gebhart/patrepeval huggingface dataset:
Place and Grid Cells in a Loop: Implications for Memory Function and Spatial Coding (2017)

Place cells in the hippocampus and grid cells in the medial entorhinal cortex have different codes for space. However, how one code relates to the other is ill understood. Based on the anatomy of the entorhinal-hippocampal circuitry, we constructed a model of place and grid cells organized in a loop to investigate their mutual influence in the establishment of their codes for space. Using computer simulations, we first replicated experiments in rats that measured place and grid cell activity in different environments, and then assessed which features of the model account for different phenomena observed in neurophysiological data, such as pattern completion and pattern separation, global and rate remapping of place cells, and realignment of grid cells. We found that (1) the interaction between grid and place cells converges quickly; (2) the spatial code of place cells does not require, but is altered by, grid cell input; (3) plasticity in sensory inputs to place cells is key for pattern completion but not pattern separation; (4) grid realignment can be explained in terms of place cell remapping as opposed to the other way around; (5) the switch between global and rate remapping is self-organized; and (6) grid cell input to place cells helps stabilize their code under noisy and/or inconsistent sensory input. We conclude that the hippocampus-entorhinal circuit uses the mutual interaction of place and grid cells to encode the surrounding environment and propose a theory on how such interdependence underlies the formation and use of the cognitive map.<b>SIGNIFICANCE STATEMENT</b> The mammalian brain implements a positional system with two key pieces: place and grid cells. To gain insight into the dynamics of place and grid cell interaction, we built a computational model with the two cell types organized in a loop. The proposed model accounts for differences in how place and grid cells represent different environments and provides a new interpretation in which place and grid cells mutually interact to form a coupled code for space.
Query length in interactive information retrieval (2003)

Query length in best-match information retrieval (IR) systems is well known to be positively related to effectiveness in the IR task, when measured in experimental, non-interactive environments. However, in operational, interactive IR systems, query length is quite typically very short, on the order of two to three words. We report on a study which tested the effectiveness of a particular query elicitation technique in increasing initial searcher query length, and which tested the effectiveness of queries elicited using this technique, and the relationship in general between query length and search effectiveness in interactive IR. Results show that the specific technique results in longer queries than a standard query elicitation technique, that this technique is indeed usable, that the technique results in increased user satisfaction with the search, and that query length is positively correlated with user satisfaction with the search.
Resonant scattering and mode coupling in two-dimensional textured planar waveguides (2001)

A heuristic formalism is developed for efficiently determining the specular reflectivity spectrum of two-dimensionally textured planar waveguides. The formalism is based on a Green's function approach wherein the electric fields are assumed to vary little over the thickness of the textured part of the waveguide. Its accuracy, when the thickness of the textured region is much smaller than the wavelength of relevant radiation, is verified by comparison with a much less efficient, exact finite difference solution of Maxwell's equations. In addition to its numerical efficiency, the formalism provides an intuitive explanation of Fano-like features evident in the specular reflectivity spectrum when the incident radiation is phase matched to excite leaky electromagnetic modes attached to the waveguide. By associating various Fourier components of the scattered field with bare slab modes, the dispersion, unique polarization properties, and lifetimes of these Fano-like features are explained in terms of photonic eigenmodes that reveal the renormalization of the slab modes due to interaction with the two-dimensional grating. An application of the formalism, in the analysis of polarization-insensitive notch filters, is also discussed.
Silencing of Transgene Expression: A Gene Therapy Perspective (2013)

none
Extracellular matrix-related genes in kidney after ischemic injury: potential role for TGF-β in repair (1998)

The renal expression of transforming growth factor-beta1 (TGF-beta1) is enhanced following induction of ischemic injury in rat. In cultured renal cells, TGF-beta stimulates the synthesis of extracellular matrix. To link TGF-beta1 expression with the regulation of extracellular matrix postischemia, we characterized the expression of several genes known to regulate extracellular matrix synthesis at various times during recovery from acute ischemic renal injury in rat. Levels of mRNA for plasminogen activator inhibitor-1 (PAI-1), tissue inhibitor of metalloprotease-1 (TIMP-1), alpha1(IV) collagen, and fibronectin-EIIIA (FN-EIIIA) mRNAs were significantly enhanced in kidneys within 12 h to 3 days after injury and remained elevated at 7-28 days postischemia relative to levels in kidneys of sham-operated controls. PAI-1 mRNA and peptide were localized in regenerating proximal tubules at 3 and 7 days postischemic injury. alpha1(IV) Collagen and FN-EIIIA mRNAs were expressed primarily in regenerating proximal tubule cells. Immunoreactivity for FN-EIIIA was enhanced in the tubular basement membrane (TBM) of regenerating proximal tubules, and alpha1(IV) collagen immunoreactivity was detected in thickened tubulointerstitial spaces. In contrast, TIMP-1 immunoreactivity was enhanced in distal nephron structures postischemia. Immunoneutralization of TGF-beta in vivo attenuated the increases in FN-EIIIA, alpha1(IV) collagen, PAI-1, and TIMP-1 mRNAs by 52%, 73%, 43%, and 27%, respectively. These data are consistent with TGF-beta expression postischemic injury participating in renal regeneration of extracellular matrix homeostasis in the proximal TBM.
ENERGY TRANSFER FROM SODIUM N‐ALKYL CARBAZOLE SULFONATE TO ZINC TETRAPHENYLPORPHYRIN IN MICELLAR SOLUTIONS (1982)

Abstract— In order to study energy transfer to zinc tetraphenylporphyrin (ZnTPP) in micellar solution, a series of surface active agents of sodium N‐alkyl carbazole sulfonate, were synthesized. The energy transfer efficiency from the carbazole group near the surface to ZnTPP located in the core of sodium lauryl sulfate (NaLS) micelles was found to be 30%, as observed through the fluorescence of ZnTPP. The critical micelle concentrations (CMC) of the sodium N‐alkyl carbazole sulfonate surfactants, determined by scattering, were 2 times 10 ‐4 M, 3 times 10 ‐5 M and 3 times 10 ‐6 M, respectively, for alkyl: octyl, dodecyl and hexadecyl. The sensitivity of the CMC of NaLS to the presence of foreign surfactants and solubilizates was also investigated.
The Development of a Substitute Bird Model (1981)

A comprehensive program was conducted to develop a model synthetic bird for use in engine blade impact testing. A hydrodynamic theory of the impact event was used to aid in determining the bird properties which had to be duplicated in the model. Of the two candidate models studied extensively, it was determined that a projectile fabricated from commercial gelatin impregnated with phenolic mircoballoons most nearly duplicated the impact loading history of real birds.
Quantitative History Match of 4D Seismic Response and Production Data in the Valhall Field (2005)

Abstract Permanent ocean-bottom seismic cables have been installed in the Valhall Field, offshore Norway. Five seismic surveys were acquired from the permanent system between October 2003 and April 2005, in addition to two towed-streamer surveys acquired in 1992 and 2002. The various 3D seismic data sets show strong time-lapse or 4D effects resulting from primary production. During the same time period an extensive drilling program has provided high-quality data on reservoir pressure, pressure gradients, and reservoir fluid distribution in the field. This paper outlines how changes in seismic attributes were generated synthetically from a reservoir simulation model and compared against observed 4D seismic data in one area of the field. An objective function describing the misfit between the simulated and measured data was defined using both seismic and conventional production data. BP's Top-Down Reservoir Modelling (TDRM) technology1 was used to generate multiple reservoir descriptions that would minimize the objective function. This involved computer-assisted history matching with a genetic algorithm that varied more than 60 parameters in the reservoir simulator to improve the overall history match.
Comparison of Seven Antibiotic Treatments with No Treatment for Bacteriological Efficacy Against Bovine Mastitis Pathogens (1999)

Milk culture results were retrospectively reviewed from 9007 cases of subclinical mastitis affecting cows housed in dairy herds located in New York and northern Pennsylvania. Cases included in this analysis had at least one mastitis pathogen isolated from the initial milk sample, were recultured within 1 mo, had permanent cow identification, and had records of whether mastitis was treated with an antibiotic or no treatment at all. Overall bacteriological cure rate for 21 mastitis pathogens was 68% (6097 of 9007). Antibiotic treated cases had a higher cure rate (75%) than did untreated cases (65%). Antibiotic treatments that significantly differed from the untreated cure rate of 65% were amoxicillin (82%), erythromycin (76%), cloxacillin (73%), and pirlimycin (44%). Cure rates for antibiotic treatments with cephapirin, hetacillin, or penicillin did not differ from the untreated cure rate. Agents for which some antibiotics were associated with increased cure rates compared with no treatment were Streptococcus agalactiae, streptococci other than Strep. agalactiae, and coagulase-negative staphylococci. The antibiotic most commonly associated with higher cure rates was amoxicillin. Most of the 21 mastitis agents showed no difference in bacteriologic cure rates between any of the 7 antibiotic treatments and no treatment.
High-dimensional neural network potentials for metal surfaces: A prototype study for copper (2012)

The atomic environments at metal surfaces differ strongly from the bulk, and, in particular, in case of reconstructions or imperfections at ``real surfaces,'' very complicated atomic configurations can be present. This structural complexity poses a significant challenge for the development of accurate interatomic potentials suitable for large-scale molecular dynamics simulations. In recent years, artificial neural networks (NN) have become a promising new method for the construction of potential-energy surfaces for difficult systems. In the present work, we explore the applicability of such high-dimensional NN potentials to metal surfaces using copper as a benchmark system. A detailed analysis of the properties of bulk copper and of a wide range of surface structures shows that NN potentials can provide results of almost density functional theory (DFT) quality at a small fraction of the computational costs.
Hydrodynamic stability of swimming in ostraciid fishes: role of the carapace in the smooth trunkfish<i>Lactophrys triqueter</i>(Teleostei:Ostraciidae) (2003)

The hydrodynamic bases for the stability of locomotory motions in fishes are poorly understood, even for those fishes, such as the rigid-bodied smooth trunkfish Lactophrys triqueter, that exhibit unusually small amplitude recoil movements during rectilinear swimming. We have studied the role played by the bony carapace of the smooth trunkfish in generating trimming forces that self-correct for instabilities. The flow patterns, forces and moments on and around anatomically exact, smooth trunkfish models positioned at both pitching and yawing angles of attack were investigated using three methods: digital particle image velocimetry (DPIV), pressure distribution measurements, and force balance measurements. Models positioned at various pitching angles of attack within a flow tunnel produced well-developed counter-rotating vortices along the ventro-lateral keels. The vortices developed first at the anterior edges of the ventro-lateral keels, grew posteriorly along the carapace, and reached maximum circulation at the posterior edge of the carapace. The vortical flow increased in strength as pitching angles of attack deviated from 0 degrees, and was located above the keels at positive angles of attack and below them at negative angles of attack. Variation of yawing angles of attack resulted in prominent dorsal and ventral vortices developing at far-field locations of the carapace; far-field vortices intensified posteriorly and as angles of attack deviated from 0 degrees. Pressure distribution results were consistent with the DPIV findings, with areas of low pressure correlating well with regions of attached, concentrated vorticity. Lift coefficients of boxfish models were similar to lift coefficients of delta wings, devices that also generate lift through vortex generation. Furthermore, nose-down and nose-up pitching moments about the center of mass were detected at positive and negative pitching angles of attack, respectively. The three complementary experimental approaches all indicate that the carapace of the smooth trunkfish effectively generates self-correcting forces for pitching and yawing motions--a characteristic that is advantageous for the highly variable velocity fields experienced by trunkfish in their complex aquatic environment. All important morphological features of the carapace contribute to producing the hydrodynamic stability of swimming trajectories in this species.
Potentielle Antiöstrogene vom Typ des 1,2‐Diphenyl‐1‐pyridyl‐but‐1‐ens Teil 1: Synthese (1991)

Abstract Es wird über die Synthese potentieller Antiöstrogene vom Typ des 1,2‐Diphenyl‐1‐pyridyl‐but‐1‐ens berichtet. Die Herstellung der Schlüsselverbindungen 1‐(4‐Methoxyphenyl)‐1‐(4‐ bzw. 3‐pyridyl)‐2‐phenyl‐but‐1‐en(E/Z‐1c bzw. E/Z‐2c) erfolgte durch Kupplung des entspr. 4‐Methoxyphenylpyridylketons mit Propiophenon mit TiCl 4 /Zn als Reduktionsmittel. Durch Etherspaltung wurden die Phenole 1 und 2 und daraus durch Umsetzung mit 2‐Dimethylaminoethylchlorid die Tam‐analogen Verbindungen 1b,o und 2b,o bzw. durch Acetylierung die Derivate 1a und 2a erhalten.
Electrical stimulation therapy of the lower esophageal sphincter is successful in treating GERD: long-term 3-year results (2015)

LES-EST is safe and effective for treating patients with GERD over long-term, 3-year duration. There was a significant and sustained improvement in esophageal acid exposure and reduction in GERD symptoms and PPI use. Further, no new GI side effects or adverse events were reported.
Activation of NF-kappaB/Rel occurs early during neoplastic transformation of mammary cells (2000)

NF-kappaB/Rel is a family of transcription factors which are expressed in all cells; however, in most non-B cells, they are sequestered in the cytoplasm in inactive complexes with specific inhibitory proteins, termed IkappaBs. We have recently shown that NF-kappaB/Rel factors are aberrantly activated in human breast cancer and rodent mammary tumors, and function to promote tumor cell survival and proliferation. Here, we have examined the time-course of induction of NF-kappaB/Rel factors upon carcinogen treatment of female Sprague-Dawley (S-D) rats in vivo and in human mammary epithelial cells (HMECs) in culture. We observed that NF-kappaB/Rel activation is an early event, occurring prior to malignant transformation. In S-D rats, increased NF-kappaB/Rel binding was detected in nuclear extracts of mammary glands from 40% of animals 3 weeks post-treatment with 15 mg/kg 7,12-dimethylbenz[a]anthracene (DMBA); this is prior to formation of tumors which normally begin to be detected after 7-9 weeks. In non-tumorigenic MCF-10F cells, in vitro malignant transformation upon treatment with either DMBA or benzo[a]pyrene (B[a]P) resulted in a 4- to 12-fold increase in activity of classical NF-kappaB (p65/p50). NF-kappaB induction was corrrelated with a decrease in the stability of the NF-kappaB-specific inhibitory protein IkappaB-alpha. Ectopic expression of the transactivating p65 subunit of NF-kappaB in MCF-10F cells induced the c-myc oncogene promoter, which is driven by two NF-kappaB elements, and endogenous c-Myc levels. Furthermore, reduction mammoplasty-derived HMECs, immortalized following B[a]P exposure, showed dysregulated induction of classical NF-kappaB prior to malignant transformation. Together these findings suggest that activation of NF-kappaB plays an early, critical role in the carcinogen-driven transformation of mammary glands.
Transcriptional control of osteoblast growth and differentiation (1996)

Osteoblast differentiation is a multistep series of events modulated by an integrated cascade of gene expression that initially supports proliferation and the sequential expression of genes associated with the biosynthesis, organization, and mineralization of the bone extracellular matrix. Transcriptional control defines regulatory events operative both developmentally and for support of bone tissue-specific properties. This review focuses on components of transcriptional regulation that function in growth control during osteoblast proliferation and those that postproliferatively contribute to maturation of the bone phenotype. Emphasis is on transcription of the cell cycle-regulated histone gene and the bone-specific osteocalcin gene as paradigms for genes with promoter elements exhibiting responsiveness to a broad spectrum of physiological regulatory signals. Additionally, the potential contributions provided by the three-dimensional organization of the histone and osteocalcin gene promoters to integration of regulatory activities at multiple, independent, and overlapping regulatory domains are explored.
Mid-Infrared Spectral Characteristics of Lipid Molecular Structures in <i>Brassica carinata</i> Seeds: Relationship to Oil Content, Fatty Acid and Glucosinolate Profiles, Polyphenols, and Condensed Tannins (2014)

The objectives of this study were to quantify lipid-related inherent molecular structures using a Fourier transform infrared spectroscopy (FT-IR) technique and determine their relationship to oil content, fatty acid and glucosinolate profile, total polyphenols, and condensed tannins in seeds from newly developed yellow-seeded and brown-seeded Brassica carinata lines. Canola seeds were used as a reference. The lipid-related molecular spectral band intensities were strongly correlated to the contents of oil, fatty acids, glucosinolates, and polyphenols. The regression equations gave relatively high predictive power for the estimation of oil (R² = 0.99); all measured fatty acids (R² > 0.80), except C14:0, C20:3n-3, C22:2n-9, and C22:2n-6; 3-butenyl, 2-OH-3-butenyl, 4-OH-3-CH3-indolyl, and total glucosinolates (R² > 0.686); and total polyphenols (R² = 0.935). However, further study is required to obtain predictive equations based on large numbers of samples from diverse sources to illustrate the general applicability of these regression equations.
Harmonic distortion on the basilar membrane in the basal turn of the guinea‐pig cochlea (1998)

1. Mechanical responses to pure-tone stimuli were recorded from the basilar membrane in the basal turn of the guinea-pig cochlea using a displacement-sensitive laser interferometer. The harmonic content of the responses was evaluated using Fourier analysis. 2. Harmonic distortion products were observed in many of the basilar membrane responses. Response components locked to twice the frequency of the stimulus (i.e. 2F0) were the largest of the distortion products. 3. The second harmonic responses showed a bimodal frequency distribution at low to moderate sound pressure levels: one peak occurred around the preparation's best or most sensitive frequency (i.e. when F0 approximately 17 kHz), and another occurred around one-half of the best frequency (when F0 approximately 8.5 kHz). 4. The absolute levels of most distortion products increased progressively with increasing stimulus strength. When expressed with respect to the levels of the fundamental responses, however, the distortion levels usually decreased with increasing stimulus strength. 5. The levels of the distortion decreased (in both absolute and relative terms) with deterioration in the physiological condition of the cochlea. 6. Maximum second harmonic distortion levels amounted to approximately 3.5 and approximately 28 % of the fundamental responses to tones near and below the best frequency, respectively. 7. The above findings are shown to be consistent with a highly simplified model of cochlear mechanics which incorporates an asymmetric, saturating non-linearity in a positive feedback loop.
TouchViz (2013)

As more applications move from the desktop to touch devices like tablets, designers must wrestle with the costs of porting a design with as little revision of the UI as possible from one device to the other, or of optimizing the interaction per device. We consider the tradeoffs between two versions of a UI for working with data on a touch tablet. One interface is based on using the conventional desktop metaphor (WIMP) with a control panel, push buttons, and checkboxes -- where the mouse click is effectively replaced by a finger tap. The other interface (which we call FLUID) eliminates the control panel and focuses touch actions on the data visualization itself. We describe our design process and evaluation of each interface. We discuss the significantly better task performance and preference for the FLUID interface, in particular how touch design may challenge certain assumptions about the performance benefits of WIMP interfaces that do not hold on touch devices, such as the superiority of gestural vs. control panel based interaction.
Carboxyl‐containing polyesters and polyurethanes from dibenzyl <scp>L</scp>‐tartrate (1984)

Abstract We have prepared polyesters from succinyl chloride, adipoly chloride, and telephthaloyl chloride with dibenzyl L ‐tartrate, polyurethanes from hexamethylene diisocyanate, tolune 2,4‐diisocyanate, and methylene‐bis(4‐phenyl isocyanate) with dibenzyl L ‐tartrate. The molecular weights of these polymers were generally low except for one of the polyurethanes. These polymers were reduced to give those having carboxyl side groups. Potency for inducing interferon was tested for one of the polymers. The result was not encouraging in showing low activity.
BAT: Bisulfite Analysis Toolkit (2017)

Here, we present <b>BAT</b>, a modular bisulfite analysis toolkit, that facilitates the analysis of bisulfite sequencing data. It covers the essential analysis steps of read alignment, quality control, extraction of methylation information, and calling of differentially methylated regions, as well as biologically relevant downstream analyses, such as data integration with gene expression, histone modification data, or transcription factor binding site annotation.