gebhart/patrepeval huggingface dataset:
Lipase-catalyzed resolution of chiral 2-amino 1-alcohols (1987)

Lipase-catalyzed resolution of 2-amino 1-alcohols was readily accomplished provided that the amino group was protected as an N-alkoxycarbonyl derivative. Racemic 2-amino-l-butanol and 2-amino-1-propanol were chosen as model compounds, and the resolution was achieved both by hydrolysis of their ester derivatives and by transesterification in ethyl acetate. In either case the (R) enantiomers reacted faster, and at low conversion, the (R) form in high optical purity was obtained as alcohol by hydrolysis and as acetate by transesterification. The two procedures can therefore be considered as complementary with respect to the final product composition. By using commercially available lipase preparations both (R)-(-) and (S)-(+) enantiomers of 2-amino 1-alcohols were isolated in high enantiomeric excesses (≥95%). © 1987, American Chemical Society. All rights reserved.
The Mitochondrial Permeability Transition Regulates Cytochrome c Release for Apoptosis during Endoplasmic Reticulum Stress by Remodeling the Cristae Junction (2007)

The role of the mitochondrial permeability transition (MPT) in apoptosis and necrosis is controversial. Here we show that the MPT regulates the release of cytochrome c for apoptosis during endoplasmic reticulum (ER) stress by remodeling the cristae junction (CJ). CEM cells, HCT116 colon cancer cells, and murine embryo fibroblast cells were treated with the ER stressor thapsigargin (THG), which led to cyclophilin D-dependent mitochondrial release of the profusion GTPase optic atrophy 1 (OPA1), which controls CJ integrity, and cytochrome c, leading to apoptosis. Interference RNA knockdown of Bax blocked OPA1 and cytochrome c release after THG treatment but did not prevent the MPT, showing that Bax was essential for the release of cytochrome c by MPT. In isolated mitochondria, MPT led to OPA1 and cytochrome c release independently of voltage-dependent anion channel and the outer membrane, indicating that the MPT is an inner membrane phenomenon. Last, the MPT was regulated by the electron transport chain but not mitochondrial reactive oxygen species, since THG-induced cell death was not blocked by antioxidants and did not occur in cells lacking mitochondrial DNA. Our results show that the MPT regulates CJ remodeling for cytochrome c-dependent apoptosis induced by ER stress and that mitochondrial electron transport is indispensable for this process.
A Powerful Generative Model Using Random Weights for the Deep Image Representation (2016)

To what extent is the success of deep visualization due to the training? Could we do deep visualization using untrained, random weight networks? To address this issue, we explore new and powerful generative models for three popular deep visualization tasks using untrained, random weight convolutional neural networks. First we invert representations in feature spaces and reconstruct images from white noise inputs. The reconstruction quality is statistically higher than that of the same method applied on well trained networks with the same architecture. Next we synthesize textures using scaled correlations of representations in multiple layers and our results are almost indistinguishable with the original natural texture and the synthesized textures based on the trained network. Third, by recasting the content of an image in the style of various artworks, we create artistic images with high perceptual quality, highly competitive to the prior work of Gatys et al. on pretrained networks. To our knowledge this is the first demonstration of image representations using untrained deep neural networks. Our work provides a new and fascinating tool to study the representation of deep network architecture and sheds light on new understandings on deep visualization. It may possibly lead to a way to compare network architectures without training.
Effects of the Hydroxyl Group on Phenyl Based Ligand/ERRγ Protein Binding (2014)

Bisphenol-A (4,4'-dihydroxy-2,2-diphenylpropane, BPA, or BPA-A) and its derivatives, when exposed to humans, may affect functions of multiple organs by specific binding to the human estrogen-related receptor γ (ERRγ). We carried out atomistic molecular dynamics (MD) simulations of three ligand compounds including BPA-A, 4-α-cumylphenol (BPA-C), and 2,2-diphenylpropane (BPA-D) binding to the ligand binding domain (LBD) of a human ERRγ to study the structures and energies associated with the binding. We used the implicit Molecular Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA) method to estimate the free energies of binding for the phenyl based compound/ERRγ systems. The addition of hydroxyl groups to the aromatic ring had only a minor effect on binding structures and a significant effect on ligand/protein binding energy in an aqueous solution. Free binding energies of BPA-D to the ERRγ were found to be considerably less than those of BPA-A and BPA-C to the ERRγ. These results are well correlated with those from experiments where no binding affinities were determined in the BPA-D/ERRγ complex. No conformational change was observed for the helix 12 (H-12) of ERRγ upon binding of these compounds preserving an active transcriptional conformation state.
Corto Maltese and the process of endless semiosis (2019)

Corto Maltese from the eponymous series is usually regarded as one of the last great romantic heroes in comic books. This qualification is related to his persistent idealism. In various episodes, he typically ends up renouncing the material gains (e. g. a treasure he is after) in the name of friendship and solidarity. Corto Maltese consequently appears as a politically subversive figure, but in fact romantic individualism is an ambivalent ideology, which has developed together with – and not in opposition to – the dominant social-economic relations. The author of the article therefore proposes that we understand the subversive essence of the Corto Maltese series slightly differently, from the perspective of Deleuze-Guattarian schizophrenia, where stable structures of meaning are replaced by the world of unpredictable transitions. The analysis of the series points out the most important elements that could be understood as examples of endless semiosis.
Observation of the cesium clock transition using laser-cooled atoms in a vapor cell (1991)

Cesium atoms in a vapor cell have been trapped and cooled by using light from laser diodes. The 6S F = 4, m = 0 → 6S F = 3, m = 0 hyperfine clock transition was excited as these atoms then fell 2.5 cm in darkness. We observed a linewidth of 8 Hz with good signal-to-noise ratio. This gave a short-term fractional frequency resolution of 6.5×10-12sec, and there is potential for substantial improvement. The apparatus is extremely simple and compact, consisting of a small cesium vapor cell and two diode lasers.
Single layer patch arrays exploiting a quasibalanced feeder to improve the radiation pattern (1999)

Sources of radiation and surface wave excitation from microstrip feeders are reviewed, and instances when the commonly used approximations break down are illustrated. The conditions for cancellation of radiation from novel symmetric feeder structures are shown. Radiation patterns from prototype antennas made for the 28 GHz band with gains of 18 and 27 dBi will be compared, and a set of ‘good practice’ design rules are presented.
Band gap determination of semiconductor powders via surface photovoltage spectroscopy (1999)

Surface photovoltage spectroscopy (SPS) is introduced as a powerful tool for band gap determination of semiconductor powders. The main advantage of SPS is that scattering and reflection do not interfere with the spectra. Therefore, it does not suffer from the inherent limitations of transmission/reflection based spectroscopies, most notably diffuse reflectance spectroscopy (DRS). The principles of the approach are presented and its usefulness is demonstrated by comparing it with DRS for band gap determination of GaAs, InP, CdTe, CdSe, and CdS semiconductor powders.
Vitamin B12 and folate during pregnancy and offspring motor, mental and social development at 2 years of age (2011)

Insufficiency of vitamin B12 (B12) and folate during pregnancy can result in low concentrations in the fetus and have adverse effects on brain development. We investigated the relationship between maternal B12 and folate nutrition during pregnancy and offspring motor, mental and social development at two years of age (2 y). Mothers (n = 123) and their offspring (62 girls, 61 boys) from rural and middle-class urban communities in and around Pune city were followed through pregnancy up to 2 y. Maternal B12 and folate concentrations were measured at 28 and 34 weeks of gestation. At 2 y, the Developmental Assessment Scale for Indian Infants was used to determine motor and mental developmental quotients and the Vineland Social Maturity Scale for the social developmental quotient. Overall, 62% of the mothers had low B12 levels (<150 pmol/l) and one mother was folate deficient during pregnancy. Maternal B12 at 28 and 34 weeks of gestation was associated with offspring B12 at 2 y (r = 0.29, r = 0.32, P < 0.001), but folate was not associated with offspring folate. At 2 y, motor development was associated with maternal folate at 28 and 34 weeks of gestation. Mental and social development quotients were associated positively with head circumference and negatively with birth weight. In addition, pregnancy B12 and folate were positively associated with mental and social development quotients. Maternal B12 and folate during intrauterine life may favorably influence brain development and function. Pregnancy provides a window of opportunity to enhance fetal psychomotor (motor and mental) development.
Descriptive names in X.500 (1989)

This paper presents a new name form for the OSI X.500 directory system. The primary function of the directory is to provide a name-to-object look-up facility for OSI objects. The directory consists of a set of agents and a database which is distributed among the agents. The directory database is structured as a tree where each node, or entry, corresponds to an object. An entry consists of a set of attributes where one or more attributes are designated as the object name relative to the entry's immediate superior. X.500 defines a name as an ordered sequence of entry names starting from the root and terminating at the object. Therefore, a user must know the names of all the superiors of an object. In contrast, the descriptive name form is an unordered set of attributes. Only enough attributes need be given to distinguish the object from other objects. As a result, users do not have to know or understand the underlying hierarchy of the directory in order to do name look-up.
Expander-compressor for a more efficient use of CO2 as refrigerant (1998)

L'efficacite thermodynamique du processus transcritique avec du dioxyde de carbone, a une temperature de 30-45°C, a la sortie de l'echangeur de chaleur haute pression, peut etre sensiblement amelioree si l'on utilise une machine de detente-compression. Il est montre que, non seulement la puissance frigorifique specifique augmente, mais aussi que l'utilisation du surplus de travail de detente, pour la compression du deuxieme etage, permet une amelioration remarquable. Pour la realisation de la machine de detente-compression, il a ete propose l'utilisation d'une machine a piston fonctionnant sur la base du piston libre. Cette machine est efficace: principe simple de fonctionnement, utilisation de plusieurs parametres, compatibilite. Grâce a la haute pression de la machine, il est possible d'obtenir un rendement de 78 %, ce qu'il est impossible d'obtenir avec une machine de detente simple.
Carbonic Anhydrase Inhibitors as Anticonvulsant Agents (2007)

Seizures is one of the most common neurological disorders in clinical medicine. Triggering mechanisms by which seizures form remain unclear, but are related to a rapid change in ionic composition, including an increase of intracellular potassium concentration and pH shifts within the brain. pH buffering of extra- and intracellular spaces is mainly carried out by the CO2 / HCO3 - buffer, the equilibration of the two species being assured by the zinc enzyme carbonic anhydrase (CA, EC 4.2.1.1). Some carbonic anhydrase inhibitors (CAIs) are used as anticonvulsants in the treatment of epilepsy. In this review, we will describe the link between CA and seizures on the basis of several putative mechanisms. Several CA isozymes have been pointed out for their contribution to epileptiform activity. An overview of the CA isozyme expression in the brain and of their specifics roles is also discussed. This article reviews the research achievements published on CA inhibitors, clinically used as anticonvulsant and those under development. Keywords: Carbonic anhydrase, brain, seizures, epilepsy, pH, GABA (γ-aminobutyric), sulfonamides
Development of high-performance multi-layer resist process with hardening treatment (2007)

In the manufacture of devices beyond the 45 nm node, it is important to employ a high-performance multi-layer resist (MLR) process that uses silicon containing ARC (Si-ARC) and spin on carbon (SOC). We examined an additional hardening process of SOC by H<sub>2</sub> plasma treatment in order to improve the etching durability of the MLR. The dry etching durability of H<sub>2</sub>-plasma-hardened SOC film showed a drastic improvement, while the wiggling features of the MLR without H<sub>2</sub> treatment observed after SiO<sub>2</sub> etching disappeared completely. The hardening mechanism of SOC was analyzed by Fourier transform infrared spectroscopy (FTIR) with gradient shaving preparation (GSP) and Raman spectrometry. The formation of diamond-like amorphous carbon at a depth of approximately 50 nm was observed and was attributed to the improvement in the dry etching durability. In addition, the MLR stack with hardening has good reflectivity characteristics. The simulated reflectivity at the interface between the bottom of the resist and top surface of the MLR stack with hardening below 0.6% was attained over a wide range of Si-ARC thicknesses and hyper NA (~1.3) regions. The measured refractive indices of the hardened SOC film at 193 nm had a high value at the surface; however, they gradually decreased toward the inner region and finally became the same as those of untreated SOC. This might be the origin of the estimated excellent reflectivity characteristics.
Authorization for digital rights management in the geospatial domain (2005)

Since information is available in digital format, the protection of intellectual property and copyright fraud has become an important issue. This is, because the digital content can be copied without quality loss and with a reasonable effort of time, equipment and money. After copying, it can be distributed using the Internet, again with little effort of time and money. In such an environment, the loss of revenue for the music and film industry -- not only due to sites like Napster -- is becoming so tremendous, that mechanisms as described under the Digital Rights Management become important. In the geospatial domain, Spatial Data Infrastructures emerge that have the potential to provide high quality and up-to-date geographic information. This enables the endeavor of new market potentials and the creation of new business cases. However, the establishment of Digital Rights Management for geographic information is important in the first place. This paper introduces requirements for geospatial Digital Rights Management and illustrates the difference to known requirements for the music industry. The major contribution of this paper is the description of geospatial access control -- named GeoXACML -- as it can possibly be a solution to the authorization requirement for Digital Rights Management in the geospatial domain.
Modeling Alzheimer's disease in transgenic mice. (1994)

Alzheimer's disease is a common neurodegenerative disorder of unknown etiology characterized by the accumulation of beta amyloid plaques and neurofibrillary tangles in the brain. Attempts have been made to engineer an animal model of the disease using a variety of transgenic approaches. So far the models have only been partially successful. The methods used and the models generated are discussed.
5.3: Digital Paper™: Reflective Displays Using Interferometric Modulation (2000)

Abstract Reflective displays have been fabricated using Interferometric Modulators (IMods), which are interference based MEMS devices. The displays have exhibited reflectivities in excess of 80%, contrast ratios greater than 12:1, viewing angles up to ± 60°, and drive voltages < 5 volts. They are being developed for portable electronic applications, and their status will be discussed.
A critical review on lithium–air battery electrolytes (2013)

Metal-air batteries, utilizing the reduction of ambient oxygen, have the highest energy density because most of the cell volume is occupied by the anode while the cathode active material is not stored in the battery. Lithium metal is a tempting anode material for any battery because of its outstanding specific capacity (3842 mA h g(-1) for Li vs. 815 mA h g(-1) for Zn). Combining the high energy density of Li with ambient oxygen seems to be a promising option. Specifically, in all classes of electrolytes, the transformation from Li-O2 to Li-air is still a major challenge as the presence of moisture and CO2 reduces significantly the cell performance due to their strong reaction with Li metal. Thus, the quest for electrolyte systems capable of providing a solution to the imposed challenges due to the use of metallic Li, exposure to the environment and handling the formation of reactive discharged product is still on. This extended Review provides an expanded insight into electrolytes being suggested and researched and also a future vision on challenges and their possible solutions.
Python in the NERSC Exascale Science Applications Program for Data (2017)

We describe a new effort at the National Energy Research Scientific Computing Center (NERSC) in performance analysis and optimization of scientific Python applications targeting the Intel Xeon Phi (Knights Landing, KNL) manycore architecture. The Python-centered work outlined here is part of a larger effort called the NERSC Exascale Science Applications Program (NESAP) for Data. NESAP for Data focuses on applications that process and analyze high-volume, high-velocity data sets from experimental or observational science (EOS) facilities supported by the US Department of Energy Office of Science. We present three case study applications from NESAP for Data that use Python. These codes vary in terms of "Python purity" from applications developed in pure Python to ones that use Python mainly as a convenience layer for scientists without expertise in lower level programming languages like C, C++ or Fortran. The science case, requirements, constraints, algorithms, and initial performance optimizations for each code are discussed. Our goal with this paper is to contribute to the larger conversation around the role of Python in high-performance computing today and tomorrow, highlighting areas for future work and emerging best practices.
Electron Transfer by Neuronal Nitric-oxide Synthase Is Regulated by Concerted Interaction of Calmodulin and Two Intrinsic Regulatory Elements (2006)

The nitric-oxide synthases (NOSs) are modular, cofactor-containing enzymes, divided into a heme-containing oxygenase domain and an FMN- and FAD-containing reductase domain. The domains are connected by a calmodulin (CaM)-binding sequence, occupancy of which is required for nitric oxide (NO) production. Two additional CaM-modulated regulatory elements are present in the reductase domains of the constitutive isoforms, the autoregulatory region (AR) and the C-terminal tail region. Deletion of the AR reduces CaM stimulation of electron flow through the reductase domain from 10-fold in wild-type nNOS to 2-fold in the mutant. Deletion of the C terminus yields an enzyme with greatly enhanced reductase activity in the absence of CaM but with activity equivalent to that of wild-type enzyme in its presence. A mutant in which both the AR and C terminus were deleted completely loses CaM modulation through the reductase domain. Thus, transduction of the CaM effect through the reductase domain of nNOS is dependent on these elements. Formation of nitric oxide is, however, still stimulated by CaM in all three mutants. A CaM molecule in which the N-terminal lobe was replaced by the C-terminal lobe (CaM-CC) supported NO synthesis by the deletion mutants but not by wild-type nNOS. We propose a model in which the AR, the C-terminal tail, and CaM interact directly to regulate the conformational state of the reductase domain of nNOS.
Transitioning from Face-to-Face to Online Instruction (2009)

This article briefly reviews two important goals in online education: interaction and presence. These are important goals in online education because they are linked to learning and motivation to learn. The article provides guidelines and an extended example of how to design an online course in information security in a manner that will enhance interaction and presence. This article’s contribution is to provide guidelines with a corresponding extended and concrete example for those who are tasked with designing and delivering online courses. Although the guidelines and example were targeted to the field of information security, they can be readily adopted by other disciplines.
Comparison of three different kits for extraction of high-quality RNA from frozen blood (2014)

Extraction of high-quality RNA is a crucial step in gene expression profiling. To achieve optimal RNA extraction from frozen blood, the performance of three RNA extraction kits- TRI reagent, PAXgene blood RNA system (PAXgene) and NucleoSpin RNA blood kit (NucleoSpin)- was evaluated. Fifteen blood specimens collected in tubes containing potassium ethylenediaminetetraacetic acid (EDTA) and stored at -80°C for approximately 5 years were randomly selected. The yield and purity of RNA, RIN (RNA integrity number) values and cycle threshold (Ct) values were assessed. Mean RNA yields with TRI reagent, PAXgene and NucleoSpin were 15.6 ± 8.7 μg/ml, 3.1 ± 1.7 μg/ml and 9.0 ± 5.5 μg/ml, respectively. Mean A260/280 ratios of RNA for the three kits were 1.7 ± 0.1, 2.0 ± 0.1, and 2.0 ± 0.0, and mean RIN values recorded as 3.2 ± 0.8, 6.0 ± 1.1, and 6.4 ± 0.9, respectively. The Ct values of housekeeping genes, 18S rRNA, β-actin, RPLP0 and HPRT1, were as follows: TRI reagent (19.2 ± 1.6, 30.6 ± 1.8, 29.9 ± 1.4 and 36.3 ± 1.3), PAXgene 16.6 ± 1.4, 26.4 ± 1.3, 28.2 ± 1.8 and 33.8 ± 1.1), and NucleoSpin (16.3 ± 1.5, 27.2 ± 1.3, 27.0 ± 1.6 and 32.9 ± 1.6). RNA yield using TRI reagent was 1.7 times higher than that with NucleoSpin and 5 times higher than that with PAXgene. However, the purity and integrity of TRI-extracted RNA was lower than that extracted with PAXgene and NucleoSpin. Moreover, the Ct values of housekeeping genes after extraction with TRI reagent were approximately 1.7-3.8 times higher than those obtained with PAXgene and NucleoSpin. The PAXgene and NucleoSpin kits produced similar results in terms of RNA purity and integrity and subsequent gene amplification. However, RNA yields from NucleoSpin were 2.9-fold higher, compared to PAXgene. Based on these findings, we conclude that NucleoSpin is the most effective kit for extraction of abundant and high-quality RNA from frozen blood.