gebhart/patrepeval huggingface dataset:
Nucleic Acid Analysis Using an Expanded Genetic Alphabet to Quench Fluorescence (2004)

Organic chemistry has made possible the synthesis of molecules that expand on Nature's genetic alphabet. Using the previously described nonstandard DNA base pair constructed from isoguanine and 5-methylisocytosine, we report a highly specific and sensitive method that allows for the fast and specific quantitation of genetic sequences in a closed tube format. During PCR amplification, enzymatic site-specific incorporation of a quencher covalently linked to isoguanine allows for the simultaneous detection and identification of multiple targets. The specificity of method is then established by analysis of thermal denaturation or melting of the amplicons. The appropriate functions of all reactions are further verified by incorporation of an independent target into the reaction mixture. We report that the method is sensitive down to the single copy level, and specificity is demonstrated by multiplexed end-point genotypic analysis of four targets simultaneously using four separate fluorescent reporters. The method is general enough for quantitative and qualitative analysis of both RNA and DNA using previously developed primer sets. Though the method described employs the commonly used PCR, the enzymatic incorporation of reporter groups into DNA site-specifically should find broad utility throughout molecular biology.
Strained multiquantum-well corrugation-pitch-modulated distributed feedback laser with ultranarrow (3.6 kHz) spectral linewidth (1993)

Introducing a 1% compressive strained multiquantum-well (MQW) active layer into a corrugation-pitch-modulated distributed feedback (CPM-DFB) laser reduces the linewidth floor (residual linewidth for extrapolated infinite output power) to 2 kHz and results in a linewidth-power product of 140 kHz mW. Strained MQW CPM-DFB lasers produced a 55 mW output with a spectral linewidth of only 3.6 kHz.
Biochemical and biological properties of the human N-ras p21 protein. (1987)

We characterized the normal (Gly-12) and two mutant (Asp-12 and Val-12) forms of human N-ras proteins produced by Escherichia coli. No significant differences were found between normal and mutant p21 proteins in their affinities for GTP or GDP. Examination of GTPase activities revealed significant differences between the mutant p21s: the Val-12 mutant retained 12% of wild-type GTPase activity, whereas the Asp-12 mutant retained 43%. Both mutant proteins, however, were equally potent in causing morphological transformation and increased cell motility after their microinjection into quiescent NIH 3T3 cells. This lack of correlation between transforming potency and GTPase activity or guanine nucleotide binding suggests that position 12 mutations affect other aspects of p21 function.
Pressure Dependence of Enzyme Catalysis (1992)

Pressure effects on enzyme function are strongly influenced by environmental factors such as temperature, pH, salt and substrate concentrations, and pressure itself. This article examines these effects in relation to volume changes associated with enzymatic reactions and enzyme denaturation. Depending on the experimental conditions, elevated pressure can enhance or inhibit enzyme activity and increase or decrease enzyme stability. Difficulties inherent in the design and interpretation of high pressure experiments are discussed, as are economic considerations pertaining to high pressure enzyme technology.
Circulating tumor DNA analysis detects minimal residual disease and predicts recurrence in patients with stage II colon cancer (2016)

Detection of circulating tumor DNA (ctDNA) after resection of stage II colon cancer may identify patients at the highest risk of recurrence and help inform adjuvant treatment decisions. We used massively parallel sequencing-based assays to evaluate the ability of ctDNA to detect minimal residual disease in 1046 plasma samples from a prospective cohort of 230 patients with resected stage II colon cancer. In patients not treated with adjuvant chemotherapy, ctDNA was detected postoperatively in 14 of 178 (7.9%) patients, 11 (79%) of whom had recurred at a median follow-up of 27 months; recurrence occurred in only 16 (9.8 %) of 164 patients with negative ctDNA [hazard ratio (HR), 18; 95% confidence interval (CI), 7.9 to 40; P < 0.001]. In patients treated with chemotherapy, the presence of ctDNA after completion of chemotherapy was also associated with an inferior recurrence-free survival (HR, 11; 95% CI, 1.8 to 68; P = 0.001). ctDNA detection after stage II colon cancer resection provides direct evidence of residual disease and identifies patients at very high risk of recurrence.
Continuous Glucose Monitoring Using a Novel Glucose/Galactose Binding Protein: Results of a 12-Hour Feasibility Study with the Becton Dickinson Glucose/Galactose Binding Protein Sensor (2011)

The BD prototype sensor demonstrated competitive accuracy relative to a GOx-based sensor and a YSI blood standard with a single calibration and minimal warm-up. Current development work is focused on the design and manufacture of a commercially feasible device that will include marked enhancements to device robustness and longevity.
A cellular single-stranded DNA-dependent ATPase associated with simian virus 40 chromatin. (1983)

A single-stranded DNA-dependent ATPase from monkey kidney tissue culture cells (CV-1) has been found associated with SV40 chromatin. This ATPase activity is distinguishable from the ATPase activity of T-antigen by the following properties: the Km for ATP, elution from phosphocellulose, and stimulation of the ATPase activity by single-stranded DNA but not by double-stranded DNA. The ATPase has been isolated and characterized from the nuclei of uninfected cells. ATP hydrolysis is dependent on single-stranded DNA and a divalent cation. The km values for ATP and single-stranded DNA are 0.024 mM and 0.09 microgram/ml, respectively. The affinity of the ATPase for single-stranded DNA is sufficiently high that the enzyme co-sediments with single-stranded DNA in glycerol gradients. The binding of single-stranded DNA is independent of ATP and MgCl2; however, ATP hydrolysis increases the exchange of enzyme between different DNA molecules. Form I (superhelical) SV40 DNA is also a substrate for ATPase binding, but relaxed Form I, Form II (nicked circular), and double-stranded linear SV40 DNAs are not substrates. Because the DNA helix within chromatin is not under the same kind of tortional strain as Form I DNA, we hypothesize that the ATPase is bound to the single-stranded regions of replication forks in the SV40 chromatin.
Tumor-induced perturbations of cytokines and immune cell networks (2014)

Until recently, the intrinsically high level of cross-talk between immune cells, the complexity of immune cell development, and the pleiotropic nature of cytokine signaling have hampered progress in understanding the mechanisms of immunosuppression by which tumor cells circumvent native and adaptive immune responses. One technology that has helped to shed light on this complex signaling network is the cytokine antibody array, which facilitates simultaneous screening of dozens to hundreds of secreted signal proteins in complex biological samples. The combined applications of traditional methods of molecular and cell biology with the high-content, high-throughput screening capabilities of cytokine antibody arrays and other multiplexed immunoassays have revealed a complex mechanism that involves multiple cytokine signals contributed not just by tumor cells but by stromal cells and a wide spectrum of immune cell types. This review will summarize the interactions among cancerous and immune cell types, as well as the key cytokine signals that are required for tumors to survive immunoediting in a dormant state or to grow and spread by escaping it. Additionally, it will present examples of how probing secreted cell-cell signal networks in the tumor microenvironment (TME) with cytokine screens have contributed to our current understanding of these processes and discuss the implications of this understanding to antitumor therapies.
Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high‐salinity stresses using a full‐length cDNA microarray (2002)

Full-length cDNAs are essential for functional analysis of plant genes in the post-sequencing era of the Arabidopsis genome. Recently, cDNA microarray analysis has been developed for quantitative analysis of global and simultaneous analysis of expression profiles. We have prepared a full-length cDNA microarray containing approximately 7000 independent, full-length cDNA groups to analyse the expression profiles of genes under drought, cold (low temperature) and high-salinity stress conditions over time. The transcripts of 53, 277 and 194 genes increased after cold, drought and high-salinity treatments, respectively, more than fivefold compared with the control genes. We also identified many highly drought-, cold- or high-salinity- stress-inducible genes. However, we observed strong relationships in the expression of these stress-responsive genes based on Venn diagram analysis, and found 22 stress-inducible genes that responded to all three stresses. Several gene groups showing different expression profiles were identified by analysis of their expression patterns during stress-responsive gene induction. The cold-inducible genes were classified into at least two gene groups from their expression profiles. DREB1A was included in a group whose expression peaked at 2 h after cold treatment. Among the drought, cold or high-salinity stress-inducible genes identified, we found 40 transcription factor genes (corresponding to approximately 11% of all stress-inducible genes identified), suggesting that various transcriptional regulatory mechanisms function in the drought, cold or high-salinity stress signal transduction pathways.
The influence of tibial-patellofemoral location on function of the knee in patients with the posterior stabilized condylar knee prosthesis. (1986)

Function of the knee and patellofemoral symptoms were correlated with the position of the implant in 101 consecutive patients with 116 posterior stabilized condylar knee prostheses. All of the patients were followed for a minimum of two and a half years with sequential physical examinations, radiographs, and functional evaluation of the knee. In sixteen knees (14 per cent), clicking or catching of the patella in terminal extension or painless crepitation throughout the arc of flexion developed without lowering the functional knee-evaluation score. Pain or mechanical problems, or both, that lowered the functional knee-evaluation score occurred in another fourteen knees (12 per cent), within the first postoperative year. Of these fourteen, eight required revision solely for patellofemoral complaints. Critical analysis of the tibial-patellofemoral mechanical axis identified three surgical variables that were found to markedly affect the functional result of the prosthesis: the distance from the center line of the tibial prosthesis to the center line of the tibial plateau, a change in the position of the joint line of the prosthesis relative to the hip and ankle, and the patellar height, measured as the perpendicular distance from the inferior pole of the patellar implant to the joint line of the prosthesis. Functional knee scores, range of motion, patellofemoral pain or mechanical symptoms, the need for revision, and the necessity of manipulation could all be statistically significantly correlated with the three independent variables. In addition, a range of neutral alignment was developed.(ABSTRACT TRUNCATED AT 250 WORDS)
A 0.6V 32.5mW Highly Integrated Receiver for 2.4GHz ISM-Band Applications (2008)

We explore the challenges of designing RF transceivers for an ultra-low-voltage (ULV) supply with performance that is compatible to commercial standards. The ITRS roadmap projects that the aggressive device size scaling will result in supply voltage reductions to well below IV, in particular for low-power technologies. The use of alternative energy sources also requires ULV operation in some applications. Achieving sufficient linearity with low power consumption is very challenging for the ULV mixer and baseband circuits. The on-chip LO generation and distribution is difficult due to the low-voltage device bias. We present optimized mixer and filter topologies, and a polyphase LO buffer, used in a low-power ULV receiver for 2.4GHz applications like Bluetooth or Zigbee. The use of spiral inductors is kept to a minimum to avoid their excessive area. The design techniques demonstrated here can enable the continued integration of RF front-ends onto SoC devices in nano CMOS technologies without requiring dedicated supply voltages or thick oxide devices.
In Situ Hybridization in Cancer and Normal Tissue (2003)

AbstractWith recent advances in the Human Genome Project and progress in microarray and gene chip technology, an explosion of genomic information is becoming available. One of the major ways to understand this vast amount of data is by bestowing topological information to help us identify the functional relevance of specific genes and to explain the pathogenesis of disease processes. In situ hybridization is a technique that will further our understanding of the function of genes within normal tissue along with the pathogenesis of a disease process within abnormal cells. This chapter provides an overview of in situ hybridization, followed by general principles and protocols.KeywordsSodium Dodecyl SulfateHuman Papilloma VirusChromosome PaintingChromosome Painting ProbeCatalyze Signal AmplificationThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
SOX7 transcription factor: sequence, chromosomal localisation, expression, transactivation and interference with Wnt signalling (2001)

The Sox gene family consists of several genes related by encoding a 79 amino acid DNA-binding domain known as the HMG box. This box shares strong sequence similarity to that of the testis determining protein SRY. SOX proteins are transcription factors having critical roles in the regulation of diverse developmental processes in the animal kingdom. We have characterised the human SOX7 gene and compared it to its mouse orthologue. Chromosomal mapping analyses localised mouse Sox7 on band D of mouse chromosome 14, and assigned human SOX7 in a region of shared synteny on human chromosome 8 (8p22). A detailed expression analysis was performed in both species. Sox7 mRNA was detected during embryonic development in many tissues, most abundantly in brain, heart, lung, kidney, prostate, colon and spleen, suggesting a role in their respective differentiation and development. In addition, mouse Sox7 expression was shown to parallel mouse Sox18 mRNA localisation in diverse situations. Our studies also demonstrate the presence of a functional transactivation domain in SOX7 protein C-terminus, as well as the ability of SOX7 protein to significantly reduce Wnt/beta-catenin-stimulated transcription. In view of these and other findings, we suggest different modes of action for SOX7 inside the cell including repression of Wnt signalling.
Evaluation of thermal conductivity of single carbon nanotubes in air and liquid using a fluorescence temperature sensor (2013)

We propose a method for evaluating thermal conductivity of a single carbon nanotube (CNT) using a fluorescent temperature sensor in liquid and air. The CNT is fixed to sensors by photofabrication. The electrode for Joule-heating of the CNT is fabricated on the sensor. Thermal conductivity of the CNT is evaluated through the temperature difference between both ends of the CNT and the heat quantity input to the CNT. In this paper, we evaluated thermal conductivity of the same CNT in air and liquid. Calculated thermal conductivity of the CNT in air (667 ± 38 [W/m·K]) is higher than that of CNT in water (484 ± 72 [W/m·K]).
[Invasive aspergillosis in cavitary lung sarcoidosis]. (1992)

Pulmonary sarcoidosis is a granulomatous disorder of unknown origin with a favorable outcome in most patients. However in about 5-10% progressive fibrosis is observed and may lead to further complications. We report on a 49 year-old woman with sarcoidosis with fibrotic changes and cavities in both upper lobes, who developed an upper lobe infiltration resistant to antibiotic treatment. Histologic examination of bronchial biopsy specimen revealed invasive aspergillosis. Therapy with Amphotericin B and Flucytosin was followed by marked clinical and radiological improvement.
Targeted nanoparticles for quantitative imaging of sparse molecular epitopes with MRI (2004)

Before molecular imaging with MRI can be applied clinically, certain problems, such as the potential sparseness of molecular epitopes on targeted cell surfaces, and the relative weakness of conventional targeted MR contrast agents, must be overcome. Accordingly, the conditions for diagnostic conspicuity that apply to any paramagnetic MRI contrast agent with known intrinsic relaxivity were examined in this study. A highly potent paramagnetic liquid perfluorocarbon nanoparticle contrast agent ( approximately 250 nm diameter, >90,000 Gd3+/particle) was imaged at 1.5 T and used to successfully predict a range of sparse concentrations in experimental phantoms with the use of standard MR signal models. Additionally, we cultured and targeted the smooth muscle cell (SMC) monolayers that express "tissue factor," a glycoprotein of crucial significance to hemostasis and response to vascular injury, by conjugating an anti-tissue factor antibody fragment to the nanoparticles to effect specific binding. Quantification of the signal from cell monolayers imaged at 1.5 T demonstrated, as predicted via modeling, that only picomolar concentrations of paramagnetic perfluorocarbon nanoparticles were required for the detection and quantification of tissue factor at clinical field strengths. Thus, for targeted paramagnetic agents carrying high payloads of gadolinium, it is possible to quantify molecular epitopes present in picomolar concentrations in single cells with routine MRI.
Localization of BCR-ABL to F-actin regulates cell adhesion but does not attenuate CML development (2003)

We have previously found that P210BCR-ABL increases the adhesion of hematopoietic cell lines to fibronectin by a mechanism that is independent of tyrosine kinase activity. To investigate the pathway(s) by which P210BCR-ABL influences cell adhesion, we used a quantitative cell adhesion device that can discern small changes in cell adhesion to assay P210BCR-ABL with mutations in several critical domains. We expressed P210BCR-ABL mutants in 32D myeloblast cells and found that binding to fibronectin is mediated primarily by the alpha5beta1 integrin. We performed a structure/function analysis to map domains important for cell adhesion. Increased adhesion was mediated by 3 domains: (1) the N-terminal coiled-coil domain that facilitates oligomerization and F-actin localization; (2) bcr sequences between aa 163 to 210; and (3) F-actin localization through the C-terminal actin-binding domain of c-abl. We compared our adhesion results with the ability of these mutants to cause a chronic myelogenous leukemia (CML)-like disease in a murine bone marrow transplantation assay and found that adhesion to fibronectin did not correlate with the ability of these mutants to cause CML. Together, our results suggest that F-actin localization may play a pivotal role in modulating adhesion but that it is dispensable for the development of CML.
Myocardial infarction in a parturient (1994)

Myocardial infarction is rare in pregnancy. We report a 38-year-old woman with a history of smoking and pre-eclampsia in her previous pregnancy, who suffered a non-Q infarction at 18 weeks of gestation. Stenoses in the left coronary artery were verified angiographically. She delivered a healthy child vaginally under epidural anaesthesia.
A Discrete-Time Model for the Design of Type-II PLLs With Passive Sampled Loop Filters (2010)

Type-II charge-pump (CP) phase-locked loop (PLLs) are used extensively in electronic systems for frequency synthesis. Recently, a passive sampled loop filter (SLF) has been shown to offer major benefits over the conventional continuous-time loop filter traditionally used in such PLLs. These benefits include greatly enhanced reference spur suppression, elimination of CP pulse-position modulation nonlinearity, and, in the case of phase noise cancelling fractional-N PLLs, improved phase noise cancellation. The main disadvantage of the SLF to date has been the lack of a linear time-invariant (LTI) model with which to perform the system-level design of SLF-based PLLs. Without such a model, designers are forced to rely on trial and error iteration supported by lengthy transient simulations. This paper presents an accurate LTI model of SLF-based type-II PLLs that eliminates this disadvantage.
Expression of the costimulatory molecule B7-H3 is associated with prolonged survival in human pancreatic cancer (2009)

We demonstrate for the first time that B7-H3 is abundantly expressed in pancreatic cancer and that tumor-associated B7-H3 expression significantly correlates with prolonged postoperative survival. Our findings suggest that B7-H3 might play an important role as a potential stimulator of antitumor immune response in pancreatic cancer.
Production of transgenic porcine blastocysts by hand-made cloning (2004)

Recently, a zona-free technique for bovine somatic cell nuclear transfer (NT) with no requirement for micromanipulation (i.e. hand-made cloning (HMC)) has been described. The present study demonstrates the application of the HMC technique in the production of transgenic porcine blastocysts. In vitro-matured zona-free porcine oocytes were bisected manually using a microblade and halves containing no chromatin (i.e. the cytoplasts) were selected. Two cytoplasts were electrofused with one transgenic fibroblast expressing enhanced green fluorescent protein and reconstructed embryos were activated in calcium ionophore (A23187) followed by 6-dimethylaminopurine. Subsequently, embryos were cultured in NCSU-23 medium supplemented with 4 mg mL(-1) bovine serum albumin for 7 days. In five replicates, 93.0 +/- 7.0% (mean +/- s.e.m.) of attempted reconstructed embryos fused and survived activation (31/31, 15/23, 28/28, 37/37 and 28/28). On Day 7 after activation, the respective blastocyst rates (per successfully reconstructed embryos) were 6% (2/31), 7% (1/15), 7% (2/28), 3% (1/37) and 7% (2/28), resulting in an average of 6.0 +/- 0.8%. Enhanced green fluorescent protein was expressed in all cells of all eight developing blastocysts. Efforts are now directed towards the production of offspring from such transgenic NT blastocysts.
Exploiting Similarities among Languages for Machine Translation (2013)

Dictionaries and phrase tables are the basis of modern statistical machine translation systems. This paper develops a method that can automate the process of generating and extending dictionaries and phrase tables. Our method can translate missing word and phrase entries by learning language structures based on large monolingual data and mapping between languages from small bilingual data. It uses distributed representation of words and learns a linear mapping between vector spaces of languages. Despite its simplicity, our method is surprisingly effective: we can achieve almost 90% precision@5 for translation of words between English and Spanish. This method makes little assumption about the languages, so it can be used to extend and refine dictionaries and translation tables for any language pairs.