gebhart/patrepeval huggingface dataset:
Power laws in microrheology experiments on living cells: Comparative analysis and modeling (2006)

We compare and synthesize the results of two microrheological experiments on the cytoskeleton of single cells. In the first one, the creep function J(t) of a cell stretched between two glass plates is measured after applying a constant force step. In the second one, a microbead specifically bound to transmembrane receptors is driven by an oscillating optical trap, and the viscoelastic coefficient Ge(omega) is retrieved. Both J(t) and Ge(omega) exhibit power law behaviors: J(t) = A0(t/t0)alpha and absolute value (Ge(omega)) = G0(omega/omega0)alpha, with the same exponent alpha approximately 0.2. This power law behavior is very robust; alpha is distributed over a narrow range, and shows almost no dependence on the cell type, on the nature of the protein complex which transmits the mechanical stress, nor on the typical length scale of the experiment. On the contrary, the prefactors A0 and G0 appear very sensitive to these parameters. Whereas the exponents alpha are normally distributed over the cell population, the prefactors A0 and G0 follow a log-normal repartition. These results are compared with other data published in the literature. We propose a global interpretation, based on a semiphenomenological model, which involves a broad distribution of relaxation times in the system. The model predicts the power law behavior and the statistical repartition of the mechanical parameters, as experimentally observed for the cells. Moreover, it leads to an estimate of the largest response time in the cytoskeletal network: tau(m) approximately 1000 s.
Biosynthesis of poly(4-hydroxybutyric acid) by recombinant strains of Escherichia coli1 (2006)

The aim of this study was the production of the homopolyester poly(4-hydroxybutyric acid) (poly(4HB)) with recombinant strains of Escherichia coli. Wild-type strains and other widely used non-recombinant strains of E. coli are not able to produce polyhydroxyalkanoic acids (PHA) as storage compounds and cannot utilize 4-hydroxybutyric acid as sole carbon source. Accordingly, hybrid plasmids of pBluescript vectors were constructed which harbored the Alcaligenes eutrophus PHA synthase gene (phaC) and the Clostridium kluyveri orfZ putatively encoding a 4-hydroxybutyric acid-coenzyme A transferase. A 3.5-kb genomic SmaI/ApaI fragment from A. eutrophus, which comprises phaC, and a 1.8-kb genomic ApaI/EcoRI fragment from C kluyveri, which contained orfZ, were inserted into the SmaI and EcoRI sites of the vectors pKS- and pSK-, respectively. The two resulting plasmids pSKSE5.3 and pKSSE5.3 comprising phaC and orfZ colinear or antilinear to lacZ, respectively, were transformed into E. coli XL1-Blue. Recombinant strains synthesized the homopolyester poly(4HB), when the cells were cultivated in Luria-Bertani broth and if glucose and 4-hydroxybutyric acid were provided as carbon sources. If glucose was omitted, a copolyester of 3-hydroxybutyric acid and 4-hydroxybutyric acid was accumulated. The homopolyester poly(4HB) was also accumulated during cultivation of these strains in M9 mineral salts medium containing glucose plus 4-hydroxybutyric acid as carbon sources. Poly(4HB) could amount up to approximately 80% (w/w) of the cell dry matter if E. coli XL1-Blue harboring pKSSE5.3 was cultivated in M9 mineral salts medium and if the cultures were not sufficiently supplied with oxygen. 4HB was also incorporated into PHA if gamma-butyrolactone was used as carbon source. If levulinic acid, 4-hydroxyvaleric acid or gamma-valerolactone were used as carbon sources, only very low amounts of PHA were accumulated which did not contain 4-hydroxyalkanoic acids as constituents.
Fast interactive exploration of 4D MRI flow data (2011)

1- or 2-directional MRI blood flow mapping sequences are an integral part of standard MR protocols for diagnosis and therapy control in heart diseases. Recent progress in rapid MRI has made it possible to acquire volumetric, 3-directional cine images in reasonable scan time. In addition to flow and velocity measurements relative to arbitrarily oriented image planes, the analysis of 3-dimensional trajectories enables the visualization of flow patterns, local features of flow trajectories or possible paths into specific regions. The anatomical and functional information allows for advanced hemodynamic analysis in different application areas like stroke risk assessment, congenital and acquired heart disease, aneurysms or abdominal collaterals and cranial blood flow. The complexity of the 4D MRI flow datasets and the flow related image analysis tasks makes the development of fast comprehensive data exploration software for advanced flow analysis a challenging task. Most existing tools address only individual aspects of the analysis pipeline such as pre-processing, quantification or visualization, or are difficult to use for clinicians. The goal of the presented work is to provide a software solution that supports the whole image analysis pipeline and enables data exploration with fast intuitive interaction and visualization methods. The implemented methods facilitate the segmentation and inspection of different vascular systems. Arbitrary 2- or 3-dimensional regions for quantitative analysis and particle tracing can be defined interactively. Synchronized views of animated 3D path lines, 2D velocity or flow overlays and flow curves offer a detailed insight into local hemodynamics. The application of the analysis pipeline is shown for 6 cases from clinical practice, illustrating the usefulness for different clinical questions. Initial user tests show that the software is intuitive to learn and even inexperienced users achieve good results within reasonable processing times.
Fine-resolution photoacoustic imaging of the eye (2010)

Purpose: Ultrasound and optical coherence tomography (OCT) are widely used techniques for diagnostic imaging of the eye. OCT provides excellent resolution, but limited penetration. Ultrasound provides better penetration, but an order-of-magnitude poorer resolution than OCT. Photoacoustic imaging is relatively insensitive to scattering, and so offers a potential means to image deeper than OCT. Furthermore, photoacoustic imaging detects optical absorption, a parameter that is independent of that detected by conventional ultrasound or OCT. Our aim was to develop a photoacoustic system suitable for imaging the eye. Methods: We developed a prototype system utilizing a focused 20 MHz ultrasound probe with a central aperture through which optics were introduced. The prototype system produced 1-&mu;J, 5-nsec pulses at 532 or 1064 nm with a 20-&mu;m spot size at a 500 Hz repetition rate. The photoacoustic probe was mounted onto computer-controlled linear stages and pulse-echo ultrasound and photoacoustic images obtained on ex vivo pig eyes and in vivo mouse eyes. Results: Lateral resolution was significantly improved by use of a laser spot size much smaller than the acoustic beamwidth. Photoacoustic signals were obtained primarily from melanin in ex vivo tissues and from melanin and hemoglobin in vivo. Image fusion allowed superposition of photoacoustic signals upon the anatomic features detected by conventional ultrasound. Conclusion: Photoacoustic imaging detects the presence of clinically relevant pigments, such as melanin and oxyand deoxy-hemoglobin, and, potentially, from other pathologic pigments occurring in disease conditions (tumors, nevii, macular degeneration). Fine-resolution photoacoustic data provides information not detected in current ophthalmic imaging modalities.
National Trends in Staphylococcus aureus Infection Rates: Impact on Economic Burden and Mortality over a 6-Year Period (1998-2003) (2007)

The inpatient S. aureus infection rate and economic burden of S. aureus infections for US hospitals increased substantially from 1998 to 2003, whereas the in-hospital mortality rate decreased.
Processing and proliferative effects of human progastrin in transgenic mice. (1996)

Incompletely processed gastrins have been postulated to play a role in growth of the gastrointestinal tract, but few studies have examined the effects of progastrin on mucosal proliferation in vivo. Human gastrin gene expression and progastrin processing were therefore studied in transgenic mice containing a human gastrin (hGAS) minigene, and compared to processing in mice bearing an insulin gastrin (INS-GAS) transgene that overexpresses amidated gastrin. Progastrin processing was studied using region-specific antisera and radioimmunoassays, biosynthetic labeling, immunoprecipitation, and HPLC. Proliferative effects due to overexpression of processed and unprocessed gastrin in INS-GAS and hGAS mice, respectively, were determined using routine histology and BrdU incorporation. The pancreatic islets of INS-GAS mice were able to produce carboxyamidated G-17, resulting in a twofold elevation of serum amidated gastrin, marked thickening of the oxyntic mucosa, and an increased BrdU labeling index (LI) of the gastric body. In contrast, livers of adult hGAS mice expressed abundant human gastrin mRNA and human progastrin but were unable to process this peptide to the mature amidated form, resulting in markedly elevated serum progastrin levels and normal amidated gastrin levels. Nevertheless, there was a marked increase in the BrdU labeling index of the colon in hGAS mice (LI 7.46+/-1.90%), as well as in INS-GAS mice (LI 6.16+/-1.17%), compared to age-matched, wild type control mice (LI 4.01+/-0.98%, P < 0.05). These studies suggest that incompletely processed gastrin precursors may contribute to colonic mucosal proliferation in vivo.
Active NF-E2-related Factor (Nrf2) Contributes to Keep Endothelial NO Synthase (eNOS) in the Coupled State (2009)

The aim of our study was to examine in detail the impact of NF-E2-related factor (Nrf2) activation on endothelial cell function with focus on redox homeostasis and the endothelial nitric oxide synthase (eNOS) system. We administered 2-cyano-3,12-dioxooleana-1,9-dien-28-oic imidazolide (CDDO-IM), a known activator of Nrf2, to primary human umbilical vein endothelial cells. Activation of Nrf2 by CDDO-IM increased the amount of bioavailable nitric oxide (NO), a major contributor to vascular homeostasis, in naive and stressed cells. Concomitantly, intracellular reactive oxygen species were dose-and time-dependently reduced. In apparent contrast to elevated NO levels, eNOS protein expression was transiently decreased in an Nrf2-dependent manner. Employing pharmacological inhibitors as well as a small interfering RNA approach, we identified de novo protein synthesis of heme oxygenase 1 (HO-1) and its enzymatic activity as cause for the observed reduction of eNOS. We hypothesize that under redox stress, when the availability of tetrahydrobiopterin, a pivotal stoichiometric cofactor for eNOS, is limited, activation of Nrf2 leads (a) to transient reduction of eNOS protein levels and (b) to an antioxidant defense in human umbilical vein endothelial cells. Both activities ensure that a stoichiometric ratio of eNOS and tetrahydrobiopterin is sustained and that the risk of eNOS uncoupling is reduced. Our study is the first to provide a causal link between Nrf2 activation and eNOS expression and NO levels, respectively.
Memory for pain: Relation between past and present pain intensity (1985)

Memory for the intensity of past physical pain depends critically on the intensity of present pain. When their present pain intensity was high, patients with chronic headaches of myofascial origin rated their maximum, usual, and minimum levels of prior pain as being more severe than their hourly pain diaries indicated. When their present pain intensity was low, the same patients remembered all 3 levels of prior pain as being less severe than they actually had been. The results show that pain produces systematic distortions of memory similar to those associated with alterations of affect or mood, and suggest a resolution to a conspicuous conflict in the current pain literature.
Autoantibodies to IL-1 alpha in sera from rapidly progressive idiopathic pulmonary fibrosis. (2001)

To clarify the clinical significance of autoantibodies to interleukin-1 alpha (IL-1 alpha autoantibodies) in rapidly progressive idiopathic pulmonary fibrosis (IPF), we measured the level of IL-1 alpha autoantibodies in serum of 11 patients on the first hospital day, when patients were admitted due to severe symptoms, and on the 21st hospital day. IL-1 alpha autoantibodies in serum were measured using radioimmunoassay, and the limitation of this assay for IL-1 alpha autoantibodies was 5 ng/ml. These antibodies were detected in 5 of 11 patients on the first hospital day. On the 21st hospital day, these antibodies were detected in all patients, and its level was increased compared with that on the first hospital day. IL-1 alpha autoantibodies that appeared in patients corresponded to that of IgG. The half life of exogenous autoantibodies was investigated following administration of autoantibody rich plasma obtained from healthy blood donors to 6 control patients (CP) and 6 progressive IPF patients. These autoantibody levels in their serum were less than 5 ng/ml before administration. Serum was obtained at the indicated time after administration of IL-1 alpha autoantibodies and the level of these autoantibodies in serum was measured, then the half life was calculated. Half life of exogenous IL-1 alpha autoantibodies in progressive IPF patients was significantly shorter than that in CP (71.3 +/- 31.8 hr vs 352.0 +/- 98.3 hr, p < 0.01). These findings suggested that IL-1 alpha autoantibodies were generated in response to the inflammatory process of rapidly progressive IPF and may act as a regulatory factor for IL-1 alpha.
Cloning and nucleotide sequence of a gene from Lactobacillus sake Lb706 necessary for sakacin A production and immunity (1993)

Sakacin A is an antilisterial bacteriocin produced by Lactobacillus sake Lb706. In order to identify genes involved in sakacin A production and immunity, the plasmid fraction of L. sake Lb706 was shotgun cloned directly into a sakacin A-nonproducing and -sensitive variant, L. sake Lb706-B, by using the broad-host-range vector pVS2. Two clones that produced sakacin A and were immune to the bacteriocin were obtained. A DNA fragment of approximately 1.8 kb, derived from a 60-kb plasmid of strain Lb706 and present in the inserts of both clones, was necessary for restoration of sakacin A production and immunity in strain Lb706-B. The sequence of the 1.8-kb fragment from one of the clones was determined. It contained one large open reading frame, designated sakB, potentially encoding a protein of 430 amino acid residues. Hybridization and nucleotide sequence analyses revealed that the cloned sakB complemented a mutated copy of sakB present in strain Lb706-B. The sakB gene mapped 1.6 kb from the previously cloned structural gene for sakacin A (sakA) on the 60-kb plasmid. The putative SakB protein shared 22% amino acid sequence identity (51% similarity if conservative changes are considered) to AgrB, the deduced amino acid sequence of the Staphylococcus aureus gene agrB. The polycistronic agr (accessory gene regulator) locus is involved in the regulation of exoprotein synthesis in S. aureus. Similar to the AgrB protein, SakB had some features in common with a family of transmembrane histidine protein kinases, involved in various adaptive response systems of bacteria.(ABSTRACT TRUNCATED AT 250 WORDS)
Automatic detection and correction of spelling errors in a large data base (1980)

Abstract On‐line bibliographic search systems tend to increase the visibility of spelling errors through the use of indexes of unique terms; even low error rates in a data base can result in large numbers of misspelled terms in these indexes. This article describes the techniques used to detect and correct spelling errors in the data base of Chemical Abstracts Service. A computer program for spelling error detection achieves a high level of performance using hashing techniques for dictionary look‐up and compression. Heuristic procedures extend the dictionary and increase the proportion of misspelled words in the words flagged. Automatic correction procedures are applied only to words which are known to be misspelled; other corrections are performed manually during the normal editorial cycle. The constraints imposed on the selection of a spelling error detection technique by a complex data base, human factors, and high‐volume production are discussed.
Microfluidic sub-millisecond mixers for the study of chemical reaction kinetics (2002)

We present a micromachined, high Reynolds number (2000-6000), sub-millisecond liquid mixer for the study of chemical reaction kinetics. This 1 cm/spl times/1 cm/spl times/1 mm bulk micromachined silicon mixer is capable of initiating and quenching (starting and stopping) chemical reactions in intervals as short as 100 /spl mu/s. The centimeter sized mixer chip contains two tee mixers connected by one channel which serves as a reaction chamber. Each tee mixer consists of opposing channels where liquids meet head-on and exit into a third channel forming the base of a "T". Our mixer performance was characterized by employing two carefully chosen chemical reactions with reaction time constants of 3 ms and 9 ms along with visualization techniques using dyes and acid-base indicators.
Learning both Weights and Connections for Efficient Neural Networks (2015)

Neural networks are both computationally intensive and memory intensive, making them difficult to deploy on embedded systems. Also, conventional networks fix the architecture before training starts; as a result, training cannot improve the architecture. To address these limitations, we describe a method to reduce the storage and computation required by neural networks by an order of magnitude without affecting their accuracy by learning only the important connections. Our method prunes redundant connections using a three-step method. First, we train the network to learn which connections are important. Next, we prune the unimportant connections. Finally, we retrain the network to fine tune the weights of the remaining connections. On the ImageNet dataset, our method reduced the number of parameters of AlexNet by a factor of 9x, from 61 million to 6.7 million, without incurring accuracy loss. Similar experiments with VGG-16 found that the number of parameters can be reduced by 13x, from 138 million to 10.3 million, again with no loss of accuracy.
Blood Lipid Mediator Sphingosine 1-Phosphate Potently Stimulates Platelet-derived Growth Factor-A and -B Chain Expression through S1P1-Gi-Ras-MAPK-dependent Induction of Krüppel-like Factor 5 (2004)

Platelet-derived growth factors (PDGFs), potent mitogens and chemoattractants for mesenchymal cell types, play essential roles in development of several organs including blood vessels, kidney, and lung, and are also implicated in the pathogenesis of atherosclerosis and malignancies. Blood lipid mediator sphingosine 1-phosphate (S1P) regulates migration, proliferation, and apoptosis in a variety of cell types through multiple G protein-coupled receptors of the Edg family, and is necessary for vascular formation at the developmental stage. We found in the present study that S1P induced severalfold increases in the mRNA and protein levels of PDGF-A and -B chains in vascular smooth muscle cells and neointimal cells. S1P stimulation of PDGF mRNA and protein expression was abolished by the small interfering RNA duplexes targeting S1P(1)/Edg1 receptor subtype. S1P stimulated the small GTPase Ras in a G(i)-dependent manner, and activated ERK and p38 MAPK in G(i)- and Ras-dependent manners. Pertussis toxin pretreatment, adenovirus-mediated Asn(17)Ras expression, the MEK inhibitor PD98059, or the p38 MAPK inhibitor SB203580 markedly suppressed PDGF mRNA and protein up-regulation, indicating the involvement of G(i)-Ras-ERK/p38 MAPK in S1P stimulation of PDGF expression. S1P stimulated expression of the transcription factor KLF5 in manners dependent on G(i), Ras, and ERK/p38 MAPK. Down-regulation of KLF5 by small interfering RNA duplexes abolished S1P-induced PDGF-A and -B chain expression. On the other hand, overexpression of KLF5 stimulated basal and S1P-induced PDGF expression. Either S1P stimulation or KLF5 overexpression increased the PDGF-B promoter activity in a cis-element-dependent manner. These results reveal the S1P(1)-triggered, G(i)-Ras-ERK/p38 MAPK-KLF5-dependent, stimulatory regulation of PDGF gene transcription in vascular smooth muscle cells.
Epidemiology and Burden of Chronic Constipation (2011)

Chronic constipation is an important component of clinical gastroenterology practice worldwide. Based on the definition, either self‐reported or using Rome criteria, chronic constipation can affect from 2% to 27% of the population. Constipation is physically and mentally troublesome for many patients, and can significantly interfere with their daily living and well‐being. Although only a proportion of patients with constipation seek medical care, most of them use prescribed or over‐the‐counter medication to improve their condition. The health care costs of constipation are significant as evidenced by the hundreds of million dollars spent yearly on laxatives alone. Because constipation is more common in older patients and life expectancy is increasing, an increase in the prevalence of constipation is expected in the years to come, with the associated impact on quality of life and socioeconomic burden.
Power cycling induced failure mechanisms in the viewpoint of rough temperature environment (2008)

Applications of power electronic devices in hybrid electric cars demand a higher allowed junction temperature of the power devices, if compact inverters close to the engine which use the combustion engine cooling circuit (with water temperatures up to T=115deg C) are required. Main challenge is the packaging technology. This paper reports on different power cycling tests, failure mechanisms and possible improvements.
Colorimetric Cu2+ detection with a ligation DNAzyme and nanoparticles (2007)

Using a Cu(2+)-dependent DNA ligation DNAzyme, a colorimetric sensor for Cu2+ has been developed based on directed assembly of DNA-functionalized gold nanoparticles by the ligation product, and such ligation DNAzyme-based sensors are intrinsically more sensitive than cleavage DNAzyme systems due to the lack of background.
A deletion mutation causes hemophilia B in Lhasa Apso dogs (1996)

Hemophilia B is a bleeding disorder caused by a deficiency of clotting factor IX (FIX). A colony of FIX deficient Lhasa Apso dogs has been established and the molecular basis of hemophilia B has been determined. The plasma factor IX levels were < 1% of normal canine levels in affected dogs. A complex deletion mutation at nucleotides 772-777 was found when hepatocyte cDNA from a hemophilia B dog was sequenced. The sequence was identical to the normal canine sequence except for a deletion including nucleotides 772-776 and a C-->T transition at nucleotide 777. The mutation results in mRNA instability and a premature termination codon in the nucleotide sequence encoding the activation peptide. The mutation was verified by sequencing genomic DNA from an FIX-deficient dog. A genetic test for the detection of heterozygous animals was established using heteroduplex analysis. Although hemophilia B has been described in many dog breeds, this is only the second mutation to be sequenced. The Lhasa Apso dog model should be valuable for evaluating novel strategies for treating hemophilia B such as gene therapy.