gebhart/patrepeval huggingface dataset:
Skeletal troponin I as a marker of exercise-induced muscle damage (1997)

The utility of skeletal troponin I (sTnI) as a plasma marker of skeletal muscle damage after exercise was compared against creatine kinase (CK), myoglobin (Mb), and myosin heavy chain (MHC) fragments. These markers were serially measured in normal physical education teacher trainees after four different exercise regimens: 20 min of level or downhill (16% decline) running (intensity: 70% maximal O2 uptake), high-force eccentric contractions (70 repetitions), or high-force isokinetic concentric contractions of the quadriceps group (40 repetitions). Eccentrically biased exercise (downhill running and eccentric contractions) promoted greater increases in all parameters. The highest plasma concentration were found after downhill running (median peaks: 309 U/l CK concentration (-CK-)), 466 microgram/l Mb concentration (-Mb-), 1,021 microU/l MHC concentration (-MHC-), and 27.3 microgram/l sTnI concentration ([sTnI]). Level running produced a moderate response (median peaks: 178 U/l -CK-, 98 microgram/l -Mb-, 501 microU/l -MHC-, and 6.6 microgram/l [sTnI]), whereas the concentric contraction protocol did not elicit significant changes in any of the markers assayed. sTnI increased and peaked in parallel to CK and stayed elevated (>2.2 microgram/l) for at least 1-2 days after exercise. In contrast to MHC, sTnI is an initial, specific marker of exercise-induced muscle injury, which may be partly explained by their different intracellular compartmentation with essentially no (MHC <0.1%) or a small soluble pool (sTnI: median 3.4%).
Phenotypic characterization of rat hepatoma cell lines and lineage-specific regulation of gene expression by differentiation agents (1998)

Hepatoma cell lines can be characterized by their expression of hepatocyte- and biliary-specific genes and by their response to differentiating agents in a lineage-dependent manner. These characteristics can be used to map the maturational lineage position of the cell lines. Tissue-specific gene expression and regulation by heparin, dimethylsulfoxide (DMSO), and sodium butyrate (SB) were examined in three rat hepatoma cell lines and two rat liver epithelial cell lines. Based on antigenic profiles and gene expression in serum-supplemented medium, the hepatoma cell lines could be organized in distinct categories of hepatic differentiation. All three hepatomas expressed the following five genes: gamma-glutamyl transpeptidase (GGT), glutathione-S-transferase pi (Yp), glutamine synthetase, and alpha 5 and beta 1 integrin. Cell line H4AzC2 also expressed alpha-fetoprotein (AFP), albumin. IGF II receptor, and the biliary/oval cell antigens OC.2 and OC.3, a phenotype characteristic of fetal hepatocytes. FTO-2B cells lacked AFP, OC.2, and OC.3 but expressed albumin and IGF II receptor in addition to the five commonly expressed genes, consistent with a more hepatocyte-like phenotype. Cell line H5D-7 expressed neither albumin nor the IGF II receptor, but did express OC.2, OC.3, and alpha 3 integrin in addition to the five commonly expressed genes, characteristic of biliary epithelial cells. Regulation of gene expression by heparin, DMSO, and SB was examined in cells cultured in hormonally defined medium. The patterns of regulation of AFP, albumin, GGT, and Yp were dependent upon the state of differentiation of the cell. FTO-2B cells regulated genes in a manner similar to that of E16 fetal hepatocytes, H4AzC2 regulated genes characteristic of both hepatocytic and biliary lineages, and H5D.7 regulated only biliary genes. Suppression of GGT by DMSO was uniformly observed. The three cell lines expressed equal amounts of HNF-4, but FTO-2B cells expressed more HNF-3 beta and less HNF-3 alpha, while the reverse was true of H4AzC2 and H5D.7 cells.
Liposomal Formulations of Cyclosporin A: A Biophysical Approach to Pharmacokinetics and Pharmacodynamics (2001)

There are about 20 publications about liposomal formulations of Cyclosporin A (CyA) in the pharmaceutical and preclinical literature. Liposomal formulations were developed in order to reduce the nephrotoxicity of CyA and to increase pharmacological effects. However, conflicting results have been published as to the therapeutic properties of these formulations. This is also true for the change in pharmacokinetics and organ distribution of the liposomally encapsulated CyA as compared to conventionally formulated CyA. Using biophysical methods, it could be shown that CyA is not tightly entrapped in liposomal membranes, despite its high lipophilicity. CyA shows retardation only at high lipid concentrations in blood, following a massive injection of liposomes. This effect may diminish nephrotoxicity, as could be demonstrated by in vitro studies using a model tubule system. The results of these studies can be used to predict the formulation behavior in vivo and to optimize liposomal formulations. When applied in an early phase of the drug formulation process, these types of biophysical experiments can also help minimize animal experiments. However, these basic interaction studies cannot cover all physiological, pharmacological, and toxic effects in animals and humans.
Spontaneous Formation of Indium-Rich Nanostructures on InGaN(0001) Surfaces (2000)

InGaN(0001) surfaces prepared by molecular beam epitaxy have been studied using scanning tunneling microscopy and first-principles total energy calculations. Nanometer-size surface structures are observed consisting of either vacancy islands or ordered vacancy rows. The spontaneous formation of these structures is shown to be driven by significant strain in the surface layers and by the relative weakness of the In-N bond compared to Ga-N. Theory indicates that In will preferentially bind at the edges and interior of the structures, thereby giving rise to an inhomogeneous In distribution at the surface.
Experimental study of dual-core photonic crystalfibre (2000)

The authors report the fabrication and characterisation of photonic crystal (‘holey’) fibres in which multiple cores are created by filling in selected air-holes with glass. The guidance mechanism is modified total internal reflection. Using a tunable diode laser, the inter-core coupling is investigated as a function of air-hole spacing.
Copy number alterations of <i>c‐MYC</i> and <i>PTEN</i> are prognostic factors for relapse after prostate cancer radiotherapy (2012)

Despite the use of PSA, Gleason score, and T-category as prognosticators in intermediate-risk prostate cancer, 20-40% of patients will fail local therapy. In order to optimize treatment approaches for intermediate-risk patients, additional genetic prognosticators are needed. Previous reports using array comparative genomic hybridization (aCGH) in radical prostatectomy cohorts suggested a combination of allelic loss of the PTEN gene on 10q and allelic gain of the c-MYC gene on 8q were associated with metastatic disease. We tested whether copy number alterations (CNAs) in PTEN (allelic loss) and c-MYC (allelic gain) were associated with biochemical relapse following modern-era, image-guided radiotherapy (mean dose 76.4 Gy). We used aCGH analyses validated by fluorescence in-situ hybridization (FISH) of DNA was derived from frozen, pre-treatment biopsies in 126 intermediate-risk prostate cancer patients. Patients whose tumors had CNAs in both PTEN and c-MYC had significantly increased genetic instability (percent genome alteration; PGA) compared to tumors with normal PTEN and c-MYC status (p < 0.0001). We demonstrate that c-MYC gain alone, or combined c-MYC gain and PTEN loss, were increasingly prognostic for relapse on multivariable analyses (hazard ratios (HR) of 2.58/p = 0.005 and 3.21/p = 0.0004; respectively). Triaging patients by the use of CNAs within pre-treatment biopsies may allow for better use of systemic therapies to target sub-clinical metastases or locally recurrent disease and improve clinical outcomes.
Nanopores Discriminate among Five C5-Cytosine Variants in DNA (2014)

Individual DNA molecules can be read at single nucleotide precision using nanopores coupled to processive enzymes. Discrimination among the four canonical bases has been achieved, as has discrimination among cytosine, 5-methylcytosine (mC), and 5-hydroxymethylcytosine (hmC). Two additional modified cytosine bases, 5-carboxylcytosine (caC) and 5-formylcytosine (fC), are produced during enzymatic conversion of hmC to cytosine in mammalian cells. Thus, an accurate picture of the cytosine epigenetic status in target cells should also include these C5-cytosine variants. In the present study, we used a patch clamp amplifier to acquire ionic current traces caused by phi29 DNA polymerase-controlled translocation of DNA templates through the M2MspA pore. Decision boundaries based on three consecutive ionic current states were implemented to call mC, hmC, caC, fC, or cytosine at CG dinucleotides in ∼4400 individual DNA molecules. We found that the percentage of correct base calls for single pass reads ranged from 91.6% to 98.3%. This accuracy depended upon the identity of nearest neighbor bases surrounding the CG dinucleotide.
Properties of the adenovirus IVa2 gene product, an effector of late-phase-dependent activation of the major late promoter (1996)

The adenovirus major late promoter is strongly activated after the onset of viral DNA replication. Sequence elements located downstream of the major later promoter start site have previously been shown to be essential for this activation. Two proteins (DEF-A and DEF-B) bind to these elements in a late-phase-dependent manner. DEF-B has been identified as the product of adenovirus intermediate gene IVa2 (pIVa2) (C. Tribouley, P. Lutz, A. Staub, and C. Kedinger, J. Virol. 68:4450-4457, 1994). Here we show that pIVa2, while monomeric in solution, binds to its recognition sequence as a dimer and that two 20-residue amphipathic alpha helices play an essential role in this DNA-binding activity. Attempts to purify DEF-A have failed, but its chromatographic behavior, together with its immunological properties, established that pIVa2 is also a component of this heteromeric protein. In addition, the time course of pIVa2 synthesis during infection correlated with simultaneous detection of the binding of both DEF-A and DEF-B complexes to the downstream elements. Finally, as revealed by immunomicroscopy, pIVa2 is targeted to the nucleus, where it distributes to restricted locations in the nucleoplasm, as well as to the nucleoli. Altogether, these results demonstrate that pIVa2 plays a critical role in the transition from the early to the late phase of the lytic cycle. Furthermore, pIVa2 may serve additional functions yet to be uncovered, as suggested by its presence within the cell nucleolus.
New fadB homologous enzymes and their use in enhanced biosynthesis of medium‐chain‐length polyhydroxyalkanoates in <i>fadB</i> mutant <i>Escherichia coli</i> (2004)

Recombinant Escherichia coli harboring the medium-chain-length (MCL) polyhydroxyalkanoate (PHA) synthase gene has been shown to accumulate MCL-PHAs from fatty acids when FadB is inactive. However, the enzymes in fadB mutant E. coli responsible for channeling the beta-oxidation intermediates to PHA biosynthesis have not been fully elucidated. Only recently, two enzymes encoded by yfcX and maoC have been found to be partially responsible for this. In this study, we identified five new FadB homologous enzymes in E. coli: PaaG, PaaF, BhbD, SceH, and YdbU, by protein database search, and examined their roles in the biosynthesis of MCL-PHAs in an fadB mutant E. coli strain. Coexpression of each of these genes along with the Pseudomonas sp. 61-3 phaC2 gene did not allow synthesis of MCL-PHA from fatty acid in recombinant E. coli W3110, which has a fully functional beta-oxidation pathway, but allowed MCL-PHA accumulation in an fadB mutant E. coli WB101. In particular, coexpression of the paaG, paaF, and ydbU genes resulted in a MCL-PHA production up to 0.37, 0.25, and 0.33 g/L, respectively, from 2 g/L of sodium decanoate, which is more than twice higher than that obtained with E. coli WB101 expressing only the phaC2 gene (0.16 g/L). These results suggest that the newly found FadB homologous enzymes, or at least the paaG, paaF, and ydbU genes, are involved in MCL-PHA biosynthesis in an fadB mutant E. coli strain and can be employed for the enhanced production of MCL-PHA.
Using Games to Embody Spiking Neural Networks for Neuromorphic Hardware (2014)

Adding value to action-selection through reinforcement-learning provides a mechanism for modifying future decisions of real and artificial entities. This behavioral-level modulation is vital for performing in complex and dynamic environments. In this paper we focus on three classes of biologically inspired feed-forward spiking neural networks capable of action-selection via reinforcement-learning embodied in a minimal virtual agent. Their ability to learn two simple games through reinforcement and punishment is explored under varying levels of noise and feedback. There is no bias or understanding of the task inherent to the networks and all of the dynamics emerge based on environmental interactions. Value of an action takes the form of reinforcement and punishment signals assumed to be provided by the environment or a user. The variation in the four classes arises from different levels of network complexity based on differences in network architecture, the nature of network interactions including the interplay between excitation, inhibition and reinforcement, and the degree of bio-fidelity of the model. A novel aspect of these models is that they obey the constraints of neuromorphic hardware that are currently under development, including the DARPA SyNAPSE neuromorphic chips for very low power spiking model implementations. The simulation results demonstrate the performance of these models for a variant of classic pong as well as a first-person view selection task. Embodying models in games allows for the creation of environments with varying levels of detail that are ideal for testing spiking neural networks. In addition, the performance results suggest that these models could serve as building blocks for the control of more complex robotic systems
Raising high-density lipoprotein cholesterol with reduction of cardiovascular risk: the role of nicotinic acid – a position paper developed by the European Consensus Panel on HDL-C* (2004)

Reduction of low-density lipoprotein cholesterol (LDL-C) is presently the primary focus of lipid-lowering therapy for prevention and treatment of coronary heart disease (CHD). However, the high level of residual risk among statin-treated patients in recent coronary prevention studies indicates the need for modification of other major components of the atherogenic lipid profile. There is overwhelming evidence that a low plasma level of high-density lipoprotein cholesterol (HDL-C) is an important independent risk factor for CHD. Moreover, a substantial proportion of patients with or at risk of developing premature CHD typically exhibit distinct lipid abnormalities, including low HDL-C levels. Thus, therapeutic intervention aimed at raising HDL-C, within the context of reducing global cardiovascular risk, would benefit such patients, a viewpoint increasingly adopted by international treatment guidelines. Therapeutic options for patients with low HDL-C include treatment with statins, fibrates and nicotinic acid, either as monotherapy or in combination. Of these options, nicotinic acid is not only the most potent agent for raising HDL-C but is also effective in reducing key atherogenic lipid components including triglyceride-rich lipoproteins (mainly very low-density lipoproteins [VLDL] and VLDL remnants), LDL-C, and lipoprotein(a). The principal features of the atherogenic lipid profile in type 2 diabetes and the metabolic syndrome make them logical targets for nicotinic acid therapy, either alone or in combination with a statin. The lack of comprehensive European data on the prevalence of low HDL-C levels highlights a critical need for education on the importance of raising HDL-C in CHD prevention and treatment. The development of a reliable and accurate assay for HDL-C, as well as clarification of criteria for low and optimal levels of HDL-C in both men and women, constitute critical factors in the reliable identification and treatment of patients at elevated risk of CHD due to low HDL-C. Based on the available evidence, the European Consensus Panel recommends that the minimum target for HDL-C should be 40 mg/dL (1.03 mmol/L) in patients with CHD or with a high level of risk for CHD, including patients at high global risk with type 2 diabetes or the metabolic syndrome.
Role of anaerobic bacteria in the metabolic welfare of the colonic mucosa in man. (1980)

Suspensions of isolated epithelial cells (colonocytes) from the human colon were used to assess utilisation of respiratory fuels which are normally available to the colonic mucosa in vivo. Cells were prepared from operative specimens of the ascending colon (seven) and descending colon (seven). The fuels that were used were the short chain fatty acid n-butyrate, produced only by anaerobic bacteria in the colonic lumen, together with glucose and glutamine, normally present in the circulation. The percentage oxygen consumption attributable to n-butyrate, when this was the only substrate, was 73% in the ascending colon and 75% in the descending colon. In the presence of 10 mM glucose these proportions changed to 59% and 72%. Aerobic glycolysis was observed in both the ascending and descending colon. Glucose oxidation accounted for 85% of the oxygen consumption in the ascending colon and 30% in the descending colon. In the presence of 10 mM n-butyrate these proportions decreased to 41% in the ascending colon and 16% in the descending colon. Based on the assumption that events in the isolated colonocytes reflect utilization of fuels in vivo, the hypothesis is put forward that fatty acids of anaerobic bacteria are a major source of energy for the colonic mucosa, particularly of the distal colon.
Single and Tandem Axial <i>p-i-n</i> Nanowire Photovoltaic Devices (2008)

Nanowires represent a promising class of materials for exploring new concepts in solar energy conversion. Here we report the first experimental realization of axial modulation-doped p-i-n and tandem p-i-n(+) -p(+)-i-n silicon nanowire (SiNW) photovoltaic elements. Scanning electron microscopy images of selectively etched nanowires demonstrate excellent synthetic control over doping and lengths of distinct regions in the diode structures. Current-voltage (I-V) characteristics reveal clear and reproducible diode characteristics for the p-i-n and p-n SiNW devices. Under simulated one-sun solar conditions (AM 1.5G), optimized p-i-n SiNW devices exhibited an open circuit voltage (Voc) of 0.29 V, a maximum short-circuit current density of 3.5 mA/cm(2), and a maximum efficiency of 0.5%. The response of the short-circuit current versus Voc under varying illumination intensities shows that the diode quality factor is improved from n=1.78 to n=1.28 by insertion of the i-type SiNW segment. The temperature dependence of Voc scales as -2.97 mV/K and extrapolates to the crystalline Si band gap at 0 K, which is in excellent agreement with bulk properties. Finally, a novel single SiNW tandem solar cell consisting of synthetic integration of two photovoltaic elements with an overall p-i-n(+) -p(+)-i-n structure was prepared and shown to exhibit a Voc that is on average 57% larger than that of the single p-i-n device. Fundamental studies of such well-defined nanowire photovoltaics will enable their intrinsic performance limits to be defined.
Tracking self-occluding articulated objects in dense disparity maps (1999)

In this paper, we present an algorithm for real-time tracking of articulated structures in dense disparity maps derived from stereo image sequences. A statistical image formation model that accounts for occlusions plays the central role in our tracking approach. This graphical model (a Bayesian network) assumes that the range image of each part of the structure is formed by drawing the depth candidates from a 3-D Gaussian distribution. The advantage over the classical mixture of Gaussians is that our model takes into account occlusions by picking the minimum depth (which could be regarded as a probabilistic version of z-buffering). The model also enforces articulation constraints among the parts of the structure. The tracking problem is formulated as an inference problem in the image formation model. This model can be extended and used for other tasks in addition to the one described in the paper and can also be used for estimating probability distribution functions instead of the ML estimates of the tracked parameters. For the purposes of real-time tracking, we used certain approximations in the inference process, which resulted in a real-time two-stage inference algorithm. We were able to successfully track upper human body motion in real time and in the presence of self-occlusions.
Spin Relaxation and Decoherence of Holes in Quantum Dots (2005)

We investigate heavy-hole spin relaxation and decoherence in quantum dots in perpendicular magnetic fields. We show that at low temperatures the spin decoherence time is 2 times longer than the spin relaxation time. We find that the spin relaxation time for heavy holes can be comparable to or even longer than that for electrons in strongly two-dimensional quantum dots. We discuss the difference in the magnetic-field dependence of the spin relaxation rate due to Rashba or Dresselhaus spin-orbit coupling for systems with positive (i.e., GaAs quantum dots) or negative (i.e., InAs quantum dots) g factor.
An interactive analysis method for multidimensional images using a Hilbert curve (1995)

Abstract To analyze multidimensional images we need a mapping of feature vectors from a multidimensional space to a lower dimensional space. In general, these are performed using linear transformation methods, such as principal component analysis, etc. Linear transformation requires many rotations of data from several points of view because the mapping is not one‐to‐one. Here, a new interactive method for classifying multispectral images using a Hilbert curve is presented. The Hilbert curve is a one‐to‐one mapping from N ‐dimensional space to one‐dimensional space and preserves the neighborhood as much as possible. Hilbert curve is a kind of space filling curves, and provides a continuous scan. The merit of the system presented is that the user can extract category clusters without computing any distance in N ‐dimensional space easily. The method presented here is explained in brief. Clusters are extracted from 1‐D data mapped by a Hilbert curve interactively, i.e., a pixel is classified as a category. The user can analyze multidimensional images hierarchically from gross data distribution to fine data distribution. To realize the real time response from the system, data tables storing the addresses and the occurrences of data are used. Here, the address is defined by using the coordinates in N ‐dimensional space, and a part of mapping which cannot preserve the neighborhood is utilized. In the experiments ex‐extracting categories from LANDSAT data, it is confirmed that the user can obtain the real time response from the system after once making the data tables.