In total, 47 genes were differentially expressed more than 1.5 times. Most of the differentially regulated genes in this study were associated with the extracellular matrix (ECM) and cell motility. In detail, the respective groups were matrix-organizing proteins, ECM proteins, cell adhesion proteins, extracellular communication and cytoskeleton motility proteins. Genes known to be differentially regulated during haSMC migration and invasion, like TIMP 2, TIMP 3, and MMP 3, were confirmed by the array data. Reduced expression of several cytoskeletal proteins, like vimentin, fibronectin, cytokeratins and beta1 integrin, was shown in the invasive phenotype. Further, angio-associated protein, alpha E-catenin and atrial brain natriuretic peptide receptor were downregulated whereas TFPI 2 was strongly upregulated in invasive haSMCs. In conclusion, several relevant potential candidate genes for the quiescent and the invasive SMC phenotype were identified and genes already known to be differentially regulated by previous analysis were confirmed.
The ORF <i>YNL274c</i> (<i>GOR1</i>) codes for glyoxylate reductase in <i>Saccharomyces cerevisiae</i> (2006)

The enzyme glyoxylate reductase reversibly reduces glyoxylate to glycolate, or alternatively hydroxypyruvate to D-glycerate, using either NADPH or NADH as a co-factor. The enzyme has multiple metabolic roles in different organisms. In this paper we show that GOR1 (ORF YNL274c) encodes a glyoxylate reductase and not a hydroxyisocaproate dehydrogenase in Saccharomyces cerevisiae, even though it also has minor activity on alpha-ketoisocaproate. In addition, we show that deletion of the glyoxylate reductase-encoding gene leads to higher biomass concentration after diauxic shift.
Pseudo Mask Augmented Object Detection (2018)

In this work, we present a novel and effective framework to facilitate object detection with the instance-level segmentation information that is only supervised by bounding box annotation. Starting from the joint object detection and instance segmentation network, we propose to recursively estimate the pseudo ground-truth object masks from the instance-level object segmentation network training, and then enhance the detection network with top-down segmentation feedbacks. The pseudo ground truth mask and network parameters are optimized alternatively to mutually benefit each other. To obtain the promising pseudo masks in each iteration, we embed a graphical inference that incorporates the low-level image appearance consistency and the bounding box annotations to refine the segmentation masks predicted by the segmentation network. Our approach progressively improves the object detection performance by incorporating the detailed pixel-wise information learned from the weakly-supervised segmentation network. Extensive evaluation on the detection task in PASCAL VOC 2007 and 2012 [12] verifies that the proposed approach is effective.
Thiazolidinediones and Rexinoids Induce Peroxisome Proliferator-Activated Receptor-Coactivator (PGC)-1α Gene Transcription: An Autoregulatory Loop Controls PGC-1α Expression in Adipocytes via Peroxisome Proliferator-Activated Receptor-γ Coactivation (2006)

Thiazolidinediones (TZDs) are insulin-sensitizing drugs currently used to treat type 2 diabetes. They are activators of peroxisome proliferator-activated receptor (PPAR)-gamma, and adipose tissue constitutes a major site for their biological effects. PPAR coactivator (PGC)-1alpha is a transcriptional coactivator of PPARgamma and other transcription factors. It is involved in the control of mitochondrial biogenesis, and its activity has been linked to insulin sensitization. Here we report that PGC-1alpha gene expression in brown and white adipocytes is a direct target of TZDs via PPARgamma activation. Activators of the retinoid X receptor also induce PGC-1alpha gene expression. This is due to the presence of a PPARgamma-responsive element in the distal region of the PGC-1alpha gene promoter that binds PPARgamma/retinoid X receptor heterodimers. Moreover, there is a positive autoregulatory loop of control of the PGC-1alpha gene through coactivation of PPARgamma responsiveness to TZDs by PGC-1alpha itself. These data indicate that some of the effects of TZDs, especially promotion of mitochondrial biogenesis and oxidative pathways in adipose depots, entail PGC-1alpha up-regulation via enhanced transcription of the PGC-1alpha gene.
Characterization of enhancement-mode AlGaN/GaN high electron mobility transistor using N2O plasma oxidation technology (2011)

In this study, an enhancement-mode (E-mode) AlGaN/GaN high electron mobility transistor (HEMT) using N2O plasma oxidation process has been performed. Before the gate metal deposition, the AlGaN barrier layer was treated by 135 W N2O plasma for 240 s. The surface native oxide of AlGaN was removed and a 4 nm high quality Ga2O3/Al2O3 compound insulator was simultaneously formed. The threshold voltage of conventional depletion-mode (D-mode) GaN HEMT was −3.6 V and this value can be shifted to +0.17 after N2O plasma oxidation treatment beneath the gate metal. This 4 nm Ga2O3/Al2O3 compound insulator oxidized by N2O can suppress the polarization charge density for E-mode operation of gate terminal and the gate leakage was also reduced simultaneously.
Insights into the molecular basis of a bispecific antibody's target selectivity (2015)

Bispecific antibodies constitute a valuable class of therapeutics owing to their ability to bind 2 distinct targets. Dual targeting is thought to enhance biological efficacy, limit escape mechanisms, and increase target selectivity via a strong avidity effect mediated by concurrent binding to both antigens on the surface of the same cell. However, factors that regulate the extent of target selectivity are not well understood. We show that dual targeting alone is not sufficient to promote efficient target selectivity, and report the substantial roles played by the affinity of the individual arms, overall avidity and valence. More particularly, various monovalent bispecific IgGs composed of an anti-CD70 moiety paired with variants of the anti-CD4 mAb ibalizumab were tested for preferential binding and selective depletion of CD4(+)/CD70(+) T cells over cells expressing only one of the target antigens that resulted from antibody dependent cell-mediated cytotoxicity. Variants exhibiting reduced CD4 affinity showed a greater degree of target selectivity, while the overall efficacy of the bispecific molecule was not affected.
Incident Detection Methods Using Probe Vehicles with On-board GPS Equipment (2015)

Mobile communication instruments have made detecting traffic incidents possible by using floating traffic data. This paper studies the properties of traffic flow dynamics during incidents and proposes incident detection methods using floating data collected by probe vehicles equipped with on-board global positioning system (GPS) equipment. The proposed algorithms predict the time and location of traffic congestion caused by an incident. The detection rate and false rate of the models are examined using a traffic flow simulator, and the performance measures of the proposed methods are compared with those of previous methods.
Low power PCM CODEC and filter system (1981)

Describes the architecture and circuit design technology for a low-power single-channel PCM CODEC and filter system. This system consists of 2 CMOS LSIs-the encoder/decoder chip using the C-R D/A conversion technique and the dual channel filter chip using the switched capacitor technique. Experimental results show how these operate with 71 mW power consumption and meet the requirements.