gebhart/patrepeval huggingface dataset:
Spike Correlations – What Can They Tell About Synchrony? (2011)

Sensory and cognitive processing relies on the concerted activity of large populations of neurons. The advent of modern experimental techniques like two-photon population calcium imaging makes it possible to monitor the spiking activity of multiple neurons as they are participating in specific cognitive tasks. The development of appropriate theoretical tools to quantify and interpret the spiking activity of multiple neurons, however, is still in its infancy. One of the simplest and widely used measures of correlated activity is the pairwise correlation coefficient. While spike correlation coefficients are easy to compute using the available numerical toolboxes, it has remained largely an open question whether they are indeed a reliable measure of synchrony. Surprisingly, despite the intense use of correlation coefficients in the design of synthetic spike trains, the construction of population models and the assessment of the synchrony level in live neuronal networks very little was known about their computational properties. We showed that many features of pairwise spike correlations can be studied analytically in a tractable threshold model. Importantly, we demonstrated that under some circumstances the correlation coefficients can vanish, even though input and also pairwise spike cross correlations are present. This finding suggests that the most popular and frequently used measures can, by design, fail to capture the neuronal synchrony.
Crystal structure of human interferon-α2 (1996)

We have reported the comparison of epitope predictions from site-directed mutagenesis experiments with those from the 2.8 A structure of the Fab Jel42 antibody-HPr complex (Prasad et a!. 1993. J. Biol. Chem., 268, 10705-10708). We now report the 2.5 A structure of the Jel42-HPr complex which provides further details of antibodv-antigen recognition.
Effects of Media and Temperature on Storage of In Vivo- and In Vitro-Produced Bovine Blastocysts. (2010)

In vitro produced embryos have lower cryotolerance than the in vivo counterparts, resulting in lower pregnancy rates when they are cryopreserved and transferred; thus, transporting fresh embryos (not frozen) is a viable alternative to obtain good pregnancy outcomes. The aim of this work was to evaluate different systems for transportation of fresh in vivo- and in vitro- produced embryos up to 8h. In vivo produced embryos were collected nonsurgically from superovulated cows. Also, oocytes were collected from slaughterhouse ovaries, matured, fertilized, and the resulting embryos cultured in vitro by standard procedures in a chemically defined medium. Day 0 of culture was ~18 h after the onset of in vitro fertilization. Seven days after fertilization or insemination, respectively, in vitro- and in vivo-produced embryos were blocked by quality and stage and allocated to different treatments in a 2 x 2 x 2 factorial design, with factors: embryo origin (in vivo (n=32) vs. in vitro (n=69)), media (mPBS with 0.05% PVA vs. HCDM2 with 0.4% BSA), and temperature (25 vs. 37°C). The embryos were blindly and subjectively evaluated for stage (5=early blastocyst, 6=blastocyst, 7=expanded blastocyst and 8=hatched blastocyst) and quality (1=excellent, 2=good, 3=fair and 4=dead) by a single person every 2 h during an 8 h period (Time). An ANCOVA model to adjust storage time as a covariate was used; main effects and first, second, and third order interactions of fixed factors were included in the model. Second order interactions were not significant and dropped from the model. Two way significant interactions for embryo quality were: temperature X embryo, media X time and temperature X time (P < 0.05). In vitro-produced embryos were better kept at 25°C (quality 1.56 vs. 2.00) whereas in vivo produced embryos quality was best at 38°C (quality 2.02 vs. 1.75). HCDM2 medium resulted in better quality embryos with time. Quality of embryos with time was better under 25°C. There were no embryo X media or time interactions (P > 0.1). For stage, significant interactions were temperature X embryo and media X time (P < 0.05). In vivo produced embryos progressed better in stage at 25°C whereas in vitro embryos performed better at 38°C. Embryos placed in mPBS progressed faster than in HCDM2. In summary, HCDM2 was better for long time embryo transportation, 25°C was best for in vitro produced embryos, whereas for in vivo produced embryos 38°C was best. For short time of transportation (2 h) both temperatures are appropriate. However, 25°C is better suited for long time transportation (8 h). Research supported by Fondos Mixtos del Estado de Chihuahua-CONACYT, Grant No. CHIH-2008-C01-91923.
Expression of two zinc transporters in the hippocampus of spontaneously epileptic rats (2009)

Objective To explore the correlation between hippocampal zinc transporter 1 and 3 expressions and epilepsy in spontaneously epileptic rats (ESRs) and normal rats, and observe the alternations of zinc homeostasis in zinc-containing neurons after seizure. Methods Western blot and RT-PCR were used to detect zinc transporter 1 and 3 expressions in the hippocampus of both ESRs with recurrent seizures and normal Wistar rats. Results At both the mRNA and protein levels, hippocampal zinc transporter 1 expression in ESRs with recurrent seizures was significantly higher than that in normal Wistar rats, while hippocampal zinc transporter 3 protein expression was comparable between the two groups. Conclusion Hippocampal zinc transporter 1 expression is up-regnlated and Zn2+ in the hippocampal neurons, especially the post-synaptic neurons, can be elevated in ESRs after recurrent seizure. Up-regulated zinc transporter 1 expression in the hippocampus may protect the neurons against seizure-induced injuries by decreasing Zn2+ levels in the neurons.

Key words: 
Epilepsy; Zinc; Zinc transporter
Efficient Solution of Parabolic Equations by Krylov Approximation Methods (1992)

Numerical techniques for solving parabolic equations by the method of lines is addressed. The main motivation for the proposed approach is the possibility of exploiting a high degree of parallelism in a simple manner. The basic idea of the method is to approximate the action of the evolution operator on a given state vector by means of a projection process onto a Krylov subspace. Thus, the resulting approximation consists of applying an evolution operator of a very small dimension to a known vector which is, in turn, computed accurately by exploiting well-known rational approximations to the exponential. Because the rational approximation is only applied to a small matrix, the only operations required with the original large matrix are matrix-by-vector multiplications, and as a result the algorithm can easily be parallelized and vectorized. Some relevant approximation and stability issues are discussed. We present some numerical experiments with the method and compare its performance with a few explicit and implicit algorithms.
An Approach to Tuning Hyperparameters in Parallel: A Performance Study Using Climate Data CyberTraining: Big Data + High-Performance Computing + Atmospheric Sciences (2019)

The ability to predict violent storms and bad weather conditions with current models can be difficult due to the immense complexity associated with weather simulation. For example when predicting a tornado caution must be used when attempting to quickly classify a weather pattern as tornadic or not tornadic. Thus one can use machine learning to quickly classify these weather patterns but great care must be taken to obtain the maximal amount of accuracy while maintaining prediction wall time. We then create a general framework for determining hyperparameters with tensorflow and keras and use it for training a convolutional neural network that specializes in classifying storms as tornadic or not tornadic based on important factors like vorticity. We demonstrate our framework’s ability to determine optimal hyperparameter values for batch size, epochs, and learning rate by examining accuracy and training time with regards to a small amount of application data. In the context of training time we leverage both CPUs and GPUs and found the performance of GPUs to be vastly superior in time taken to train the various networks than CPUs.
In vitro mineralization of gelatin-polyacrylic acid complex matrices (2004)

Abstract Gelatin-polyacrylic acid (gel-PAA) matrices were obtained by slow diffusion of polyacrylic acid into gelatin gels. The matrices were submitted to uniaxial stretching, which induces a preferential orientation of the collagen molecules, and used as biomimetic substrates for the nucleation of hydroxyapatite from simulated body fluid (SBF). The relative amount of hydroxyapatite deposited from 1.5SBF increases as a function of polyelectrolyte content in the matrices, up to about 30 wt%. In the absence of PAA, the inorganic phase is laid down on the surface of the gelatin matrices as hemispherical aggregates. At variance, hydroxyapatite deposition in the gel-PAA composite matrices at relatively low PAA content occurs preferentially in the spaces between the layers on the surface of the matrices and displays a tablet-like morphology. At high polyelectrolyte concentration, an almost uniform layer of hydroxyapatite covers the whole surface of the matrices. The preferential orientation of the (002) hydroxyapatite reflection indicates a close relationship between the inorganic crystals and the collagen molecules. Keywords: BIOACTIVITYHYDROXYAPATITEGELATINPOLYACRYLIC ACIDSBF
The genetics of the bitter taste receptor T2R38 in upper airway innate immunity and implications for chronic rhinosinusitis (2016)

N/A. Laryngoscope, 127:44-51, 2017.
Stochastic natural gradient descent draws posterior samples in function space (2018)

Recent work has argued that stochastic gradient descent can approximate the Bayesian uncertainty in model parameters near local minima. In this work we develop a similar correspondence for minibatch natural gradient descent (NGD). We prove that for sufficiently small learning rates, if the model predictions on the training set approach the true conditional distribution of labels given inputs, the stationary distribution of minibatch NGD approaches a Bayesian posterior near local minima. The temperature $T = εN / (2B)$ is controlled by the learning rate $ε$, training set size $N$ and batch size $B$. However minibatch NGD is not parameterisation invariant and it does not sample a valid posterior away from local minima. We therefore propose a novel optimiser, "stochastic NGD", which introduces the additional correction terms required to preserve both properties.
Characterization of Measles Virus-Specific Proteins Synthesized In Vivo and In Vitro from Acutely and Persistently Infected Cells (1979)

Measles virus protein synthesis has been analyzed in acutely and persistently infected cells. To assess the role of measles in subacute sclerosing panencephalitis (SSPE), measles viral proteins synthesized in vivo or in vitro were tested for reactivity with serum from a guinea pig(s) immunized with measles virus and sera from patients with SSPE. Guinea pig antimeasles virus serum immunoprecipitates the viral polypeptides of 78,000 molecular weight (glycosylated [G]), 70,000 molecular weight (phosphorylated [P]), 60,000 molecular weight (nucleocapsid [N]), and 35,000 molecular weight (matrix [M]) from cells acutely infected with measles virus as well as from chronically infected cells, but in the latter case, immunoprecipitated M protein has a reduced electrophoretic migration. Sera of SSPE patients immunoprecipitated all but the G protein in acutely infected cells and only the P and N proteins from chronically infected cells. In immunoprecipitates of viral polypeptides synthesized in a reticulocyte cell-free translation system, in response to mRNA from acutely or persistently infected cells, the 78,000-molecular-weight form of the G protein was not detected among the cell-free products of either mRNA. Guinea pig antimeasles virus serum immunoprecipitated P, N, and M polypeptides from the products of either form of mRNA, whereas SSPE serum immunoprecipitated the P and N polypeptides but not the M polypeptide. The differences in immunoreactivity of the antimeasles virus antiserum and the SSPE serum are discussed in terms of possible modifications of measles virus proteins in SSPE.
Incidence of Acute Primary Angle-closure Glaucoma in Singapore (1997)

There is a high incidence of APACG in Singapore, with elderly women being the highest risk group. Chinese Singaporeans are at higher risk than other ethnic groups (Malay and Indian). There is often a substantial delay before these patients consult a physician. The onset of APACG seems to be associated with meteorological factors.
Effect of IL-6 on proliferation and IG production of human EBV-transformed cell lines in serum free culture media. (1990)

To optimalize growth and Ig production of EBV transformed B cells for large scale tissue culture, we analyzed five stable monoclonal EBV-B cell lines for their responsiveness to interleukin (IL)-6 in standard medium with 5% FCS and in several serum-free media. As we previously demonstrated these cell lines were found to be heterogeneous with regard to their production of Il-1, Il-6 and lymphotoxin. We could not demonstrate an effect of Il-6 on proliferation on any of the cell lines in either standard medium with 5% FCS or in any of the serum-free culture media. In standard medium, cell lines capable of Il-6 production showed a slight elevation of Ig production in response to exogenous Il-6. Only one cell line, that did not secrete any of the lymphokines tested, responded strongly to Il-6 with a 12 times elevated IgM production. In contrast, in serum-free medium supplemented with Bovine Serum Albumin (BSA), Il-6 raised Ig secretion of all cell lines. This study shows that in some serum-free culture media EBV cell lines can be propagated as well as in standard medium with FCS. Responsiveness of these cells to cytokines is heterogeneous and is at least partially influenced by the culture medium used.
X-ray fluorescence measurements of arsenic micro-distribution in human nail clippings using synchrotron radiation (2013)

Arsenic (As) distribution in nail clippings from three healthy human subjects was investigated using the microbeam experimental setup of the hard x-ray micro-analysis (HXMA) beamline from the Canadian Light Source (CLS) synchrotron. A pair of toenail and fingernail clippings was collected from each of three subjects (one contributed two fingernail clippings). The fingernail and toenail clippings were embedded in polyester resin and cut in cross-sectional slices with an average thickness of 270 µm. Nine nail clipping cross sections were analyzed from the three subjects. The same method was used to produce five cross sections of nail phantom clippings with concentrations of As ranging from 0 to 20 µg g−1, in increments of 5 µg g−1. These samples were used to produce a calibration line for the As Kα peak. The energy of the x-ray beam was set at 13 keV for optimal excitation of As and the beam size was 28 × 10 µm2. Each sample was analyzed using a point-by-point scanning technique in a 45° beam-sample and 90° beam-detector geometry. The dwelling time was set at 30 s for the human nail clippings and 20 s for the nail phantom clippings, using a step size of 50 µm in both the horizontal and vertical directions for all samples. As concentration for each point was calculated based on the calibration line parameters and the fitted amplitude of the observed As Kα peak. As concentration maps were produced for each nail clipping cross section. The maps show that small regions (<0.1 mm2) with higher As concentrations (>1 µg g−1) are located predominantly in the ventral and dorsal layers of the nail. The results are in agreement with findings reported in a recent study and can be linked to nail histology and keratin structure.
Supplementary Figure 2 from Whole-Body <i>Sleeping Beauty</i> Mutagenesis Can Cause Penetrant Leukemia/Lymphoma and Rare High-Grade Glioma without Associated Embryonic Lethality (2023)

Supplementary Figure 2 from Whole-Body &lt;i&gt;Sleeping Beauty&lt;/i&gt; Mutagenesis Can Cause Penetrant Leukemia/Lymphoma and Rare High-Grade Glioma without Associated Embryonic Lethality
Structure of a Membrane-Embedded Prenyltransferase Homologous to UBIAD1 (2014)

Membrane-embedded prenyltransferases from the UbiA family catalyze the Mg2+-dependent transfer of a hydrophobic polyprenyl chain onto a variety of acceptor molecules and are involved in the synthesis of molecules that mediate electron transport, including Vitamin K and Coenzyme Q. In humans, missense mutations to the protein UbiA prenyltransferase domain-containing 1 (UBIAD1) are responsible for Schnyder crystalline corneal dystrophy, which is a genetic disease that causes blindness. Mechanistic understanding of this family of enzymes has been hampered by a lack of three-dimensional structures. We have solved structures of a UBIAD1 homolog from Archaeoglobus fulgidus, AfUbiA, in an unliganded form and bound to Mg2+ and two different isoprenyl diphosphates. Functional assays on MenA, a UbiA family member from E. coli, verified the importance of residues involved in Mg2+ and substrate binding. The structural and functional studies led us to propose a mechanism for the prenyl transfer reaction. Disease-causing mutations in UBIAD1 are clustered around the active site in AfUbiA, suggesting the mechanism of catalysis is conserved between the two homologs.
Electrical conductivity of fractured media: A computational study of the self-consistent method (2012)

Effective medium theory can be used to link conductivity estimation methods with prior knowledge about the distribution of fractures in the investigated geological structure. In the literature, little work has been presented on assessing the accuracy of effective medium approximations for dense networks of finite-sized fractures. We present here a systematic computational study, comparing the conductivity predictions of the popular self-consistent method with results from numerical finite-element simulations. Our results show that the self-consistent method is accurate within acceptable error bounds for a range of parameter values, in some cases even beyond the percolation limit. We also compare the percolation thresholds predicted by self-consistent theory with the thresholds obtained by a numerical percolation algorithm. For the cases we have studied, the percolation thresholds agree to a remarkable degree.
Encapsulating peritoneal sclerosis (2013)

Chronic peritoneal dialysis (PD) can be complicated by encapsulating peritoneal sclerosis (EPS), a rare but the most severe complication associated with long-term PD. Morbidity and mortality are still high (range from 25% to 55%) especially in the first year after diagnosis. The international Society for Peritoneal Dialysis (ISPD) defined EPS by clinical signs of abdominal pain, bowel obstruction or weight loss in late stages of the disease. Clinical symptoms, radiologic findings and histologic criteria are the three diagnostic pillars.
Application of the Multigrid Data Assimilation Scheme to the China Seas’ Temperature Forecast (2008)

Abstract Correlation scales have been used in the traditional scheme of three-dimensional variational data assimilation (3DVAR) to estimate the background (or first guess) error covariance matrix (the 𝗕 matrix in brief) for the numerical forecast and reanalysis of ocean for decades. However, it is challenging to implement this scheme. On the one hand, determining the correlation scales accurately can be difficult. On the other hand, the positive definite of the 𝗕 matrix cannot be guaranteed unless the correlation scales are sufficiently small. Xie et al. indicated that a traditional 3DVAR only corrects certain wavelength errors, and its accuracy depends on the accuracy of the 𝗕 matrix. Generally speaking, the shortwave error cannot be sufficiently corrected until the longwave error is corrected. An inaccurate 𝗕 matrix may mistake longwave errors as shortwave ones, resulting in erroneous analyses. A new 3DVAR data assimilation scheme, called a multigrid data assimilation scheme, is proposed in this paper for quickly minimizing longwave and shortwave errors successively. By assimilating the sea surface temperature and temperature profile observations into a numerical model of the China Seas, this scheme is applied to a retroactive real-time forecast experiment and favorable results are obtained. Compared to the traditional scheme of 3DVAR, this new scheme has higher forecast accuracy and lower root-mean-square errors. Note that the new scheme demonstrates greatly improved numerical efficiency in the analysis procedure.
Comparative study of the chemical composition of Trigonella foenum-graecum L. essential oil (2023)

Fenugreek is a well-known aromatic plant. Its leaves and seeds are commonly used for their many health benefits and the species is cultivated worldwide. For the first time, essential oils (EOs) from seeds of the Bulgarian and Indian populations were obtained by secondary distillation of hydrolat to extract the residual essential oil therein. They were analyzed by gas chromatography-mass spectrometry and the chemical composition of the two samples was compared. Thirty-six compounds were identified and although the results showed some differences in the component composition of the two essential oils, the major constituents identified in both oils were cubenol, γ -n-amylbutyrolactone and palmitic acid. Moreover, oxygenated sesquiterpenes were the predominant fraction in Bulgarian and Indian seeds oils. Information is limited regarding menthol and γ -n-amylbutyrolactone, which were found in the present study in both oils. The performed analysis confirmed the presence of phytol in fenugreek seeds regardless of the extraction method of the essential oil.
Solid State Reactions in the Fe-Sn System under Mechanical Alloying and Grinding (1998)

Structure-phase transformations in the 68Fe-32Sn system by mechanical alloying from pure elements and mechanical grinding of a multi-phase alloy for different conditions of mechanical treatment in planetary ball mills were studied by X-ray diffraction, 57 Fe Mossbauer spectroscopy and magnetic measurements. The initial stages of structure-phase transformations by mechanical alloying and grinding were found to be different. However, the final product in all cases was nanocrystalline supersaturated solid solution of Sn in α-Fe with the bcc lattice parameter a= 0.2995 nm, the magnetic moment per Fe atom μ Fe =1.9 μ B and the Curie temperature T c =700 K.