gebhart/patrepeval huggingface dataset:
PaccMann: Prediction of anticancer compound sensitivity with multi-modal attention-based neural networks (2018)

We present a novel approach for the prediction of anticancer compound sensitivity by means of multi-modal attention-based neural networks (PaccMann). In our approach, we integrate three key pillars of drug sensitivity, namely, the molecular structure of compounds, transcriptomic profiles of cancer cells as well as prior knowledge about interactions among proteins within cells. Our models ingest a drug-cell pair consisting of SMILES encoding of a compound and the gene expression profile of a cancer cell and predicts an IC50 sensitivity value. Gene expression profiles are encoded using an attention-based encoding mechanism that assigns high weights to the most informative genes. We present and study three encoders for SMILES string of compounds: 1) bidirectional recurrent 2) convolutional 3) attention-based encoders. We compare our devised models against a baseline model that ingests engineered fingerprints to represent the molecular structure. We demonstrate that using our attention-based encoders, we can surpass the baseline model. The use of attention-based encoders enhance interpretability and enable us to identify genes, bonds and atoms that were used by the network to make a prediction.
A Bacteroides ruminicola 1,4-beta-D-endoglucanase is encoded in two reading frames (1991)

Escherichia coli transformed with a plasmid containing a Bacteroides ruminicola endoglucanase (carboxymethyl cellulase [CMCase]) gene produced three immunologically cross-reacting CMCases which had molecular weights of 40,500, 84,000, and 88,000, while B. ruminicola produced CMCases with molecular weights of 82,000 and 88,000. The two B. ruminicola enzymes (purified from culture supernatants) had different N-terminal amino acid sequences, but each enzyme was encoded by the same gene (three independent clones had the same DNA sequence). The 88,000-molecular-weight CMCase (88K CMCase) gene appeared to contain two open reading frames which overlapped for 18 bp and were -1 out of frame, and each open reading frame contained several stop codons near the overlap region. The two 88K CMCase open reading frames had enough DNA to produce a protein of 106K, but the mobility of the enzyme in sodium dodecyl sulfate gels gave a value which was 20% lower. On the basis of the -1 frame shift and the large deviation in theoretical versus actual size, it appears that an unusual event (e.g., ribosomal hopping or RNA splicing) is involved in either the translation or the transcription of the 88K B. ruminicola CMCase gene. The 82K CMCase was completely encoded in the second reading frame, and its size was in agreement with the DNA sequence.
An <em>In Vitro</em> Adult Mouse Muscle-nerve Preparation for Studying the Firing Properties of Muscle Afferents (2014)

Muscle sensory neurons innervating muscle spindles and Golgi tendon organs encode length and force changes essential to proprioception. Additional afferent fibers monitor other characteristics of the muscle environment, including metabolite buildup, temperature, and nociceptive stimuli. Overall, abnormal activation of sensory neurons can lead to movement disorders or chronic pain syndromes. We describe the isolation of the extensor digitorum longus (EDL) muscle and nerve for in vitro study of stretch-evoked afferent responses in the adult mouse. Sensory activity is recorded from the nerve with a suction electrode and individual afferents can be analyzed using spike sorting software. In vitro preparations allow for well controlled studies on sensory afferents without the potential confounds of anesthesia or altered muscle perfusion. Here we describe a protocol to identify and test the response of muscle spindle afferents to stretch. Importantly, this preparation also supports the study of other subtypes of muscle afferents, response properties following drug application and the incorporation of powerful genetic approaches and disease models in mice.
Preparation of a Highly Porous Binderless Activated Carbon Monolith from Rubber Wood Sawdust by a Multi-Step Activation Process for Application in Supercapacitors (2011)

Binderless activated carbon monoliths (ACMs) with high porosity that were prepared from self-adhesive pre-carbonized rubber wood sawdust were studied as electrodes for supercapacitors, focusing on the influence of activation time on the physical and electrochemical properties of the ACMs. The ACMs were activated under a flow of CO2 gas at a rate of 0.5 liters per minute and at a temperature of 900 oC. Activation time varied from 1 to 6 hours and with a multi-step heating profile. The ACM was characterized physically (density, porosity, structure and surface morphology) and electrochemically (specific capacitance, equivalent series resistance, energy and power density). This study found that the combined effects from the length of activation time, binderless property and multi-step heating had the greatest influence on the physical and electrochemical properties of the ACM. The optimum ACM was activated for 5 hours and had a specific capacitance, equivalent series resistance, energy and power density of 138 F g-1, 0.49 Ohm, 2.63 Wh kg-1 and 291 W kg-1, respectively.
(Invited) Static Induction Transistor Logic (1978)

Static induction transistor (SIT) seems to correspond to field effect transistor (FET) and bipolar transistor (BPT) in backward biased and forward biased mode, respectively. In each mode, characteristics are much superior both theoretically and experimentally. Integrating SIT into IIL structure, operation with very low power, very low energy and fast speed is shown even when very primitive and easy processing has applied, as the first stage. Future of this kind of integrated circuit, including memory circuit, which shows very high packing density, very high speed and very low energy operation, is discussed.
Wavelength division multiplexing in long-haul transoceanic transmission systems (2005)

Wavelength division multiplexing (WDM) technology used in long-haul transmission systems has steadily progressed over the past few years. Newly installed state-of-the-art transoceanic systems now have terabit per second maximum capacity, while being flexible enough to have an initial deployed capacity at a fraction of the maximum. The steady capacity growth of these long-haul fiber-optic cable systems has resulted from many improvements in WDM transmission techniques and an increased understanding of WDM optical propagation. Important strides have been made in areas of dispersion management, gain equalization, modulation formats, and error-correcting codes that have made possible the demonstration of capacities approaching 4 Tb/s over transoceanic distances in laboratory experiments.
Asymmetric synthesis towards (3<i>Z</i>,6<i>R</i>)-3-methyl-6-isopropenyl-3,9-decadien-1-yl acetate, a component of the California red scale pheromone (1985)

The key chiral synthons, (R)-3-isopropenyl-6-heptenoic acid and (R)-3-isopropenyl-6-heptenal, needed for the synthesis of (3Z,6R)-3-methyl-6-isopropenyl-3,9-decadien-1-yl acetate, a component of the sex pheromone of the California red scale, Aonidiellaaurantii, have been prepared by asymmetric synthesis. The chiral acid was synthesized in 86% ee by an asymmetric 1,4-addition of isopropenylmagnesium bromide to the l-ephedrine amide derived from (E)-2,6-heptadienoic acid, followed by base hydrolysis. Acid hydrolysis gave the chiral 3-(3-buten-1-yl)-4,4-dimethylbutyrolactone. The chiral aldehyde was prepared in greater than 99% ee by an asymmetric 1,4-addition of isopropenylmagnesium bromide to the imine derived from (S)-(+)-tert-butyl 2-amino-3,3-dimethylbutyrate and (E)-2,6-heptadienal. The 1,4-addition reactions of n-butyllithium or isopropenyllithium to (4S,5S)-(+)-2-[1-(E-1,5-hexadienyl)]-4-methoxymethyl-5-phenyl-2-oxazoline gave the addition products, and sequential mild hydrolysis and reduction of these adducts yielded chiral 3-n-butyl-6-hepten-1-ol for the former adduct but a mixture of products was obtained from the latter adduct.
Development, application, and verification of a digital model of the 3-phase current regulator function of a switched reluctance cycloconverter controller (2002)

The verification of digital control and application to a switched reluctance cycloconverter (SRC) system is addressed. Specifically addressed is the development of the digital model and testing and verification of a digital synthesis of the model for a major functional unit of the controller of a 400 Hz AC SRC system. A general functional framework is first developed for the implementation of a complete SRC controller. The resulting framework consists of two main functional components: the feedback control software function which can be implemented with a digital signal processor and the 3-phase current regulator (3PCR) function which must be implemented with hardwired digital logic and can be prototyped with a complex programmable logic device (CPLD). The focus is next on the 3PCR functionality of the SRC system controller, development of a digital model of the 3PCR function, and its CPLD prototype synthesis and verification. Finally, how a Simulink and CPLD post-synthesis simulation test environment were used to verify the successful synthesis of the digitized 3PCR function of the controller for digital CPLD technology is described.
Effect of lysine and methionine supplementation to a soy protein concentrate diet for red sea bream Pagrus major (2001)

The supplemental effect of amino acids (AAs) to a soy protein concentrate (SPC) diet for red sea bream Pagrus major was evaluated for different-sized fish. The fish were fed artificial diets based on 52% SPC for 60 days in juvenile (mean weight 11.7 g) and for 153 days in yearling (mean weight 178 g). To these diets L-lysine hydrochloric acid (LS), DL-methionine (MS) and both L-lysine and DL-methionine (LMS) were supplemented. A control diet without AA supplementation (NOS) and a reference diet based on brown fish meal (BFM) were also tested. In the juvenile fish, the growth performance of the MS group was significantly higher than the NOS group. The growth performance was further improved by the dietary supplementation of both Lys and Met (LMS group). Lenticular opacity was not observed in these two dietary groups. On the other hand, the growth performance of the NOS and LS groups was lowest, and the incidence of lenticular opacity of the LS group was higher rather than the NOS group. In the yearling fish, feed conversion of the LMS group was slightly higher than the NOS group, but the growth performance of the LMS group was similar to the NOS group. These parameters were similar or slightly lower in the LS or MS groups compared with the NOS group. Lenticular opacity was not observed in any dietary groups for yearling fish. In both juvenile and yearling fish, the performances of the BFM groups were superior to the other dietary groups. The results for juvenile fish indicate that the quality of the SPC diet is improved by the Met supplementation, and further improved by both Lys and Met supplementation. Furthermore, the results in the present study suggest that the AA requirement of red sea bream changes with growth and/or age.
Everyone's Magnetism (1998)

If you were to tell a child playing with a horseshoe magnet and pieces of iron that his uncle has a much bigger magnet that can lift everything and everybody, the child would probably believe you and might even ask for a ride on the magnet. If a physicist were present at such a conversation, he or she—armed with knowledge and experience—would probably smile condescendingly. The physicist would know well that only a very few materials—such as iron or nickel—are strongly magnetic, while the rest of the world's materials are not; to be precise, the rest of the world is a billion (109) times less magnetic. This number seems obviously too large to allow common substances (water, for example) to be lifted even by the most powerful magnets; a billionfold increase in magnetic fields can be found only on neutron stars. In this case, however, knowledge and experience would mislead the physicist: In fact, all materials can be lifted by using magnetic fields that are rather standard these days. In principle, even a child can be levitated by a magnet, as we shall see below.
Probiotic gut effect prevents the chronic psychological stress‐induced brain activity abnormality in mice (2013)

These data suggest that chronic stress-induced abnormal brain plasticity and reduction in neurogenesis can be prevented by a pretreatment with the Probio'Stick(®) formulation, suggesting that probiotics modulate neuroregulatory factors and various signaling pathways in the central nervous system involved in stress response.
Food Allergy: Only a Pediatric Disease? (2010)

Epidemiologic studies report an increase in food allergies in industrialized countries, but mainly focus on children and young adults. This leads to the impression that food allergies do not occur in the older population. However, age-related changes dramatically affect both the innate as well as the adaptive immune system - a phenomenon known as immunosenescence. Deficiencies in micronutrients, especially zinc and iron, as well as vitamin D, in the elderly may also contribute to the development of allergies. A further risk factor of the elderly in developing food allergies could also be the decreased digestive ability of the stomach due to atrophic gastritis or anti-ulcer medication. In these settings, undigested proteins may persist and become allergenic. In fact, mouse models indicate that these pharmaceuticals support the induction of Th2 responses not only in young adult, but also in aged animals. Previous reports have already suggested that allergies are underdiagnosed among the elderly. Based on our own recent study conducted in a geriatric nursing home, we also suggest that food allergies may be underestimated.
Science in General Education (2013)

General education must develop in students an appreciation of the power of science, how it works, why it is an effective knowledge generation tool, and what it can deliver. Knowing what science has discovered is desirable but less important.
Axenic Culture Studies of a New Marine Phycomycete Possessing an Unusual Type of Asexual Reproduction (1964)

Investigations of a nonfilamentous fungus (Schizochytrium aggregatum gen. et sp. nov.) reveal that it proliferates zoosporangia by successive bipartitioning of the thallus. Thus, its vegetative reproduction differs from that of other fungi, but resembles that of some possibly primitive chlorosphaeracean algae. Organism development is described from growth on natural substrates and synthetic media. Inoculation experiments involving diverse algae and phanerogam materials suggest that S. aggregatum is largely a saprophyte of vascular plant detritus in the littoral zone—a conclusion consonant with the results of a survey of its apparent distribution in coastal waters. This obligately marine organism requires 2.5-3.0% NaCl for optimal growth and does not develop in media which differ radically from sea water in potassium content. Neither KCl nor CaCl2 can replace NaCl, and increased levels of KC1 do not mitigate the inhibitory effects of high concentrations of NaCl. The fungus grows well at 12–25 C and gives maximal yields when provided with cellobiose or the cleavage products of starch as carbon sources.
3D Sound Effects with Transaural Audio Beam Projection (2009)

This paper investigates the suitability of transaural reproduction using directional audio\n\n\n\nbeams generated by parametric array in air to produce 3D sound through objective\n\n\n\nevaluation. The 3D sound performance is evaluated by using a binaural hearing model to\n\n\n\nestimate the relevant spatial cues. The reproduced spatial cues from the audio beam\n\n\n\nprojection are compared to the cues from conventional loudspeakers and headphones. It is\n\n\n\nshown that audio beam projection is capable of retaining cues more closely than\n\n\n\nconventional loudspeakers. This suggests that transaural audio beam projection gives a\n\n\n\nbetter 3D perception performance than conventional loudspeaker and it is a viable means\n\n\n\nto reproduce 3D sound effects.
A Domain-Specific Conceptual Query System (2022)

This thesis presents the architecture and implementation of a query system resulted from a domain-specific conceptual data modeling and querying methodology. The query system is built for a high level conceptual query language that supports dynamically user-defined domain-specific functions and application-specific functions. It is DBMS-independent and can be translated to SQL and OQL through a normal form. Currently, it has been implemented in neuroscience domain and can be applied to any other domain.
Towards Low-Latency Energy-Efficient Deep SNNs via Attention-Guided Compression (2021)

Deep spiking neural networks (SNNs) have emerged as a potential alternative to traditional deep learning frameworks, due to their promise to provide increased compute efficiency on event-driven neuromorphic hardware. However, to perform well on complex vision applications, most SNN training frameworks yield large inference latency which translates to increased spike activity and reduced energy efficiency. Hence,minimizing average spike activity while preserving accuracy indeep SNNs remains a significant challenge and opportunity.This paper presents a non-iterative SNN training technique thatachieves ultra-high compression with reduced spiking activitywhile maintaining high inference accuracy. In particular, our framework first uses the attention-maps of an un compressed meta-model to yield compressed ANNs. This step can be tuned to support both irregular and structured channel pruning to leverage computational benefits over a broad range of platforms. The framework then performs sparse-learning-based supervised SNN training using direct inputs. During the training, it jointly optimizes the SNN weight, threshold, and leak parameters to drastically minimize the number of time steps required while retaining compression. To evaluate the merits of our approach, we performed experiments with variants of VGG and ResNet, on both CIFAR-10 and CIFAR-100, and VGG16 on Tiny-ImageNet.The SNN models generated through the proposed technique yield SOTA compression ratios of up to 33.4x with no significant drops in accuracy compared to baseline unpruned counterparts. Compared to existing SNN pruning methods, we achieve up to 8.3x higher compression with improved accuracy.
Preparation and characterization of ZnS–polymer nanocomposite films with high refractive index (2003)

Novel ZnS–poly(urethane-methacrylate macromer) (PUMM) nanocomposite films with high refractive index were prepared by incorporating thiophenol (PhSH)–4-thiomethyl styrene (TMSt)-capped ZnS nanoparticles into a urethane-methacrylate macromer (UMM), followed by spin-coating and ultraviolet radiation initiated free radical polymerization. PhSH–TMSt-capped colloidal ZnS solution was synthesized by reacting zinc acetate with H2S in N,N-dimethylformamide. UMM macromer was synthesized by reacting 2-hydroxyethyl methacrylate (HEMA) with isocyanate group terminated polythiourethane oligomer which was obtained from polyaddition of 2,2′-dimercaptoethyl sulfide (MES) with 2,4-tolylene diisocyanate (TDI). Thiol-capped ZnS nanoparticles were characterized and found to be 2.0–5.0 nm in diameter with a cubic phase structure. The chemical composition of these ZnS nanoparticles was determined to be Zn2+ ∶ S2− ∶ RS− = 1 ∶ 0.6 ∶ 0.6 using chemical analysis methods. The weight fraction of ZnS nanoparticles in the films was measured by TGA, and it accords well with that of theoretical calculation. FTIR and DSC studies show that ZnS nanoparticles were successfully immobilized into the polymer matrix and the resulting nanocomposite films have a good thermal stability. TEM images indicate that the ZnS nanoparticles were uniformly dispersed in the polymer matrix and the particles remained their original size (2–5 nm) before incorporation into the polymer matrix. The XPS depth profiling technique demonstrates that the ZnS nanoparticles were also dispersed homogeneously in the depth scales of the polymer matrix. The nanocomposite films show high optical transparency in the visible region (T > 95% at 550 nm) and high refractive index in the range of 1.645–1.796 at 632.8 nm as the content of thiol-capped ZnS nanoparticles linearly increased from 0 to 86 wt%.
Presencia de multilatinas en Europa: Tipología y estrategia empresarial (2013)

El sentido de los flujos de inversiones directas entre países desarrollados y emergentes ha cambiado recientemente. El exceso de recursos acumulados en los emergentes ha generado un cambio de tendencia, ya que en la última década han tomado relevancia flujos desde ellos hacia mercados maduros como el europeo o el estadounidense, en los que se da una crecien-te presencia de multinacionales procedentes de áreas menos desarrolladas. Este trabajo pre-tende estudiar el impacto de aquellas que proceden de América Latina (Brasil y México funda-mentalmente) comprobando si el proceso es relevante. Más de 700 empresas de Latinoamérica tienen presencia en la UE. Estudiar sus características, estrategias y comportamientos es el fin último de nuestra investigación. Para llevar a cabo el cometido hemos elaborado una base de datos seleccionando más de 170 empresas y a partir de ella hemos identificado patrones de com-portamiento en su proceso de internacionalización hacia Europa mediante el análisis clúster.
Self-mixing flow sensor using a monolithic VCSEL array with parallel readout (2010)

The self-mixing sensing technique is a compact, interferometric sensing technique that can be used for measuring fluid flows. In this work, we demonstrate a parallel readout self-mixing flow velocity sensing system based on a monolithic Vertical-Cavity Surface-Emitting Laser (VCSEL) array. The parallel sensing scheme enables high-resolution full-field imaging systems employing electronic scanning with faster acquisition rates than mechanical scanning systems. The self-mixing signal is acquired from the variation in VCSEL junction voltage, thus markedly reducing the system complexity. The system was validated by measuring velocity distribution of fluid in a custom built diverging-converging planar flow channel. The results obtained agree well with simulation and demonstrate the feasibility of high frame-rate and resolution parallel self-mixing sensors.
Experimental single flux quantum NDRO Josephson memory cell (1979)

Single flux quantum nondestructive readout (NDRO) Josephson memory cells which store an energy of only ~6/spl times/10/SUP -20/ J have been successfully fabricated and operated for the first time. Margin enhancement due to quantization, and low operating currents render this cell an attractive basis for a <1 ns access-time Josephson cache memory designed with a 2.5 /spl mu/m technology.
7-Azabicycloheptane Carboxylic Acid: A Proline Replacement in a Boroarginine Thrombin Inhibitor (1999)

[formula: see text] The synthesis of thrombin inhibitor 3, which incorporates conformationally constrained 7-azabicycloheptane carboxylic acid (1) as a proline replacement, is described. The inhibition constant (Ki(thrombin) = 2.9 nM) indicates that 1 is a reasonable replacement of proline in the formation of a beta-turn tripeptide mimetic.
4th International Conference on Molecular Simulation 2016 (2017)

Molecular simulation, as a powerful tool for investigating science of matter at a molecular level, is widely applied in interdisciplinary fields between chemistry, physics, biology, engineering and...