gebhart/patrepeval huggingface dataset:
Highly sensitive and quantitative detection of rare pathogens through agarose droplet microfluidic emulsion PCR at the single-cell level (2012)

Genetic alternations can serve as highly specific biomarkers to distinguish fatal bacteria or cancer cells from their normal counterparts. However, these mutations normally exist in very rare amount in the presence of a large excess of non-mutated analogs. Taking the notorious pathogen E. coli O157:H7 as the target analyte, we have developed an agarose droplet-based microfluidic ePCR method for highly sensitive, specific and quantitative detection of rare pathogens in the high background of normal bacteria. Massively parallel singleplex and multiplex PCR at the single-cell level in agarose droplets have been successfully established. Moreover, we challenged the system with rare pathogen detection and realized the sensitive and quantitative analysis of a single E. coli O157:H7 cell in the high background of 100,000 excess normal K12 cells. For the first time, we demonstrated rare pathogen detection through agarose droplet microfluidic ePCR. Such a multiplex single-cell agarose droplet amplification method enables ultra-high throughput and multi-parameter genetic analysis of large population of cells at the single-cell level to uncover the stochastic variations in biological systems.
Low frequency noise in heavily doped polysilicon thin film resistors (1998)

Low frequency noise and current–voltage measurements in several heavily doped polysilicon resistors of varying geometry and both p and n type, and over a limited range of temperatures from −60 to 50 °C were conducted for the first time. We found that the noise in p-type polysilicon was independent of temperature, but not the n-type polysilicon. For the p-type resistors, linear current–voltage characteristics were observed, and the relative noise spectral density was independent of bias and inversely proportional to frequency. For the n-type resistors, linear current–voltage characteristics were observed, and the relative noise spectral density was independent of bias. Finally, the normalized noise level in the linear n-type resistors was almost an order of magnitude lower than for the p-type resistors. We believe that this difference is because n-type dopants segregate to the grain boundaries, thus passivating some of the traps there. Boron (p-type dopant), on the other hand, does not segregate to the grain boundaries, leaving more unpassivated grain-boundary traps which capture and emit more carriers, resulting in more low frequency noise.
Optimization of Phase Change Material Heat Sinks for Low Duty Cycle High Peak Load Power Supplies (2011)

A power electronic device's lifetime depends on its maximum operating temperature and the temperature swings it is subjected to. Heat sinks employing phase change materials (PCMs) can be employed to achieve a temperature reduction, but only for a limited duration. This makes such heat sinks appropriate for use in applications with high peak loads but with low duty cycles. The heat sink is modeled using the thermal resistors and capacitors (RCs) network approach, and an optimization procedure for designing a hybrid air-cooled heat sink containing PCM is developed, yielding a maximum possible temperature reduction for a given application. It is shown that air-cooled heat sinks employing pure PCMs are best suited for applications with pulses width lengths of several minutes with a period of several tens of minutes. In order to achieve a faster response of the PCM, the concept of PCM-metal foam is explored and modeled. Experimental data is presented which confirms the validity of the thermal RC network approach.
2′-5′ Oligoadenylate Synthetase Plays a Critical Role in Interferon-γ Inhibition of Respiratory Syncytial Virus Infection of Human Epithelial Cells (2002)

Respiratory syncytial virus (RSV), associated with bronchiolitis and asthma, is resistant to the antiviral effects of type-I interferons (IFN), but not IFN-gamma. However, the antiviral mechanism of IFN-gamma action against RSV infection is unknown. The molecular mechanism of IFN-gamma-induced antiviral activity was examined in this study using human epithelial cell lines HEp-2 and A549. Exposure of these cells to 100-1000 units/ml of IFN-gamma, either before or after RSV infection, results in a significant decrease in RSV infection. After 1 h of exposure, IFN-gamma induces protein expression of IFN regulatory factor-1 (IRF-1) but not IRF-2, double-stranded RNA-activated protein kinase, and inducible nitric-oxide synthase in these cells. The mRNA for IRF-1, p40, and p69 isoforms of 2'-5' oligoadenylate synthetase (2-5 AS) are detectable, respectively, at 1 and 4 h of IFN-gamma exposure. Studies using cycloheximide and antisense oligonucleotides to IRF-1 indicate a direct role of IRF-1 in activating 2-5 AS. Cells transfected with 2-5 AS antisense oligonucleotides inhibit the antiviral effect of IFN-gamma. A stable cell line of HEp-2 overexpressing RNase L inhibitor, RLI-14, which exhibits an IFN-gamma-induced gene expression pattern similar to that of the parent cell line, shows a significant reduction in RNase L activity and IFN-gamma-mediated antiviral effect, compared with HEp-2 cells. These results provide direct evidence of the involvement of 2-5 AS in IFN-gamma-mediated antiviral activity in these cells.
NEBcutter: a program to cleave DNA with restriction enzymes (2003)

NEBcutter, version 1.0, is a program available via a web server (http://tools.neb.com/NEBcutter) that will accept an input DNA sequence and produce a comprehensive report of the restriction enzymes that will cleave the sequence. It produces a variety of outputs including restriction enzyme maps, theoretical digests and links into the restriction enzyme database, REBASE (http://www.neb.com/rebase). Importantly, its table of recognition sites is updated daily from REBASE and it marks all sites that are potentially affected by DNA methylation (Dam, Dcm, etc.). Many options exist to choose the enzymes used for digestion, including all known specificities, subsets of those that are commercially available or sets of enzymes that produce compatible termini.
Sequence specificity of human skin fibroblast collagenase. Evidence for the role of collagen structure in determining the collagenase cleavage site. (1987)

The sequence specificity of human skin fibroblast collagenase has been investigated by measuring the rate of hydrolysis of 16 synthetic octapeptides covering the P4 through P4' subsites of the substrate. The choice of peptides was patterned after potential collagenase cleavage sites (those containing either the Gly-Leu-Ala or Gly-Ile-Ala sequences) found in types I, II, and III collagens. The initial rate of hydrolysis of the P1-P1' bond of each peptide has been measured by quantitating the concentration of amino groups produced upon cleavage after reaction with fluorescamine. The reactions have been carried out under first-order conditions ([S] much less than KM) and kcat/KM values have been calculated from the initial rates. The amino acids in subsites P3 (Pro, Ala, Leu, or Asn), P2 (Gln, Leu, Hyp, Arg, Asp, or Val), P1' (Ile or Leu), and P4' (Gln, Thr, His, Ala, or Pro) all influence the hydrolysis rates. However, the differences in the relative rates observed for these octapeptides cannot in themselves explain why fibroblast collagenase hydrolyzes only the Gly-Leu and Gly-Ile bonds found at the cleavage site of native collagens. This supports the notion that the local structure of collagen is important in determining the location of the mammalian collagenase cleavage site.
New Perspectives on Treating Rheumatoid Arthritis (1995)

Patients with rheumatoid arthritis have symmetric synovitis of their peripheral joints and various degrees of joint destruction. In short-term studies, slow-acting antirheumatic drugs relieve symptoms and retard joint destruction, but many patients continue to have pain, stiffness, fatigue, and progressive disability.1 Better treatments are needed. This issue of the Journal includes reports of two randomized, controlled trials that investigated variations of widely used treatments for rheumatoid arthritis.2,3 In a six-month study of 148 patients with severe rheumatoid arthritis who had had only partial improvement with methotrexate, Tugwell et al. found greater clinical improvement with cyclosporine and methotrexate combined than . . .
CD4 + CD45RB Hi T cell transfer induced colitis in mice is accompanied by osteopenia which is treatable with recombinant human osteoprotegerin (2004)

CD4+CD45RBHi T cell transfer results in osteopenia in addition to colitis. Evidence suggests that this osteopenia was induced by inflammatory cell infiltration and not by malabsorption of calcium. Recombinant human osteoprotegerin effectively treated the osteopenia. OPG may be a useful therapeutic option for treating osteopenia in patients with IBD.
A gate-array-based programmable Reed-Solomon codec: structure-implementation-applications (2002)

The structure, implementation, and potential application of a gate-array-based programmable Reed-Solomon encoder/decoder (codec) chip set is presented. The encoder is based on a transform encoding scheme. The decoder is based on a modified version of the time-domain decoding (transform decoding without transform) algorithm. This algorithm has a regular structure, which is important for VLSI implementation. The structure and its implementation based on VLSI gate-array CMOS technology are described. The decoder can correct both errors and erasures for standard for shortened systematic and transform code words. The decoding time is independent of the number of errors or erasures in the received word. The Reed-Solomon codec can be used as a stand-alone (ST) device or as a microprocessor peripheral (MP) component. In MP mode, the codec can be directly interfaced to any 8-b, 16-b or 32-b, standard microprocessor, microcontroller, or digital signal processor (DSP). In ST mode, the codec operates as a standalone device, directly in the data symbol stream. It does not require a processor or any external buffer.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Anaerobic degradation of pimelate by newly isolated denitrifying bacteria (1994)

A C7 dicarboxylic (pimelic) acid derivative is postulated as an intermediate in anaerobic degradation of benzoate. Four strains of Gram-negative, nitrate-reducing bacteria capable of growth with both pimelate and benzoate as sole carbon and energy source were isolated. The metabolism of strain LP-1, which was enriched from activated sludge with pimelate as substrate, was studied in detail. This strain grew only with oxygen or with oxidized nitrogen compounds as electron acceptor. In the presence of nitrate, a wide range of substrates excluding C1 compounds was degraded. The new isolate was catalase- and oxidase-positive, and had one single polar flagellum. Strain LP-1 was tentatively classified within the family Pseudomonadaceae. The catabolism of pimelate and benzoate was studied in cell-free extracts of strain LP-1. Both acids were activated with coenzyme A in a Mg(2E)- and ATP-dependent reaction. The corresponding acyl-CoA synthetases were specifically induced by the respective growth substrate. Pimelate was also activated by CoA transfer from succinyl-CoA. Pimelyl-CoA was oxidized by cell-free extracts in the presence of potassium ferricyanide. Degradation to glutaryl-CoA and acetyl-CoA proceeded by a sequence of beta-oxidation-like reactions. Glutaryl-CoA dehydrogenase and glutaconyl-CoA decarboxylase activities were expressed in cells grown with pimelate or benzoate, indicating the specific involvement of these enzyme activities in anaerobic degradation of these two acids. Enzyme activities responsible for further degradation of the resulting crotonyl-CoA to acetyl-CoA via classical beta-oxidation were also detected.
Left ventricular remodeling after myocardial infarction: a corollary to infarct expansion. (1986)

Dilatation of infarcted segments (infarct expansion) may occur during recovery from myocardial infarction, but the fate of noninfarcted segments is uncertain. Accordingly, left ventricular geometric changes were assessed by left ventricular angiography and M mode echocardiography on admission and 2 weeks later in 30 patients with their first acute transmural myocardial infarction. All patients demonstrated chest pain, ST segment elevation with subsequent development of Q waves (15 anterior, 15 inferior), and elevation of cardiac enzymes. Sequential left ventricular angiographic and hemodynamic findings were available in these patients by virtue of their participation in a study of thrombolysis in acute myocardial infarction. By that study design, all patients treated successfully with thrombolytic therapy and demonstrating improvement of flow in an occluded coronary artery underwent repeat cardiac catheterization. At 2 weeks there was a significant decrease in left ventricular and pulmonary capillary wedge pressures (p less than .01), whereas both left ventricular end-diastolic (LVEDV) and end-systolic (LVESV) volume indexes increased (p less than .01). The increase in LVEDV correlated directly with the percentage of the ventriculographic silhouette that was akinetic or dyskinetic at the initial catheterization (r = .71, p less than .001). To assess regional changes in both infarcted and noninfarcted segments, serial endocardial perimeter lengths of both the akinetic-dyskinetic segments (infarction zone) and of the remainder of the cardiac silhouette (noninfarction zone) were measured in all patients who demonstrated at least a 20% increase in their LVEDV at 2 weeks after myocardial infarction. Notably, there was a mean increase of 13% in the endocardial perimeter length of infarcted segments and a 19% increase in the endocardial perimeter length of noninfarcted segments. Serial M mode echocardiographic studies showed no significant change in the wall thickness of noninfarcted myocardial segments. Hemodynamic changes that occurred in this subgroup of patients included significant decreases in left ventricular end-diastolic and pulmonary capillary wedge pressures (p less than .05) and significant increases in angiographic cardiac index (p less than .01) and LVESV index (p less than .01). We conclude that in patients who manifest cardiac dilatation in the early convalescent period after myocardial infarction, there is remodeling of the entire left ventricle including infarct expansion of akinetic-dyskinetic segments and volume-overload hypertrophy of noninfarcted segments.(ABSTRACT TRUNCATED AT 400 WORDS)
Learning why by being told what: interactive acquisition of justifications (1991)

An approach to acquiring justification that transforms why-questions into what-questions, borrowing the power of existing techniques, is discussed. The constrained dialogue has been implemented in an interactive tool, called ASK, that interviews experts and builds programs. The approach is applied to two different knowledge-acquisition problems; the acquisition of diagnostic strategy (why this action is chosen in this situation) and the acquisition of design rationale (why this device is designed this way). Generalization of the justification technique and key open problems in justification elicitation are examined.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Design of Nickel-rich Layered Oxides Using d Electronic Donor for Redox Reactions (2015)

Through first-principles calculations and experimental observations, we first present the correlation between the Ni and Mn ratio and the redox behaviors of the layered NCM cathodes. The equilibrium potentials based on redox reactions of Ni2+/Ni3+ are highly dependent on the Mn ratio (NCM523 and NCM721: ∼3.7 and 3.5 V) because of a donor electron, in the eg band, transferred from Mn to Ni owing to their crystal field splitting (CFS) with different electronegativities, leading to oxidation states of Ni2+-like and Mn4+. Considering the electronic donor (Mn) based on CFS with electronegativity of transition metals (TMs), we finally expect V as a promising doping source to provide donor electrons for Ni redox reactions in Ni-rich layered oxides, leading to be higher delithiation potentials (NCV523: 3.8 V). From our theoretical calculations in the NCV oxide, the oxidation states of Ni and V are stable Ni2+-like and V5+, respectively, and the fractional d-band fillings of Ni are the highest value as compared with NCM523 and LiNiO2 because of two donor electrons in the t2g band. Based on the underlying understanding on the CFS with electronegativity of TMs, it would be possible to design new Ni-rich layered cathodes with higher energy for use in Li-ion batteries.
cDNA cloning of a mouse mammary epithelial cell surface protein reveals the existence of epidermal growth factor-like domains linked to factor VIII-like sequences. (1990)

A 2.1-kilobase cDNA coding for a surface protein of mammary epithelial cells has been isolated from a mouse mammary gland lambda gt11 cDNA library. Sequence analysis of this cDNA reveals an open reading frame of 1389 base pairs that defines a protein with a molecular mass of 51.5 kDa. Structural analysis of the predicted sequence identifies two putative functional domains of the protein: (i) an N-terminal cysteine-rich region that is similar to epidermal growth factor-like domains of Drosophila Notch-1 protein and (ii) a large segment of the sequence that exhibited 54.5% identity with C-terminal domains of human coagulation factors VIII and V. These similarities in structure are used to predict the possible functions of the protein and its means of interaction with the cell surface. mRNA expression was detectable in mammary tissue from nonpregnant animals but was maximal in the lactating gland. In cultured cells, mRNA levels also correlated with the degree of cellular differentiation.
Interaction of tetracycline with RNA: photoincorporation into ribosomal RNA of Escherichia coli (1997)

Photolysis of [3H]tetracycline in the presence of Escherichia coli ribosomes results in an approximately 1:1 ratio of labelling ribosomal proteins and RNAs. In this work we characterize crosslinks to both 16S and 23S RNAs. Previously, the main target of photoincorporation of [3H]tetracycline into ribosomal proteins was shown to be S7, which is also part of the one strong binding site of tetracycline on the 30S subunit. The crosslinks on 23S RNA map exclusively to the central loop of domain V (G2505, G2576 and G2608) which is part of the peptidyl transferase region. However, experiments performed with chimeric ribosomal subunits demonstrate that peptidyltransferase activity is not affected by tetracycline crosslinked solely to the 50S subunits. Three different positions are labelled on the 16S RNA, G693, G1300 and G1338. The positions of these crosslinked nucleotides correlate well with footprints on the 16S RNA produced either by tRNA or the protein S7. This suggests that the nucleotides are labelled by tetracycline bound to the strong binding site on the 30S subunit. In addition, our results demonstrate that the well known inhibition of tRNA binding to the A-site is solely due to tetracycline crosslinked to 30S subunits and furthermore suggest that interactions of the antibiotic with 16S RNA might be involved in its mode of action.
Eradication of disseminated lymphomas with CpG-DNA activated T helper type 1 cells from nontransgenic mice. (2000)

Various evidence suggests that adoptive transfer of polyclonal, tumor-specific, IFN-gamma-producing CD4+ T cells [T helper type 1 (Th1) cells] should be highly efficient for tumor immune therapy. However, this approach could not be tested because very few MHC class II-restricted tumor peptides have been defined. Here we show that stimulation of freshly isolated T helper cells with syngeneic tumor cells and antigen-presenting cells in the presence of immunostimulatory CpG DNA allows the generation of large numbers of strongly polarized, tumor-specific Th1 cells within 3 weeks of culture, even when T helper cells were derived from tumor-bearing mice. A single injection of 0.5 x 10(6) A20-specific Th1 cells even eradicated disseminated A20 lymphomas and provided lifelong protection without inducing autoimmune disease. The therapy was largely independent of CD8+ cells but required IFN-gamma and CD40-CD40L interactions, suggesting that tumor-specific Th1 cells eradicate established tumors by activating proinflammatory macrophages.
Robust control of nonlinear systems using pattern recognition (2003)

Pattern-recognition based methodology implemented in the architecture of artificial neural networks can be used to model knowledge-intensive feedback control systems. The procedure for development and practical design of a neural-net based control system is described and demonstrated by the example of a nonlinear hydraulic system. The neural-net control system has been trained to provide stabilizing controls and to detect and identify malfunctioning sensors. The results of computer simulations and experiments are presented to illustrate the proposed approach. They show that the neural-net control system is capable of maintaining any desired level of liquid in a tank, for tanks of various shapes; of stabilizing the system in the presence of large disturbances; of detecting and identifying defective level sensors; and of estimating parameters in nonlinear processes.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Detection and quantification of spice adulteration by near infrared hyperspectral imaging (2011)

Black pepper is known for its diverse uses and importance in the global spice trade. This creates reason for the intentional adulteration of black pepper by fraudsters for economical gain. The potential of near (NIR) hyperspectral imaging as a rapid method for detecting the presence of adulterants (buckwheat and millet flour) in ground black pepper was evaluated. A sisuChema short wave infrared (SWIR) pushbroom imaging system with spectral range of 1000–2498 nm was used for hyperspectral image measurements. Ground black pepper was adulterated with either buckwheat or millet flour in 5% (w/w) increments from 0–100%. Exploratory principal component analysis (PCA) was performed on absorbance images for removal of non–essential information (background, bad pixels and shading errors). Multiplicative scattering correction (MSC) was applied to the cleaned image. Consequently, mean-centering was applied and the PCA model was recalculated. An adulterant dependent gradient was recognised along PC1 this is possibly due to a difference in protein and oil presence of the adulterant and black pepper. Analysis of images (mosaics of buckwheat and millet adulterated black pepper) revealed that buckwheat adulterated samples were separated from millet adulterated samples along PC4 and the loading line plot of PC4 suggests that this separation was due to a protein difference. Subsequently, partial least squares-discriminant analysis (PLS-DA) was performed on both buckwheat and millet adulterated black pepper. PLS-DA models calculated for buckwheat and millet adulterated black pepper demonstrated accuracies of 70% and 77%, respectively.