gebhart/patrepeval huggingface dataset:
Multi‐Field Surface Electrode for Selective Electrical Stimulation (2005)

We designed a 24-field array and an on-line control box that selects which and how many of 24 fields will conduct electrical charge during functional electrical stimulation. The array was made using a conductive microfiber textile, silver two-component adhesive, and the conductive ink imprint on the polycarbonate. The control box comprised 24 switches that corresponded one-to-one to the fields on the array. Each field could be made conductive or nonconductive by simple pressing of the corresponding push-button type switch on the control box. We present here representative results of the selectivity of the new electrode measured in three tetraplegic patients during functional electrical stimulation of the forearm. The task was to generate finger flexion and extension with minimal interference of the wrist movement during lateral and palmar grasps. Therapists determined the appropriate pattern that lead to effective grasping, lasting on average 5 min per stimulation channel in the first session. This optimal conductive pattern (size and shape) provided effective finger flexion and extension with minimal wrist flexion/extension and ulnar/radial deviations (<10 degrees). The optimal size and shape of the electrode in all cases had a branched pattern. The selection of the optimal stimulation site was achieved without moving the electrode. The size and shape were reproducible in the same subject from session to session, yet were different from subject to subject. The optimal electrode size and shape changed when subjects pronated and supinated their forearm. The control box includes a program that can dynamically change the number and sites of the conductive fields; hence, it is feasible to use this during functional movements. Subjects learned how to determine the optimal electrode pattern; hence, these electrodes could be effective for home usage.
MYB46 and MYB83 Bind to the SMRE Sites and Directly Activate a Suite of Transcription Factors and Secondary Wall Biosynthetic Genes (2011)

MYB46 and MYB83 are two functionally redundant Arabidopsis thaliana MYB transcription factors that act as master switches regulating secondary wall biosynthesis. Here, we report the identification of the transcriptional responsive elements and global analysis of the direct targets of MYB46 and MYB83. Using the estrogen-inducible direct activation system, we found that a number of previously identified MYB46 downstream transcription factors, including MYB43, MYB52, MYB54, MYB58, MYB63 and KNAT7, are direct targets of MYB46. Promoter deletion coupled with transactivation analysis of the MYB63 promoter led to the identification of a 7 bp sequence that is sufficient to be responsive to MYB46 activation, and therefore this sequence is designated as the secondary wall MYB-responsive element (SMRE). Further single nucleotide mutation together with electrophoretic mobility shift assay mapped the SMRE consensus sequence as ACC(A/T)A(A/C)(T/C). Genome-wide analysis of direct targets of MYB46 demonstrated that it directly regulates the expression of not only a number of downstream transcription factors, but also a suite of secondary wall biosynthetic genes, some of which are also directly activated by secondary wall NAC (SWN) master switches or by MYB46 direct targets. Furthermore, MYB83 was found to bind to the same SMRE consensus sequence and activate the same set of direct targets as MYB46. Our study has revealed that the transcription program regulating secondary wall biosynthesis involves a multileveled feed-forward loop regulatory structure in which MYB46/MYB83 together with their regulators SWNs and their direct targets regulate an array of downstream genes thereby activating the secondary wall biosynthetic program.
Sarcopenic obesity: definition, cause and consequences (2008)

Recognition of obese patients who have associated muscle problems is an essential goal for clinicians. Further research is needed to identify new target for prevention and cure of this important geriatric syndrome.
"Why 6?" Defining the operational limits of stide, an anomaly-based intrusion detector (2005)

Anomaly-detection techniques have considerable promise for two difficult and critical problems in information security and intrusion detection: detecting novel attacks, and detecting masqueraders. One of the best-known anomaly detectors used in intrusion detection is stide. Developed at the University of New Mexico, stide aims to detect attacks that exploit processes that run with root privileges. The original work on stide presented empirical results indicating that data sequences of length six and above were required for effective intrusion detection. This observation has given rise to the long-standing question, "why six?" accompanied by related questions regarding the conditions under which six may or may not be appropriate. This paper addresses the "why six" issue by presenting an evaluation framework that maps out stide's effective operating space, and identifies the conditions that contribute to detection capability, particularly detection blindness. A theoretical justification explains the effectiveness of sequence lengths of six and above, as well as the consequences of using other values. In addition, results of an investigation are presented, comparing stide's anomaly-detection capabilities with those of a competing detector.
Diversity of airway epithelial cell targets for in vivo recombinant adenovirus-mediated gene transfer. (1993)

A variety of pulmonary disorders, including cystic fibrosis, are potentially amenable to treatment in which a therapeutic gene is directly transferred to the bronchial epithelium. This is difficult to accomplish because the majority of airway epithelial cells replicate slowly and/or are terminally differentiated. Adenovirus vectors may circumvent this problem, since they do not require target cell proliferation to express exogenous genes. To evaluate the diversity of airway epithelial cell targets for in vivo adenovirus-directed gene transfer, a replication deficient recombinant adenovirus containing the Escherichia coli lacZ (beta-galactosidase [beta-gal]) gene (Ad.RSV beta gal) was used to infect lungs of cotton rats. In contrast to uninfected animals, intratracheal Ad.RSV beta gal administration resulted in beta-gal activity in lung lysate and cytochemical staining in all cell types forming the airway epithelium. The expression of the exogenous gene was dose-dependent, and the distribution of the beta-gal positive airway epithelial cells in Ad.RSV beta gal-infected animals was similar to the normal cell differential of the control animals. Thus, a replication deficient recombinant adenovirus can transfer an exogenous gene to all major categories of airway epithelial cells in vivo, suggesting that adenovirus vectors may be an efficient strategy for in vivo gene transfer in airway disorders such as cystic fibrosis.
Medizin und Theologie im Gespräch (2011)

Zusammenfassung Das Gespräch zwischen Medizin und Theologie verhilft beiden Disziplinen zu einer präziseren Sicht auf Krankheit, Sterben und Tod. Gerade wenn dabei definitorische Einigkeit nicht erreicht wird, befördert das Ringen um ein im jeweiligen Kontext angemessenes Verstehen das verantwortliche Handeln der Beteiligten. In diesem Sinn werden im Folgenden Konsequenzen aus dem medizinischen Verständnis von Sterben im klinischen Alltag aufgezeigt. Die abschließenden Thesen weiten den Horizont über den medizinischen Alltag hinaus.
Efficient object localization using Convolutional Networks (2015)

Recent state-of-the-art performance on human-body pose estimation has been achieved with Deep Convolutional Networks (ConvNets). Traditional ConvNet architectures include pooling and sub-sampling layers which reduce computational requirements, introduce invariance and prevent over-training. These benefits of pooling come at the cost of reduced localization accuracy. We introduce a novel architecture which includes an efficient ‘position refinement’ model that is trained to estimate the joint offset location within a small region of the image. This refinement model is jointly trained in cascade with a state-of-the-art ConvNet model [21] to achieve improved accuracy in human joint location estimation. We show that the variance of our detector approaches the variance of human annotations on the FLIC [20] dataset and outperforms all existing approaches on the MPII-human-pose dataset [1].
Energetics of Multistep versus One-step Hydride Transfer Reactions of Reduced Nicotinamide Adenine Dinucleotide (NADH) Models with Organic Cations and p-Quinones (1998)

Free energy changes of each elementary step involved in the formal hydride transfer (H(-)(T)) reactions (including the so-called "one-step" H(-)(T) and "multistep" H(-)(T) mechanisms) of the reduced nicotinamide adenine dinucleotide (NADH) models with various cations and quinones (17) were investigated either by direct thermodynamic measurements or by calculations from thermochemical cycles. Based on the energetic data thus derived, combined with kinetic observations (particularly kinetic isotope effects), the mechanistic characteristics of the NADH-mediated reductions were systematically analyzed. Practical guidelines that resulted from these analyses suggest that a mutistep mechanism (e(-)-H(*) or e(-)-H(+)-e(-)) would be followed if the energy gap of the initial electron transfer [DeltaG(e(-)(T))] between the NADH model compound and the reducing substrate is considerably smaller than the empirical critical limit of 1.0 V for an endothermic e(-)(T). In contrast, if DeltaG(e(-)(T)) is much greater than 1.0 V, a concerted one-step H(-)(T) may take place. The guideline also suggests that a "hybrid" mechanism is possible if the DeltaG(e(-)(T)) is in an intermdiate situation.
The Effect of Long Term Calorie Restriction on in Vivo Hepatic Proteostatis: A Novel Combination of Dynamic and Quantitative Proteomics (2012)

Calorie restriction (CR) promotes longevity. A prevalent mechanistic hypothesis explaining this effect suggests that protein degradation, including mitochondrial autophagy, is increased with CR, removing damaged proteins and improving cellular fitness. At steady state, increased catabolism must be balanced by increasing mitochondrial biogenesis and protein synthesis, resulting in faster protein replacement rates. To test this hypothesis, we measured replacement kinetics and relative concentrations of hundreds of proteins in vivo in long-term CR and ad libitum-fed mice using metabolic (2)H(2)O-labeling combined with the Stable Isotope Labeling in Mammals protocol and LC-MS/MS analysis of mass isotopomer abundances in tryptic peptides. CR reduced absolute synthesis and breakdown rates of almost all measured hepatic proteins and prolonged the half-lives of most (≈ 80%), particularly mitochondrial proteins (but not ribosomal subunits). Proteins with related functions exhibited coordinated changes in relative concentration and replacement rates. In silico expression pathway interrogation allowed the testing of potential regulators of altered network dynamics (e.g. peroxisome proliferator-activated receptor gamma coactivator 1-alpha). In summary, our combination of dynamic and quantitative proteomics suggests that long-term CR reduces mitochondrial biogenesis and mitophagy. Our findings contradict the theory that CR increases mitochondrial protein turnover and provide compelling evidence that cellular fitness is accompanied by reduced global protein synthetic burden.
Advanced Glycation End Products and Oxidative Stress in Type 2 Diabetes Mellitus (2015)

Type 2 diabetes mellitus (T2DM) is a very complex and multifactorial metabolic disease characterized by insulin resistance and β cell failure leading to elevated blood glucose levels. Hyperglycemia is suggested to be the main cause of diabetic complications, which not only decrease life quality and expectancy, but are also becoming a problem regarding the financial burden for health care systems. Therefore, and to counteract the continually increasing prevalence of diabetes, understanding the pathogenesis, the main risk factors, and the underlying molecular mechanisms may establish a basis for prevention and therapy. In this regard, research was performed revealing further evidence that oxidative stress has an important role in hyperglycemia-induced tissue injury as well as in early events relevant for the development of T2DM. The formation of advanced glycation end products (AGEs), a group of modified proteins and/or lipids with damaging potential, is one contributing factor. On the one hand it has been reported that AGEs increase reactive oxygen species formation and impair antioxidant systems, on the other hand the formation of some AGEs is induced per se under oxidative conditions. Thus, AGEs contribute at least partly to chronic stress conditions in diabetes. As AGEs are not only formed endogenously, but also derive from exogenous sources, i.e., food, they have been assumed as risk factors for T2DM. However, the role of AGEs in the pathogenesis of T2DM and diabetic complications-if they are causal or simply an effect-is only partly understood. This review will highlight the involvement of AGEs in the development and progression of T2DM and their role in diabetic complications.
Survival of Patients Undergoing Hemodialysis with Paricalcitol or Calcitriol Therapy (2003)

Patients who receive paricalcitol while undergoing long-term hemodialysis appear to have a significant survival advantage over those who receive calcitriol. A prospective, randomized study is critical to confirm these findings.
Pleiotropic effects of immobilized versus soluble recombinant HIV-1 Tat protein on CD3-mediated activation, induction of apoptosis, and HIV-1 long terminal repeat transactivation in purified CD4+ T lymphocytes (1996)

CD3 mAb and HIV-1 Tat protein co-immobilized on plastic were able to induce a strong proliferation of resting human CD4 T cells, cultured in a serum-free chemically defined medium. Blocking studies performed with heparin or peptides containing the RGD sequence demonstrated that the heparin-binding basic domain of Tat plays a predominant role in CD4+ T cell activation. Moreover, the enhanced proliferative response of CD4+ T cells to immobilized Tat appeared to be mediated by alpha 5, beta 1, and alpha v subunits of surface integrin receptors. In contrast, soluble Tat showed a dose-dependent inhibitory activity on the proliferative response of resting CD4+ T cells stimulated by CD3 mAb co-immobilized with Tat or fibronectin, but not with CD28 mAb. In transient transfection assays performed with an HIV-1 long terminal repeat (LTR)-chloramphenicol acetyltransferase (CAT) plasmid CD3 mAb co-immobilized with Tat or fibronectin or CD28 mAb significantly stimulated CAT activity over the background. On the other hand, while immobilized Tat alone had no effects on LTR transactivation, soluble Tat was able to transactivate LTR-CAT in a dose-dependent manner. When CD4+ T cells activated by CD3 mAb co-immobilized with Tat were recovered, cultured for 7 days with 25 U/ml recombinant IL-2, and given an additional activation signal by recross-linking CD3 mAb, a marked increase of apoptosis was observed with respect to cells not subjected to CD3 mAb recross-linking. While co-immobilized Tat plus CD3 mAb did not show any significant effect on activation-induced cell death, high concentrations of soluble Tat synergized with immobilized CD3 mAb in the induction of apoptosis.
Threading a database of protein cores (1995)

We present an analysis of 10 blind predictions prepared for a recent conference, "Critical Assessment of Techniques for Protein Structure Prediction." The sequences of these proteins are not detectably similar to those of any protein in the structure database then available, but we attempted, by a threading method, to recognize similarity to known domain folds. Four of the 10 proteins, as we subsequently learned, do indeed show significant similarity to then-known structures. For 2 of these proteins the predictions were accurate, in the sense that a similar structure was at or near the top of the list of threading scores, and the threading alignment agreed well with the corresponding structural alignment. For the best predicted model mean alignment error relative to the optimal structural alignment was 2.7 residues, arising entirely from small "register shifts" of strands or helices. In the analysis we attempt to identify factors responsible for these successes and failures. Since our threading method does not use gap penalties, we may readily distinguish between errors arising from our prior definition of the "cores" of known structures and errors arising from inherent limitations in the threading potential. It would appear from the results that successful substructure recognition depends most critically on accurate definition of the "fold" of a database protein. This definition must correctly delineate substructures that are, and are not, likely to be conserved during protein evolution.
Current challenges in the management of the infected patient (2010)

Bacterial resistance is an increasing problem in the hospital environment, and has been associated with poorer clinical outcomes and elevated healthcare costs. By using patient characteristics, local antibiograms, and dosing strategies to achieve an optimal pharmacodynamic profile, early appropriate empiric therapy can be utilized to improve clinical outcomes, minimize the development of resistance, and reduce healthcare costs.
VLSI circuits for adaptive digital beamforming in ultrasound imaging (1993)

For phased-array ultrasound imaging, alternative beamforming techniques and their VLSI circuits are studied to form a fully digital receive front-end hardware. In order to increase the timing accuracy in beamforming, a computationally efficient interpolation scheme to increase the sampling rate is examined. For adaptive beamforming, a phase aberration correction method with very low computational complexity is described. Image quality performance of the method is examined by processing the non-aberrated and aberrated phased-array experimental data sets of an ultrasound resolution phantom. A digital beamforming scheme based on receive focusing at the raster focal points is examined. The sector images of the resolution phantom, reconstructed from the phased-array experimental data by beamforming at the radial and raster focal points, are presented for comparison of the image resolution performances of the two beamforming schemes. VLSI circuits and their implementations for the proposed techniques are presented.
Lipid Rafts Are Enriched in Arachidonic Acid and Plasmenylethanolamine and Their Composition Is Independent of Caveolin-1 Expression:  A Quantitative Electrospray Ionization/Mass Spectrometric Analysis (2002)

Lipid rafts are specialized cholesterol-enriched membrane domains that participate in cellular signaling processes. Caveolae are related domains that become invaginated due to the presence of the structural protein, caveolin-1. In this paper, we use electrospray ionization mass spectrometry (ESI/MS) to quantitatively compare the phospholipids present in plasma membranes and nondetergent lipid rafts from caveolin-1-expressing and nonexpressing cells. Lipid rafts are enriched in cholesterol and sphingomyelin as compared to the plasma membrane fraction. Expression of caveolin-1 increases the amount of cholesterol recovered in the lipid raft fraction but does not affect the relative proportions of the various phospholipid classes. Surprisingly, ESI/MS demonstrated that lipid rafts are enriched in plasmenylethanolamines, particularly those containing arachidonic acid. While the total content of anionic phospholipids was similar in plasma membranes and nondetergent lipid rafts, the latter were highly enriched in phosphatidylserine but relatively depleted in phosphatidylinositol. Detergent-resistant membranes made from the same cells showed a higher cholesterol content than nondetergent lipid rafts but were depleted in anionic phospholipids. In addition, these detergent-resistant membranes were not enriched in arachidonic acid-containing ethanolamine plasmalogens. These data provide insight into the structure of lipid rafts and identify potential new roles for these domains in signal transduction.
Phosphoroselenoate oligodeoxynucleotides: synthesis, physico-chemical characterization, anti-sense inhibitory properties and anti-HIV activity (1989)

Oligodeoxynucleotides with a phosphorus atom in which one of the non-bridging oxygen atoms is substituted by selenium were prepared and investigated with respect to their antisense properties. A general synthesis of phosphoroselenoate analogs of oligonucleotides is described using potassium selenocyanate as the selenium donor. The compounds, characterized by 31P NMR, were shown to decompose to phosphate with a half-life of ca. 30 days. Melting temperatures of duplexes between poly(rA) or poly(rI) with oligo(dT) and oligo(dC), respectively, indicate diminished hybridization capability of phosphoroselenoate oligomers relative to both the unmodified phosphodiester oligomers and the phosphorothioate congeners. A phosphoroselenoate 17-mer is a sequence specific inhibitor of rabbit beta-globin synthesis in wheat germ extract and in injected Xenopus oocytes. In contrast phosphoroselenoate analogs are potent non-sequence specific inhibitors in rabbit reticulocyte lysate. In vitro HIV assays were carried out on a phosphoroselenoate sequence and compared with a phosphorothioate analogue that has previously been shown to exhibit anti-HIV activity (Matsukura et al., Proc. Natl. Acad. Sci. (1987) 84, 7706-7710). The phosphoroselenoate was somewhat less active, and was much more toxic to the cells.
The Role of ATP Hydrolysis for Kinesin Processivity (2002)

Conventional kinesin is a highly processive, plus-end-directed microtubule-based motor that drives membranous organelles toward the synapse in neurons. Although recent structural, biochemical, and mechanical measurements are beginning to converge into a common view of how kinesin converts the energy from ATP turnover into motion, it remains difficult to dissect experimentally the intermolecular domain cooperativity required for kinesin processivity. We report here our pre-steady-state kinetic analysis of a kinesin switch I mutant at Arg(210) (NXXSSRSH, residues 205-212 in Drosophila kinesin). The results show that the R210A substitution results in a dimeric kinesin that is defective for ATP hydrolysis and a motor that cannot detach from the microtubule although ATP binding and microtubule association occur. We propose a mechanistic model in which ATP binding at head 1 leads to the plus-end-directed motion of the neck linker to position head 2 forward at the next microtubule binding site. However, ATP hydrolysis is required at head 1 to lock head 2 onto the microtubule in a tight binding state before head 1 dissociation from the microtubule. This mechanism optimizes forward movement and processivity by ensuring that one motor domain is tightly bound to the microtubule before the second can detach.
Intra‐fraction dose delivery timing during stereotactic radiotherapy can influence the radiobiological effect (2007)

The sequence of incremental dose delivery during a radiotherapy fraction can potentially influence the radiobiological effect. This would be most noticeable during the long fractions characteristic of hypo-fractionated stereotactic radiotherapy and radiosurgery. We demonstrate here the spatio-temporal variation of dose delivery by the CyberKnife to a lung tumor and propose strategies to reduce and/or correct for any resultant dose-time cytotoxic effects.
Cardiovascular safety of ustekinumab in patients with moderate to severe psoriasis: results of integrated analyses of data from phase II and III clinical studies (2011)

The totality of available clinical data suggests neither a detrimental nor a beneficial effect of ustekinumab on serious CV events. Additional data are needed to define the net effect of ustekinumab on CV events.