gebhart/patrepeval huggingface dataset:
Microstimulation in visual area MT: effects of varying pulse amplitude and frequency (1993)

We have previously shown that perceptual judgements of motion direction are based in part on the activity of direction selective neurons in extrastriate visual area MT (Salzman et al., 1990, 1992). In those experiments, we applied low-amplitude microstimulation pulses (10 microA, 200 Hz) to clusters of MT neurons whose preferred directions were similar. The effect of microstimulation was to bias the monkeys' choices on a direction discrimination task toward the preferred direction of neurons at the stimulation site. The results suggest that microstimulation generated a directionally specific cortical signal by activating selectively neurons near the electrode tip. To test this notion more directly, we have now examined the behavioral effects of varying current amplitude, current frequency, and electrode position. In the majority of experiments, the directional bias in the monkeys' choices was reduced or eliminated as current amplitude increased to 80 microA. In addition, 80 microA stimulating pulses frequently impaired overall performance as measured by the percentage of correct responses. This decrement in performance indicated that 80 microA pulses introduced "noise" into the neural circuitry encoding motion direction, presumably by increasing current spread to activate a larger population of neurons representing all directions of motion. In contrast, increasing current frequency to 500 Hz (10 microA pulses) preserved the directional specificity of microstimulation effects. The precise position of the stimulating electrode also influenced the magnitude of microstimulation effects; in some cases, differences in position on the order of 100 microns determined whether an experiment yielded a very large effect or no effect at all. Thus, directionally specific activation of cortical circuitry within MT can be disrupted by increases in current spread or by small changes in electrode position. These observations suggest that the effects of low-amplitude microstimulation depend upon direct activation of a well-localized population of neurons.
Complex partial seizures of frontal lobe origin (1985)

Complex partial seizures of medial or orbital frontal origin were documented in 10 of 90 patients with intractable epilepsy who were studied with depth electrodes. The clinical features that, in part, served to distinguish these seizures from complex partial seizures originating elsewhere included brief, frequent attacks, complex motor automatisms with kicking and thrashing, sexual automatisms, vocalization, and frequent development of complex partial status epilepticus. The constellation of clinical characteristics was often bizarre, leading to the erroneous diagnosis of hysteria. Stereotyped attack patterns helped establish the diagnosis of epilepsy. Interictal and ictal scalp electroencephalograms were often not helpful and were sometimes misleading.
Acid Sphingomyelinase: Relation of 93Lysine Residue on the Ratio of Intracellular to Secreted Enzyme Activity (2005)

Acid sphingomyelinase (ASM) is the lysosomal enzyme responsible for the hydrolysis of sphingomyelin to ceramide and phosphocholine. An inherited deficiency of this enzymatic activity results in the Type A and B forms of Niemann-Pick disease (NPD). ASM is also readily secreted from cultured cells and can rapidly move from lysosomes to the cell surface upon stimulation by cytokines and other factors. Recent interest has focused on the role of this secreted/cell surface enzyme in ceramide-mediated signal transduction. We therefore sought to understand the mechanism(s) that might regulate intracellular targeting and secretion of this important hydrolase. Most lysosomal proteins are targeted to lysosomes in mammalian cells via the mannose 6-phosphate recognition system. Using cultured skin fibroblasts from I-cell disease patients, in which one of the enzymes responsible for mannose phosphorylation, GlcNAc-phosphotransferase, is deficient, we determined ASM activities in cell homogenates and media. The ratio of secreted to intracellular activity was approximately 8-fold greater in I-cell than in normal cells, indicating that mannose phosphorylation is important in the trafficking of this hydrolase. Most of the secreted activity required Zn+2 for full activity, supporting the concept that intracellular exposure of ASM to zinc within lysosomes is required for enzymatic activation. The recognition of lysosomal proteins by GlcNAc-phosphotransferase is mediated by protein structure, and a specific three-dimensional arrangement of lysine residues exposed on the surface of several enzymes has been shown to be critical for mannose phosphorylation. Alanine scanning mutagenesis of thirteen lysine residues in ASM demonstrated that 93lysine residue plays a critical role in ASM targeting since the K93A mutant had reduced intracellular activity, but enhanced secreted activity that was zinc responsive.
Assessing the Effect of Surface Chemistry on Gold Nanorod Uptake, Toxicity, and Gene Expression in Mammalian Cells (2007)

Through the use of various layer-by-layer polyelectrolyte (PE) coating schemes, such as the common poly(diallyldimethylammonium chloride)-poly(4-styrenesulfonic acid) (PDADMAC-PSS) system, the mammalian cellular uptake of gold nanorods can be tuned from very high to very low by manipulating the surface charge and functional groups of the PEs. The toxicity of these nanorods is also examined. Since the PE coatings are individually toxic, the toxicity of nanorods coated in these PEs is measured and cells are found to be greater than 90% viable in nearly all cases, even at very high concentrations. This viability assay may not be a complete indicator of toxicity, and thus gene-expression analysis is used to examine the molecular changes of cells exposed to PDADMAC-coated nanorods, which enter cells at the highest concentrations. Indicators of cell stress, such as heat-shock proteins, are not significantly up- or down-regulated following nanorod uptake, which suggests that PDADMAC-coated gold nanorods have negligible impact on cell function. Furthermore, a very low number of genes experience any significant change in expression (0.35% of genes examined). These results indicate that gold nanorods are well suited for therapeutic applications, such as thermal cancer therapy, due to their tunable cell uptake and low toxicity.
Generating and using gaze-based document annotations (2008)

In this paper we describe a prototypical system that is able to generate document annotations based on eye movement data. Document parts can be annotated as being read or skimmed. We further explain ideas how such gaze-based document annotations could enhance document-centered office work in the future.
Transcriptional and Posttranscriptional Plant Gene Silencing in Response to a Pathogen (1998)

Plants are able to respond to pathogen attack to restrain development of a systemic infection. The response of Brassica napus (oilseed rape) to systemic infection with the DNA virus cauliflower mosaic virus was shown to result in enhancement and subsequent suppression of viral gene expression in parallel with changes in symptom expression. Transgenes with homology to viral sequences were also affected. This phenomenon, which was shown to be mediated by both transcriptional and posttranscriptional mechanisms, might be related to regulation of highly expressed genetic elements.
Oct4 expression in adult human stem cells: evidence in support of the stem cell theory of carcinogenesis (2004)

The Oct3/4 gene, a POU family transcription factor, has been noted as being specifically expressed in embryonic stem cells and in tumor cells but not in cells of differentiated tissues. With the ability to isolate adult human stem cells it became possible to test for the expression of Oct3/4 gene in adult stem cells and to test the stem cell theory of carcinogenesis. Using antibodies and PCR primers we tested human breast, liver, pancreas, kidney, mesenchyme and gastric stem cells, the cancer cell lines HeLa and MCF-7 and human, dog and rat tumors for Oct4 expression. The results indicate that adult human stem cells, immortalized non-tumorigenic cells and tumor cells and cell lines, but not differentiated cells, express Oct4. Oct4 is expressed in a few cells found in the basal layer of human skin epidermis. The data demonstrate that adult stem cells maintain expression of Oct4, consistent with the stem cell hypothesis of carcinogenesis.
The importance of the t cell in initiating and maintaining the chronic synovitis of rheumatoid arthritis (1992)

We hope that this short review has produced convincing, although indirect, evidence that in the case of rheumatoid synovitis, the T cell is the conductor of an orchestra playing a tune written by an antigen-presenting cell. The tune develops and becomes modified with time, so that it is difficult to discern with clarity much of the original melody. We believe that it may be possible to substitute a new score that will bring this symphony to a harmonious end. We also strongly believe that this is preferable to augmenting the string section or suppressing the percussion section of the orchestra in the vain hope that in the end harmony can be achieved. The final musical analogy must be the hope that the first page of the score can be found, so that we may discover the main theme, the leitmotif, of the rheumatoid-specific antigenic peptide.
Cell-Free Synthesis of Rat Growth Hormone (1973)

Growth hormone has been synthesized in a cell-free system derived from Krebs II ascites cells, under the direction of RNA prepared from rat pituitary tumor (GC) cells. Growth hormone synthesized in the cell-free system was identified by precipitation with antiserum against growth hormone developed in baboon, followed by electrophoretic analysis of the dissolved precipitate on sodium dodecyl sulfate-polyacrylamide gels. RNA from both the membrane and the post-membrane fractions of the cytoplasm of GC cells stimulated protein synthesis in the cell-free system, but only RNA from the membrane fraction was found to direct the synthesis of growth hormone.
Theory for protein mutability and biogenesis. (1990)

Using an elementary physical model for protein folding, of self-avoiding short copolymer chains on two-dimensional square lattices, we address two questions regarding the evolution and origins of globular proteins. (i) How will protein native structures and stabilities be affected by single-and double-site mutations? (ii) What is the probability that a randomly chosen sequence of amino acids will be compact and globular under folding conditions? For a large number of different sequences, we search the conformational space exhaustively to find unequivocally the "native" conformation(s), of global minimum free energy, for each sequence. We find that replacing nonpolar residues in the core by polar residues is generally destabilizing, that surface sites are less sensitive than core sites, that some mutations increase the degeneracy of native states, and that overall it is most probable that a mutation will be neutral, having no effect on the native structure. These results support a "Continuity Principle," that small changes in sequence seldom have large effects on structure or stability of the native state. The simulations also show that (i) the number of "convergent" sequences (different sequences coding for the same native structure) is extremely large and (ii) most sequences become quite dense under folding conditions. This implies that the probability of formation of a globular protein from a random sequence of amino acids by prebiotic or mutational methods is significantly greater than zero.
Dealing with the unknown: Metabolomics and Metabolite Atlases (2010)

Metabolomics is the comprehensive profiling of the small molecule composition of a biological sample. Since metabolites are often the indirect products of gene expression, this approach is being used to provide new insights into a variety of biological systems (clinical, bioenergy, etc.). A grand challenge for metabolomics is the complexity of the data, which often include many experimental artifacts. This is compounded by the tremendous chemical diversity of metabolites. Identification of each uncharacterized metabolite is in many ways its own puzzle (compared with proteomics, which is based on predictable fragmentation patterns of polypeptides). Therefore, effective data reduction/prioritization strategies are critical for this rapidly developing field. Here we review liquid chromatography electrospray ionization mass spectrometry (LC/MS)-based metabolomics, methods for feature finding/prioritization, approaches for identifying unknown metabolites, and construction of method specific 'Metabolite Atlases'.
Polymorphic Pipeline Array: A Flexible Multicore Accelerator for Mobile Multimedia Applications. (2009)

Mobile computing in the form of smart phones, netbooks, and PDAs has become an integral part of our everyday lives. Moving ahead to the next generation of mobile devices, we believe that multimedia will become a more critical and product-differentiating feature. High definition audio and video as well as 3D graphics provide richer interfaces and compelling capabilities. However, these algorithms also bring different computational challenges than wireless signal processing. Multimedia algorithms are more complex featuring more control flow and variable computational requirements where execution time is not dominated by innermost vector loops. Further, data access is more complex where media applications typically operate on multi-dimensional vectors of data rather than single-dimensional vectors with simple strides. Thus, the design of current mobile platforms requires re-examination to account for these new application domains. In this dissertation, we focus on the design of a programmable, low-power accelerator for multimedia algorithms referred to as a Polymorphic Pipeline Array (PPA). The PPA design is inspired by coarse-grain reconfigurable architectures (CGRAs) that consist of an array of function units interconnected by a mesh style interconnect. The PPA improves upon CGRAs by attacking two major limitations: scalability and acceleration limited to innermost loops. The large number of resources are fully utilized by exploiting both Lne-grain instruction-level and coarse-grain pipeline parallelism, and the acceleration is extended beyond innermost loops to encompass the whole region of applications. Various compiler and architectural optimizations are presented for CGRAs that form the basic building blocks of PPA. Two compiler techniques are presented that systematically construct the schedule with intelligent heuristics. Modulo graph embedding leverages graph embedding technique for scheduling in CGRAs and edgecentric modulo scheduling provides a communication-oriented way to address the scheduling problem. For architectural improvement, a novel control path design is presented that leverages the token network of dataflow machines to reduce the instructionmemory power. The PPA is designed with flexibility and programmability as first-order requirements to enable the hardware to be dynamically customizable to the application. A PPA exploit pipeline parallelism found in streaming applications to create a coarsegrain hardware pipeline to execute streaming media applications.
Misoprostol Reduces Serious Gastrointestinal Complications in Patients with Rheumatoid Arthritis Receiving Nonsteroidal Anti-Inflammatory Drugs (1995)

In older patients with rheumatoid arthritis, misoprostol reduced serious NSAID-induced upper gastrointestinal complications by 40% compared with placebo.
Remote Eye-gaze Tracking System by One-point Gaze Calibration (2011)

Conventional gaze tracking systems are burdensome in that they require the user to gaze at several targets on the PC screen in the user-calibration process. The proposed calibration procedure requires the user to gaze at only one target. The implemented system consists of four camera-calibrated, wide-view video cameras arranged around the screen, with near-infrared light-emitting diode (LED) lights attached to each camera. The angle θ between the line of sight and the line connecting the center of the pupil and the camera (LED lights) is related to the vector from the center of the pupil to the corneal reflection detected from the video image. The user-calibration process makes it possible to determine three parameters, which can be achieved using three of the four cameras. Usually, the larger that angle θ is, the worse the gaze detection precision is. A weighted mean method is proposed to determine the final precise gaze point.
VR BBS Using Immersive Virtual Environment (2008)

In this research, VR BBS was developed. In this system, a user can post a photograph with a comment from cellular phone. And the users can see and reply to the photograph and comment by using common BBS on the cellular phone and PC. In addition, the user can also use BBS function in the virtual world. In this study, an immersive projection display was used to experience the virtual world. The virtual world is constructed by placing the photograph images at the position measured by GPS function of the cellular phone. In the virtual world, the user can see photographs and comments on the maps, and reply to them while walking through the world. This system enables users to share information mutually using the cellular phone, PC, and immersive projection display. This system also has a feature that the virtual world would be automatically extended when many users use this system.
Prediction of Hydrophobic (Lipophilic) Properties of Small Organic Molecules Using Fragmental Methods:  An Analysis of ALOGP and CLOGP Methods (1998)

Molecular hydrophobicity (lipophilicity), usually quantified as log P (the logarithm of 1-octanol/water partition coefficient), is an important molecular characteristic in drug discovery. ALOGP and CLOGP are two of the most widely used methods for the estimation of log P. This work describes an extensive reparametrization of the atomic log P values and a detailed comparison of the performance of ALOGP and CLOGP methods on the Pomona Medchem database. Only the “star list” compounds having precisely measured log P values were used in this analysis. While the overall results with both methods are similar, analysis shows that the CLOGP method is better for very small molecules in the range of 1−20 atoms. The two methods are almost comparable in the range of 21−45 atoms, while the ALOGP method has better accuracy for molecules with more than 45 atoms. Although the rms deviation and the correlation coefficient for CLOGP predictions were marginally better than those for corresponding ALOGP predictions, the latter showed a very stable performance for all classes of organic compounds analyzed. The ALOGP method can be used to compute estimates of most neutral organic compounds having C, H, O, N, S, Se, P, B, Si, and halogens. It also covers most zwitterionic compounds having amine and carboxylic acids and ammonium halide salts. The CLOGP method has improved considerably over the years to cover most neutral organic compounds, but it still has some undefined fragments. Finally, unlike CLOGP and other methods of predicting lipophilicity, the ALOGP method has multiple uses, such as the estimation of local hydrophobicity, the visualization of molecular hydrophobicity maps, and the evaluation of hydrophobic interactions in protein−ligand complexes.
Accurate and simple analytic representation of the electron-gas correlation energy (1992)

We propose a simple analytic representation of the correlation energy ${\mathrm{\ensuremath{\varepsilon}}}_{\mathit{c}}$ for a uniform electron gas, as a function of density parameter ${\mathit{r}}_{\mathit{s}}$ and relative spin polarization \ensuremath{\zeta}. Within the random-phase approximation (RPA), this representation allows for the ${\mathit{r}}_{\mathit{s}}^{\mathrm{\ensuremath{-}}3/4}$ behavior as ${\mathit{r}}_{\mathit{s}}$\ensuremath{\rightarrow}\ensuremath{\infty}. Close agreement with numerical RPA values for ${\mathrm{\ensuremath{\varepsilon}}}_{\mathit{c}}$(${\mathit{r}}_{\mathit{s}}$,0), ${\mathrm{\ensuremath{\varepsilon}}}_{\mathit{c}}$(${\mathit{r}}_{\mathit{s}}$,1), and the spin stiffness ${\mathrm{\ensuremath{\alpha}}}_{\mathit{c}}$(${\mathit{r}}_{\mathit{s}}$)=${\mathrm{\ensuremath{\partial}}}^{2}$${\mathrm{\ensuremath{\varepsilon}}}_{\mathit{c}}$(${\mathit{r}}_{\mathit{s}}$, \ensuremath{\zeta}=0)/\ensuremath{\delta}${\mathrm{\ensuremath{\zeta}}}^{2}$, and recovery of the correct ${\mathit{r}}_{\mathit{s}}$ln${\mathit{r}}_{\mathit{s}}$ term for ${\mathit{r}}_{\mathit{s}}$\ensuremath{\rightarrow}0, indicate the appropriateness of the chosen analytic form. Beyond RPA, different parameters for the same analytic form are found by fitting to the Green's-function Monte Carlo data of Ceperley and Alder [Phys. Rev. Lett. 45, 566 (1980)], taking into account data uncertainties that have been ignored in earlier fits by Vosko, Wilk, and Nusair (VWN) [Can. J. Phys. 58, 1200 (1980)] or by Perdew and Zunger (PZ) [Phys. Rev. B 23, 5048 (1981)]. While we confirm the practical accuracy of the VWN and PZ representations, we eliminate some minor problems with these forms. We study the \ensuremath{\zeta}-dependent coefficients in the high- and low-density expansions, and the ${\mathit{r}}_{\mathit{s}}$-dependent spin susceptibility. We also present a conjecture for the exact low-density limit. The correlation potential ${\mathrm{\ensuremath{\mu}}}_{\mathit{c}}^{\mathrm{\ensuremath{\sigma}}}$(${\mathit{r}}_{\mathit{s}}$,\ensuremath{\zeta}) is evaluated for use in self-consistent density-functional calculations.
Imaging cortical association tracts in the human brain using diffusion‐tensor‐based axonal tracking (2002)

Diffusion-tensor fiber tracking was used to identify the cores of several long-association fibers, including the anterior (ATR) and posterior (PTR) thalamic radiations, and the uncinate (UNC), superior longitudinal (SLF), inferior longitudinal (ILF), and inferior fronto-occipital (IFO) fasciculi. Tracking results were compared to existing anatomical knowledge, and showed good qualitative agreement. Guidelines were developed to reproducibly track these fibers in vivo. The interindividual variability of these reconstructions was assessed in a common spatial reference frame (Talairach space) using probabilistic mapping. As a first illustration of this technical capability, a reduction in brain connectivity in a patient with a childhood neurodegenerative disease (X-linked adrenoleukodystrophy) was demonstrated.
An Integrated Microfluidic System for Reaction, High-Sensitivity Detection, and Sorting of Fluorescent Cells and Particles (2003)

Presented is a novel approach for an integrated micro total analysis system (microTAS) based on a microfluidic on-chip device that supports ultrasensitive confocal detection of fluorescent cells and particles and subsequently allows for their precise sorting in the fluid phase with respect to spectroscopic properties, such as brightness and color. The hybrid silicone elastomer/glass chip first comprises a branched channel system to initiate fluid mixing and to hydrodynamically focus the sample solution down to a thin flow layer, matching the size of the confocal detection volume placed at that position and, thus, providing a high detection efficiency. In the subsequent on-chip module, the dispersed cells or particles can be sorted into two different output channels. The sorting process is realized by a perpendicular deflection stream that can be switched electrokinetically. The performance of the automated sorting routine is demonstrated by precise partition of a mixture of differently colored fluorescent beads. Moreover, the specifically branched channel geometry allows for direct implementation of reaction steps prior to detection and sorting, which is demonstrated by inducing a selective recognition reaction between the fluorescent protein R-phycoerythrin and a mixture of live bacterial cells exhibiting or lacking the respective surface antigens.