gebhart/patrepeval huggingface dataset:
Mining Electronic Laboratory Notebooks: Analysis, Retrosynthesis, and Reaction Based Enumeration (2012)

An approach to automatically analyze and use the knowledge contained in electronic laboratory notebooks (ELNs) has been developed. Reactions were reduced to their reactive center and converted to a string representation (SMIRKS) which formed the basis for reaction classification and in silico (retro-)synthesis. Of the SMIRKS that occurred at least five times, 98% successfully regenerated the original product. The extracted reaction rules (SMIRKS) and corresponding reactants span a virtual chemical space which showed a strong dependence on the size of the reactive center. Whereas relatively few robust reaction types were sufficient to describe a large part of all reactions, considerably more reaction rules were necessary to cover all reactions in the ELN. Furthermore, reaction sequences were extracted to identify frequent combinations and diversifying reaction steps. Based on the extracted knowledge a (retro-)synthesis tool was built allowing for de novo design of compounds which have a high chance of being synthetically accessible. In an example application of the de novo design tool, various feasible retrosynthetic routes to the query molecule were obtained. Reaction based enumeration along the top ranked route yielded a library of 29 920 compounds with diverse properties, 99.9% of which are novel in the sense that they are unknown to the public domain.
Generation of human vascularized brain organoids (2018)

The aim of this study was to vascularize brain organoids with a patient's own endothelial cells (ECs). Induced pluripotent stem cells (iPSCs) of one UC Davis patient were grown into whole-brain organoids. Simultaneously, iPSCs from the same patient were differentiated into ECs. On day 34, the organoid was re-embedded in Matrigel with 250 000 ECs. Vascularized organoids were grown in vitro for 3-5 weeks or transplanted into immunodeficient mice on day 54, and animals were perfused on day 68. Coating of brain organoids on day 34 with ECs led to robust vascularization of the organoid after 3-5 weeks in vitro and 2 weeks in vivo. Human CD31-positive blood vessels were found inside and in-between rosettes within the center of the organoid after transplantation. Vascularization of brain organoids with a patient's own iPSC-derived ECs is technically feasible.
Stochastic bidirectional training (2002)

We consider connectionist compression schemes using auto-associative networks, demonstrate the advantages gained by imposing different constraints on allowed network weights, and give a comparison with pruning of the unconstrained auto-associative network. In this paper we demonstrate the advantages for generalisation performance of constraining weights symmetrically using weight sharing, and by constraining functional symmetry by the use of enhanced backpropagation networks trained bidirectionally. In the process, we derive the stochastic bidirectional training algorithm.
Cosmic Advice For the Young Planner (1998)

Last fall, two of New England's oldest planners were sitting on the top of Mount Monadnock when they were approached by a group of graduate students. After a brief spell of friendly conversation, several students asked the wise ones for sage advice on the pitfalls of local planning. With a glint in their eyes and a sense of puckish humor they started to outline forty ways in which a newly minted planner could short circuit his/her career. And so, in what they hope will be taken with a great grain of salt, they listed the following.
A Programmable Approach to Model Compression. (2019)

Deep neural networks frequently contain far more weights, represented at a higher precision, than are required for the specific task which they are trained to perform. Consequently, they can often be compressed using techniques such as weight pruning and quantization that reduce both model size and inference time without appreciable loss in accuracy. Compressing models before they are deployed can therefore result in significantly more efficient systems. However, while the results are desirable, finding the best compression strategy for a given neural network, target platform, and optimization objective often requires extensive experimentation. Moreover, finding optimal hyperparameters for a given compression strategy typically results in even more expensive, frequently manual, trial-and-error exploration. In this paper, we introduce a programmable system for model compression called Condensa. Users programmatically compose simple operators, in Python, to build complex compression strategies. Given a strategy and a user-provided objective, such as minimization of running time, Condensa uses a novel sample-efficient constrained Bayesian optimization algorithm to automatically infer desirable sparsity ratios. Our experiments on three real-world image classification and language modeling tasks demonstrate memory footprint reductions of up to 65x and runtime throughput improvements of up to 2.22x using at most 10 samples per search. We have released a reference implementation of Condensa at this https URL.
New Sorbents for Desulfurization of Diesel Fuels via π Complexation:  Layered Beds and Regeneration (2003)

Desulfurization of a commercial diesel fuel by different layered adsorbents and regeneration of the latter were studied in a fixed-bed unit operated at ambient temperature and pressure. In general, a layered bed consisting of 12 wt % activated carbon, 22 wt % of activated alumina (Selexsorb CDX), followed by Cu(I)−Y, activated carbon/Selexsorb CDX/Cu(I)−Y, is capable of producing 41 cm3 of desulfurized diesel fuel/g of adsorbent. The matrix is capable of processing 27 cm3 of deep-desulfurized diesel with a weighted average content of 76 ppbw S. These low-sulfur fuels are suitable for fuel cell applications. For layered-bed regeneration, it was determined that calcination of the adsorbed sulfur moieties with air at 350 °C followed by autoreduction of the copper species recovered all of the original desulfurization capacity when activated aluminas are used as a guard layer. Solvent elution experiments indicate that carbon tetrachloride and N,N-dimethylformamide are suitable solvents to recover all of the adsorbed organosulfur species.
我们应该如何对待孩子——《夏山学校》中的教育思想 (2015)

一、爱与赞许 孩子们幸福与快乐的程度，全靠我们给他们的爱与赞许而定．我们一定要和孩子站在一边．与孩子站在一边就是给孩子爱，那并不是一种占有的爱，也不是一种不讲理智的爱，而是一种让孩子感觉到你爱他，也赞同他一切行为的爱．
A molecular-dynamics simulation study of dielectric relaxation in a 1,4-polybutadiene melt (2002)

We have carried out atomistic molecular dynamics simulations of a melt of 1,4-poly(butadiene) from temperatures well above the experimentally observed merging of the primary α process and secondary β process down to temperatures approaching the experimentally observed bifurcation temperature. The relaxation strength and maximum loss frequency and its temperature dependence for the combined α-β dielectric relaxation process from simulations were in good agreement with experiment. The maximum loss frequency, melt viscosity, chain normal-mode relaxation times and torsional autocorrelation times were found to exhibit nearly identical non-Arrhenius temperature dependencies well represented by a Vogel–Fulcher fit with parameters in good agreement with experimental values obtained from dielectric and viscosity measurements. The dielectric susceptibility showed increasing intensity at high frequency for the lower temperatures investigated, indicative of a breakdown in time-temperature superposition due to an emerging β process. Comparison of time scales for the chain normal-mode dynamics and dielectric relaxation revealed that the latter is associated with motions on the segmental length scale. The correspondence of time scales and temperature dependence for the dielectric relaxation and the torsional autocorrelation function further confirmed the localized nature of the dielectric relaxation and indicated that the combined α-β dielectric process is fundamentally tied to microscopic conformational dynamics of individual dihedrals. However, the mean conformational transition rates were found to exhibit Arrhenius temperature dependence, leading to a divergence of time scales between the torsional, dielectric, chain and mechanical relaxation processes and the rates of conformational transitions with decreasing temperature. This divergence was associated with the increasingly heterogeneous character of conformational dynamics in the melt with decreasing temperature. Hence, the time scale of the principal (α) relaxation in the melt is fundamentally correlated with the time scale for homogenization of conformational dynamics, and not to the time scale of the conformational transitions themselves.
A Multicast Tree Management Method Supporting Fast Failure Recovery and Dynamic Group Membership Changes in OpenFlow Networks (2016)

We propose a multicast tree management method in an OpenFlow controller that handles both fast failure recovery and dynamic multicast group membership changes. Multicast communication is an efficient tool to distribute data to many hosts in various services such as live video streaming. To use multicast in such services, multicast communication must be reliable, which means multicast communication should be restored quickly after failures, and multicast tree management mechanism should support frequent group membership changes. A conventional approach, Point to Multipoint (P2MP) MPLS, only supports fast failure recovery for reliability, and is not very effective in terms of group membership changes. A new approach using OpenFlow supports dynamic group membership changes, but does not consider fast failure recovery in physical switches whose flow entry modification is slow. Our proposed method is to control multicast trees centrally, and it uses a precomputation and pre-installation approach for tree management. A controller calculates and keeps multiple trees that cover all switches where receivers are potentially connected and that have less common nodes and edges, and installs their sub-trees covering switches where receivers are actually connected. The controller calculates the difference per tree between sub-trees before and after membership changes, and reflects them into the network. At the time of failure, the controller checks and finds a pre-installed tree that is unaffected by the failure, and installs a new rule only to a root switch to send packets through the pre-installed alternate tree. Our experiments using switches and our prototype controller show that our proposed method can restore packet delivery quickly after a failure, as well as that our proposed method can handle tree modifications faster than a method of recalculating or reinstalling a tree every time that group memberships are changed.
Ca <sup>2+</sup> sparks operated by membrane depolarization require isoform 3 ryanodine receptor channels in skeletal muscle (2007)

Stimuli are translated to intracellular calcium signals via opening of inositol trisphosphate receptor and ryanodine receptor (RyR) channels of the sarcoplasmic reticulum or endoplasmic reticulum. In cardiac and skeletal muscle of amphibians the stimulus is depolarization of the transverse tubular membrane, transduced by voltage sensors at tubular-sarcoplasmic reticulum junctions, and the unit signal is the Ca(2+) spark, caused by concerted opening of multiple RyR channels. Mammalian muscles instead lose postnatally the ability to produce sparks, and they also lose RyR3, an isoform abundant in spark-producing skeletal muscles. What does it take for cells to respond to membrane depolarization with Ca(2+) sparks? To answer this question we made skeletal muscles of adult mice expressing exogenous RyR3, demonstrated as immunoreactivity at triad junctions. These muscles showed abundant sparks upon depolarization. Sparks produced thusly were found to amplify the response to depolarization in a manner characteristic of Ca(2+)-induced Ca(2+) release processes. The amplification was particularly effective in responses to brief depolarizations, as in action potentials. We also induced expression of exogenous RyR1 or yellow fluorescent protein-tagged RyR1 in muscles of adult mice. In these, tag fluorescence was present at triad junctions. RyR1-transfected muscle lacked voltage-operated sparks. Therefore, the voltage-operated sparks phenotype is specific to the RyR3 isoform. Because RyR3 does not contact voltage sensors, their opening was probably activated by Ca(2+), secondarily to Ca(2+) release through junctional RyR1. Physiologically voltage-controlled Ca(2+) sparks thus require a voltage sensor, a master junctional RyR1 channel that provides trigger Ca(2+), and a slave parajunctional RyR3 cohort.
A Low Noise Pixel Architecture for Scientific CMOS Monolithic Active Pixel Sensors (2010)

This paper presents the design and characterisation of FORTIS (4T Test Image Sensor), which is a low noise, CMOS monolithic active pixel sensor for scientific applications. The pixels present in FORTIS are based around the four transistor (4T) pixel architecture, which is already widely used in the commercial imaging community. The sensor design contains thirteen different variants of the 4T pixel architecture to investigate the effects of changing its core parameters. The variants include differences in the pixel pitch, the diode size, the in-pixel source follower, and the capacitance of the floating diffusion node (the input node of the in-pixel source follower). Processing variations have also been studied, which include varying the resistivity of the epitaxial layer and investigating the effects of a special deep p-well layer. By varying these parameters, the 4T pixel architecture can be optimised for scientific applications where detection of small amounts of charge is required.
Le signifiant imaginaire (1975)

Metz Christian. Le signifiant imaginaire. In: Communications, 23, 1975. Psychanalyse et cinéma, sous la direction de Raymond Bellour, Thierry Kuntzel et Christian Metz. pp. 3-55.
A comprehensive copper stockpile leach model: background and model formulation (2003)

The first phase in the sign, development and implementation of a comprehensive computational model of a copper stockpile leach process is presented. The model accounts for transport phenomena through the stockpile, reaction kinetics for the important mineral species, oxgen and bacterial effects on the leach reactions, plus heat, energy and acid balances for the overall leach process. The paper describes the formulation of the leach process model and its implementation in PHYSICA+, a computational fluid dynamic (CFD) software environment. The model draws on a number of phenomena to represent the competing physical and chemical features active in the process model. The phenomena are essentially represented by a three-phased (solid liquid gas) multi-component transport system; novel algorithms and procedures are required to solve the model equations, including a methodology for dealing with multiple chemical species with different reaction rates in ore represented by multiple particle size fractions. Some initial validation results and application simulations are shown to illustrate the potential of the model.
Hyporesponsiveness to Dog Interferon Induction in vitro (1983)

SUMMARY Sera from dogs that were hyporesponsive to interferon (IFN) induction blocked virus induction of IFN in spleen cells in vitro but not IFN action in dog kidney cells. Similarly, macrophages or their culture fluids were found to block IFN induction in lymphoid cells in vitro. Lymphoid cells deprived of phagocytic cells secreted IFN continuously for 4 days, whereas lymphoid cells in the presence of phagocytic cells produced IFN for only 1 day. It was speculated that the ‘hyporeactivity factor’ in the sera from hyporesponsive dogs was macrophage-derived.
Phase 2 trial of oxaliplatin and pemetrexed as an induction regimen in locally advanced head and neck cancer (2011)

Although the response rate of oxaliplatin and pemetrexed proved less than anticipated, the combination remains an active induction regimen in HNSCC. This regimen should be evaluated further in combination with targeted agents, such as cetuximab, especially in the HPV(+) patient population.
Monoclonal Antiidiotypic Antibodies Interact with the 93 Kilodalton Thyrotropin Receptor and Exhibit Heterogeneous Biological Activities (1991)

Ten antiidiotypic monoclonal antibodies (AI mAb) reacting with the TSH receptor were produced by immunization of mice with a mouse mAb directed to a TSH epitope involved in the binding of the hormone to the receptor. The AI mAb were tested for their effects on the TSH receptor-adenylate cyclase system. Four AI mAb behave as agonists of TSH as they compete with TSH for binding to the receptor and stimulate the adenylate cyclase activity. Five AI mAb inhibited both TSH binding to the receptor and adenylate cyclase activity in the presence and absence of TSH; they were thus considered as antagonists of the hormone. One mAb inhibited only slightly the binding of TSH to the receptor and did not interfere significantly with the adenylate cyclase activity. The 10 AI mAb bound with various apparent affinities to solubilized thyroid membrane proteins but not to kidney, spleen, and liver membranes. Membrane desialylation did not significantly alter the binding of the AI mAb whereas deglycosylation modified more or less strongly the binding of mAb to thyroid membranes. It was also shown that the binding to solubilized thyroid membranes of the 10 mAb was inhibited by anti-TSH receptor autoantibodies present in patients with autoimmune disease. The mAb were further analyzed by Western blot analysis. One mAb did not react with the antigen, which suggested that it was directed to a conformational epitope. The other 9 mAb reacted with a protein of 70 kilodaltons and 5 revealed another band of 93 kilodaltons in accordance with the TSH receptor size deduced from the recently molecular cloning.
DNA damage of macrophages at an air-tissue interface induced by metal nanoparticles (2009)

An air-tissue interface model was used to assess nanoparticulate-induced DNA damage to airway macrophages. Human Mono Mac 6 cells and rat alveolar macrophages were cultured on a collagen membrane and the deposition of metal nanoparticles in nitrogen enhanced using electrostatic charge. Cells were exposed to nanoparticles of iron, gold, silver for up to 10 min, then cultured in medium for 24 hours. Damage to DNA was assessed using the Comet assay. Nanoparticle dose delivered to cells varied with metal. Significant DNA damage to macrophages was induced by all three metal nanoparticles. Transmission electron microscopy showed deposition of discrete nanoparticles of gold and silver, but not iron. We conclude that an air-tissue model is a useful method for modelling DNA damage to airway cells from inhalation of metal nanoparticles.
A Heuristic Approach to Social Network-based and Context-aware Mobile Services Recommendation (2011)

The rapid growth of the number of mobile services provides enormous potential for users to find mobile information of interest. How to use both social network analysis and contextual recommendation techniques to improve mobile services recommendation has received little notice. In this paper we introduce a new heuristic approach to search nearest neighbors for each mobile user based on both given contextual mobile user preferences and mobile social network relationships, and then predict unknown contextual mobile user preferences and finally generate contextual mobile recommendations. We evaluate it on a real-world data set and compare its performance with some classical baseline methods, showing improvements in terms of different evaluation metrics.
Optimal borehole communication using multicarrier modulation (2007)

Transmission of down-hole measurements to the surface while the oil well is being drilled (logging while drilling-LWD-telemetry) is the key to the efficient and successful recovery of hydrocarbon resources. The most promising method of telemetry uses compressional acoustic waves to transmit data along the drillstring. In this technique, telemetry signals are encoded as acoustic wave pulses that propagate through the drillstring and are subsequently received and converted back to electric signals for data recovery at the surface receiver.\nBased on the analysis of the wave propagation properties in the drillstring, I propose and design an acoustic orthogonal frequency division multiplexing (OFDM) transmission scheme to efficiently communicate through the channel. To prove the feasibility of the proposed communication technique, numerous field tests were successfully designed and implemented in various drilling oil rigs. Then I characterize the performance of the oil well telemetry system and propose a joint source-channel coding approach wherein the end-to-end distortion in reconstructing telemetry signals at the surface receiver is directly minimized. I show that the acoustic OFDM technique enables simple implementation of the joint source-channel coding design criterion and present the methodology for optimizing different transmission scheme components. Realistic LWD acoustic telemetry design examples demonstrate that the optimal design results in significant gains in system performance and throughput as compared to standard design approaches.
Caching with expiration times (2002)

Caching data together with expiration times beyond which the data is no longer valid is a standard method for promoting information consistency in distributed systems, including the Internet and WWW, large databases, and mobile telecommunications. We use the framework of competitive analysis of online algorithms and study page eviction strategies in the case where data has expiration times. We show that suitable adaptations of LRU and its generalizations, namely marking algorithms, are asymptotically optimal and, in the worst case, within a multiplicative factor 2 of the lower bounds. A key technical ingredient of our analysis is a covering invariant that captures some of the subtleties introduced by expiration times. The additional difficulty of dealing with expiration times is also reflected in our analysis of the randomized online marking algorithm, as well as the offline version of the problem for which we obtain a factor 3 approximation. We complement our theoretical findings with experiments on real and synthetic data.
STAT5 polarization promotes iTregs and suppresses human T-cell alloresponses while preserving CTL capacity (2013)

Alloreactivity negatively influences outcomes of organ transplantation or HCT from allogeneic donors. Standard pharmacologic immune suppression impairs T-cell function and jeopardizes the beneficial reconstitution of Tregs. Murine transplantation models have shown that STAT3 is highly expressed in alloreactive T cells and may be therapeutically targeted. The influence and effects of STAT3 neutralization in human alloreactivity, however, remain to be elucidated. In this study, S3I-201, a selective small-molecule inhibitor of STAT3, suppressed human DC-allosensitized T-cell proliferation and abrogated Th17 responses. STAT3 blockade significantly enhanced the expansion of potent iTregs and permitted CD8(+) cytolytic effector function. Mechanistically, S3I-201 polarized the ratio of STAT phosphorylation in favor of STAT5 over STAT3 and also achieved a significant degree of Foxp3 demethylation among the iTregs. Conversely, selective impairment of STAT5 phosphorylation with CAS 285986-31-4 markedly reduced iTregs. STAT3 represents a relevant target for achieving control over human alloresponses, where its suppression facilitates STAT5-mediated iTreg growth and function.