gebhart/patrepeval huggingface dataset:
A Computational Model of Memory, Attention, and Word Learning (2012)

There is considerable evidence that people generally learn items better when the presentation of items is distributed over a period of time (the spacing effect). We hypothesize that both forgetting and attention to novelty play a role in the spacing effect in word learning. We build an incremental probabilistic computational model of word learning that incorporates a forgetting and attentional mechanism. Our model accounts for experimental results on children as well as several patterns observed in adults. 1 Memory, Attention, and Word Learning Learning the meaning of words is an important component
LPS increases biomaterial degradation by human monocytesin vitro (1997)

Different cell lines are involved during an immunological reaction, principally lymphocytes and monocytes. Monocyte/macrophage cells, which are among the first to appear in wound-healing and infection sites, are largely implicated in phagocytosis and could be involved in calcium-phosphate degradation. Their role in these processes may relate to cytokine secretions and/or their sensitivity to certain cytokines. We tested the behavior of human monocytes placed on the surface of biphasic calcium-phosphate (BCP) tablets in the presence of two lipopolysaccharide (LPS) concentrations. After short-term culture (48 h), cytokine release (IL-1beta, IL-6) was measured by ELISA, and morphological cell events and biomaterial degradation were observed in scanning electron microscopy. BCP surface pits were noted near cells stimulated by 0.5 microg/mL LPS but were not apparent with 10 microg/mL LPS. The number of lacunae on BCP was increased after LPS treatment of human monocytes. An upmodulation of IL-1beta and IL-6 (in culture medium) released by LPS-activated human monocytes was observed, indicating good cell stimulation. This study demonstrates that LPS-activated human monocytes can degrade the surface of calcium-phosphate ceramic and confirms the role of human monocytes in biomaterial degradation.
Corrigendum: In silico serotyping of E. coli from short read data identifies limited novel O-loci but extensive diversity of O:H serotype combinations within and between pathogenic lineages (2017)

Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher and we support and invest in the microbiology community, to the benefit of everyone. This supports our principal goal to develop, expand and strengthen the networks available to our members so that they can generate new knowledge about microbes and ensure that it is shared with other communities.
Ratiometric Two-Photon Fluorescent Probe for Quantitative Detection of β-Galactosidase Activity in Senescent Cells (2014)

We reported a ratiometric two-photon fluorescent probe (SG1) for β-galactosidase (β-gal) and its application to quantitative detection of β-gal activity during cellular senescence in live cells and in aged tissues. This probe is characterized by a significant two-photon excited fluorescence, a marked blue-to-yellow emission color change in response to β-gal, easy loading, insensitivity to pH and reactive oxygen species (ROS), high photostability, and low cytotoxicity. In addition, we show that SG1 labeling is an effective tool for quantitative detection of senescence-associated β-gal activity at the subcellular level in situ. This finding demonstrates that SG1 will find useful applications in biomedical research, including studies of cell aging.
Structural integrity, meltability, and variability of thermal properties in the mixed-linker zeolitic imidazolate framework ZIF-62 (2020)

Metal-organic framework (MOF) glasses have emerged as a new class of melt-quenched glasses; however, so far, all MOF glass production has remained at lab-scale; future applications will require large-scale, commercial production of parent crystalline MOFs. Yet, control of synthetic parameters, such as uniform temperature and mixing, can be challenging, particularly, when scaling-up production of a mixed-linker MOF or a zeolitic imidazolate framework (ZIF). Here, we examine the effect of heterogeneous linker distribution on the thermal properties and melting behavior of ZIF-62. X-ray diffraction (XRD), Raman, and <sup>1</sup>H nuclear magnetic resonance spectroscopies revealed little discernable structural difference between samples of ZIF-62 synthesized in our lab and by a commercial supplier. Differential scanning calorimetry and variable temperature/isothermal XRD revealed the samples to have significantly different thermal behavior. Formation of ZIF-zni was identified, which contributed to a dramatic rise in the melting point by around 100 K and also led to the alteration of the macroscopic properties of the final glass. Parameters that might lead to the formation of unexpected phases such as an uneven distribution of linkers were identified, and characterization methods for the detection of unwanted phases are provided. Finally, the need for adequate consideration of linker distribution is stressed when characterizing mixed-linker ZIFs.
Validation of the AmpC β-Lactamase Binding Site and Identification of Inhibitors with Novel Scaffolds (2012)

AmpC β-lactamase confers resistance to β-lactam antibiotics in multiple Gram-negative bacteria. Therefore, identification of non-β-lactam compounds that inhibit the enzyme is considered crucial to the development of novel antibacterial therapies. Given the highly solvent-exposed active site, it is important to study the induced-fit movements and water-mediated interactions to improve docking accuracy and virtual screening enrichments in structure-based design of new AmpC inhibitors. Here, we tested multiple models of the AmpC binding site to investigate the importance of conserved water molecules and binding site plasticity on molecular docking. The results indicate that at least one conserved water molecule greatly improves the binding pose predictions and virtual screening enrichments of known noncovalent AmpC inhibitors. The best model was tested prospectively in the virtual screening of about 6 million commercially available compounds. Sixty-one chemically diverse top-scoring compounds were experimentally tested, which led to the identification of seven previously unknown inhibitors. These findings validate the essential features of the AmpC binding site for molecular recognition and are useful for further optimization of identified inhibitors.
Psoas Muscle Calcification and Acute Renal Failure Associated with Nontraumatic Rhabdomyolysis (1990)

We present a case of reversible psoas muscle calcification associated with acute renal failure and alcohol intoxication. The CT demonstration of calcification led to the recognition of rhabdomyolysis.
ChemInform Abstract: The Synthesis of Seven‐Membered Rings: General Strategies and the Design and Development of a New Class of Cycloaddition Reactions (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Continuous Automated Model EvaluatiOn (CAMEO)—Perspectives on the future of fully automated evaluation of structure prediction methods (2021)

The Continuous Automated Model EvaluatiOn (CAMEO) platform complements the biennial CASP experiment by conducting fully automated blind evaluations of three-dimensional protein prediction servers based on the weekly prerelease of sequences of those structures, which are going to be published in the upcoming release of the Protein Data Bank. While in CASP14, significant success was observed in predicting the structures of individual protein chains with high accuracy, significant challenges remain in correctly predicting the structures of complexes. By implementing fully automated evaluation of predictions for protein-protein complexes, as well as for proteins in complex with ligands, peptides, nucleic acids, or proteins containing noncanonical amino acid residues, CAMEO will assist new developments in those challenging areas of active research.
Wireless Sensor Network With Perpetual Motes for Terrestrial Snail Activity Monitoring (2017)

Wireless sensor networks (WSNs) are increasingly adopted in agriculture to monitor environmental variables to predict the presence of pests. Differently from these approaches, this paper introduces aWSN to detect the presence of snails in the field. The network can be used to both trigger an alarm of early pest presence and to further elaborate statistical models with the addition of environmental data as temperature or humidity to predict snail presence. In this paper we also design our own WSN simulator to account for real-life conditions as an uneven spacing of motes in the field or different currents generated by solar cells at the motes. This allows achieving more realistic network deployment in the field. Experimental tests are included in this paper, showing that our motes are perpetual in terms of energy consumption.
Salvage of the Crucified Chin (2011)

Wan, Derrick C. M.D.; Longaker, Michael T. M.D., M.B.A.; Allam, Karam A. M.D.; Perry, Adam M.D.; Kawamoto, Henry K. M.D. Author Information
Disruption of the Ao <i>pex11-1</i> Gene Involved in Peroxisome Proliferation Leads to Impaired Woronin Body Formation in <i>Aspergillus oryzae</i> (2009)

The Woronin body, a unique organelle found in the Pezizomycotina, plugs the septal pore upon hyphal damage to prevent excessive cytoplasmic bleeding. Although it was previously shown that the Woronin body buds out from the peroxisome, the relationship between peroxisomal proliferation/division and Woronin body differentiation has not been extensively investigated. In this report, we examined whether Pex11 required for peroxisomal proliferation participates in Woronin body formation in Aspergillus oryzae. A. oryzae contained two orthologous PEX11 genes that were designated Aopex11-1 and Aopex11-2. Deletion of Aopex11 genes revealed that only the DeltaAopex11-1 strain showed reduced growth and enlarged peroxisomes in the presence of oleic acid as a sole carbon source, indicating a defect in peroxisomal function and proliferation. Disruption of Aopex11-1 gene impaired the Woronin body function, leading to excessive loss of the cytosol upon hyphal injury. Dual localization analysis of the peroxisome and Woronin body protein AoHex1 demonstrated that Woronin bodies fail to fully differentiate from peroxisomes in the DeltaAopex11-1 strain. Furthermore, distribution of AoHex1 was found to be peripheral in the enlarged peroxisome or junctional in dumbbell-shaped peroxisomes. Electron microscopy of the DeltaAopex11-1 strain revealed the presence of Woronin bodies that remained associated with organelles resembling peroxisomes, which was supported from the sucrose gradient centrifugation confirming that the Woronin body protein AoHex1 overlapped with the density-shifted peroxisome in the DeltaAopex11-1 strain. In conclusion, the present study describes the role of Pex11 in Woronin body differentiation for the first time.
Pivotal role of P450–P450 interactions in CYP3A4 allostery: the case of α-naphthoflavone (2013)

We investigated the relationship between oligomerization of CYP3A4 (cytochrome P450 3A4) and its response to ANF (α-naphthoflavone), a prototypical heterotropic activator. The addition of ANF resulted in over a 2-fold increase in the rate of CYP3A4-dependent debenzylation of 7-BFC [7-benzyloxy-4-(trifluoromethyl)coumarin] in HLM (human liver microsomes), but failed to produce activation in BD Supersomes or Baculosomes containing recombinant CYP3A4 and NADPH-CPR (cytochrome P450 reductase). However, incorporation of purified CYP3A4 into Supersomes containing only recombinant CPR reproduced the behaviour observed with HLM. The activation in this system was dependent on the surface density of the enzyme. Although no activation was detectable at an L/P (lipid/P450) ratio ≥750, it reached 225% at an L/P ratio of 140. To explore the relationship between this effect and CYP3A4 oligomerization, we probed P450-P450 interactions with a new technique that employs LRET (luminescence resonance energy transfer). The amplitude of LRET in mixed oligomers of the haem protein labelled with donor and acceptor fluorophores exhibited a sigmoidal dependence on the surface density of CYP3A4 in Supersomes™. The addition of ANF eliminated this sigmoidal character and increased the degree of oligomerization at low enzyme concentrations. Therefore the mechanisms of CYP3A4 allostery with ANF involve effector-dependent modulation of P450-P450 interactions.
Clinical correlates of DHEA associated with post‐traumatic stress disorder (2006)

That greater symptom improvement was related to DHEA levels may suggest for a role for these hormones in modulating recovery from PTSD.
Bridging Sim2Real Gap Using Image Gradients for the Task of End-to-End Autonomous Driving (2022)

We present the first prize solution to NeurIPS 2021 - AWS Deepracer Challenge. In this competition, the task was to train a reinforcement learning agent (i.e. an autonomous car), that learns to drive by interacting with its environment, a simulated track, by taking an action in a given state to maximize the expected reward. This model was then tested on a real-world track with a miniature AWS Deepracer car. Our goal is to train a model that can complete a lap as fast as possible without going off the track. The Deepracer challenge is a part of a series of embodied intelligence competitions in the field of autonomous vehicles, called The AI Driving Olympics (AI-DO). The overall objective of the AI-DO is to provide accessible mechanisms for benchmarking progress in autonomy applied to the task of autonomous driving. The tricky section of this challenge was the sim2real transfer of the learned skills. To reduce the domain gap in the observation space we did a canny edge detection in addition to cropping out of the unnecessary background information. We modeled the problem as a behavioral cloning task and used MLP-MIXER to optimize for runtime. We made sure our model was capable of handling control noise by careful filtration of the training data and that gave us a robust model capable of completing the track even when 50% of the commands were randomly changed. The overall runtime of the model was only 2-3ms on a modern CPU.
Identification of an apoC-II variant (apoC-IIBethesda) in a kindred with apoC-II deficiency and type I hyperlipoproteinemia. (1988)

Apolipoprotein (apo) C-II deficiency is characterized by elevated plasma triglycerides, chylomicrons, and very low density lipoproteins, as well as reduced levels of low density and high density lipoproteins. A subject with apoC-II deficiency has been identified with an apoC-II plasma level of less than 0.05 mg/dl. The plasma apoC-II in the proband was immunochemically similar to apoC-II in normal subjects when analyzed by Ouchterlony immunodiffusion, however the apoC-II had an apparently lower molecular weight and higher pI when analyzed by two-dimensional gel electrophoresis. This apoC-II variant, designated apoC-IIBethesda, was not affected by neuraminidase treatment or reduction. Two-dimensional gel electrophoresis of the plasma of the mother of the proband revealed both normal apoC-II and apoC-IIBethesda, whereas analysis of the father and two siblings revealed apoC-II of normal electrophoretic mobility. These results were interpreted as indicating that the proband was a compound heterozygote with one allele for apoC-IIBethesda inherited from the mother and an allele coding for an abnormality which results in the virtual or complete absence of plasma apoC-II from the father. This proband represents the first example of a compound heterozygote for an apolipoprotein defect associated with a dyslipoproteinemia.
Modeling for Integration of Divisible Load Theory and Markov Chains (2005)

In this paper the equivalence between various divisible load-scheduling policies and continuous time Markov chains is demonstrated. The problem is to show optimal divisible load schedules for various network topologies have Markov chain analogs. This paper is a continuation of our initial short paper [1] that introduced this unification between divisible load theory and Markov chain models for the first time. A detailed analytical analysis of linear daisy chains and single and two level tree networks is presented in this paper. While most of the Markov chains are one dimensional in topology, the labeling of transitions is di#erent from the usual practice in queueing theory.
Micromechanism Force Sensing Using Coupled Cavity Laser Diode Sensor. (1996)

A high-resolution, high-speed microforce sensing method using a simple displacement sensor with coupled-cavity-laser is presented. A resolution of 0.5mN is achieved for frequencies up to 3kHz using a leaf spring with a stiffness coefficient of 500mN/μm. This method has been applied to detecting micro-frictional forces for micromechanical systems. The microscopic static- and kinetic-frictional forces have been measured and estimated under various magnitudes of load, neglecting the force of inertia.
Deep High Dynamic Range Imaging without Motion Artifacts Using Global and Local Skip Connections (2022)

This paper proposes a new HDR image generation method using a deep residual network. The proposed method aligns input images of three low dynamic range (LDR) images with different exposure times for the same scene based on the images with intermediate exposure times and uses them as input to the network. In the network, three LDR images and three images converted into high dynamic range (HDR) regions are input, and three LDR images with improved artifacts and an alpha map are output to generate HDR images. The method proposed through the experimental results can show HDR images without color distortion or ghosting artifact when compared to the existing method, and good performance compared to the HDR function used in consumer imaging systems.
A scaling law to determine phase morphologies during ion intercalation (2020)

A scaling law, based on the coarsening of the slowest phase, determines the morphologies of phase separating intercalation materials.
FRESH: Interactive Reward Shaping in High-Dimensional State Spaces using Human Feedback (2020)

Reinforcement learning has been successful in training autonomous agents to accomplish goals in complex environments. Although this has been adapted to multiple settings, including robotics and computer games, human players often find it easier to obtain higher rewards in some environments than reinforcement learning algorithms. This is especially true of high-dimensional state spaces where the reward obtained by the agent is sparse or extremely delayed. In this paper, we seek to effectively integrate feedback signals supplied by a human operator with deep reinforcement learning algorithms in high-dimensional state spaces. We call this FRESH (Feedback-based REward SHaping). During training, a human operator is presented with trajectories from a replay buffer and then provides feedback on states and actions in the trajectory. In or- der to generalize feedback signals provided by the human operator to previously unseen states and actions at test-time, we use a feed-back neural network. We use an ensemble of neural networks with a shared network architecture to represent model uncertainty and the confidence of the neural network in its output. The output of the feedback neural network is converted to a shaping reward that is augmented to the reward provided by the environment. We evaluate our approach on the Bowling and Skiing Atari games in the arcade learning environment. Although human experts have achieved high scores in these environments, state-of-the-art deep learning algorithms perform poorly. We observe that FRESH achieves much higher scores than state-of-the-art deep learning algorithms in both environments. FRESH also achieves a 21.4% higher score than a human expert in Bowling and does as well as an expert in Skiing.
A Simple, Efficient, and Eco-Friendly Method for the Preparation of 3-Substituted-2,3-dihydroquinazolin-4(1H)-one Derivatives (2019)

A simple, cost-effective method under environmentally benign conditions is a very important concept for the preparation of 2,3-dihydroquinazolin-4(1<i>H</i>)-one derivatives. The present work describes an efficient and eco-friendly protocol for the synthesis of 2-amino-<i>N</i>-(2-substituted-ethyl)benzamide and 3-substituted-2,3-dihydroquinazolin-4(1<i>H</i>)-one derivatives. The novel feature of this protocol is the use of 2-methyl tetrahydrofuran (2-MeTHF) as an eco-friendly alternative solvent to tetrahydrofuran (THF) in the first step. In the second step, methanol in the presence of potassium carbonate as a catalyst was used under conventional heating or microwave irradiation, which provided an eco-friendly method to afford the target products in excellent yields and purities. NMR (<sup>1</sup>H and <sup>13</sup>C), elemental analysis, and LC-MS confirmed the structures of all compounds. X-ray crystallography further confirmed the structure of the intermediate 2-amino-<i>N</i>-(2-substituted-ethyl)benzamide <b>3a</b>. The molecular structure of <b>3a</b> was monoclinic crystal, with <i>P</i>21/<i>c</i>, <i>a</i> = 13.6879 (11) Å, <i>b =</i> 10.2118 (9) Å, <i>c</i> = 9.7884 (9) Å, <i>β</i> = 105.068 (7)°, <i>V</i> = 1321.2 (2) Å3, and <i>Z</i> = 4.
2D to 3D Segmentation: Inclusion of Prior Information using Random Walk Kalman Filters (2021)

Augmented reality is a quickly advancing field that has the potential to provide surgeons with computer generated diagnostic results during surgery. Visual classification of diseased tissue generated during a diagnostic procedure, for example, trans-urethral cystoscopy of the urinary bladder, can aid a surgeon during the following resection to ensure no tissue is inadvertently missed. Work with 2D segmentation of camera images is well developed and frameworks already exist to fuse this data real-time in a 3D reconstruction. These existing frame-works, however, maintain only the most recent segmentation information when building the 3D reconstruction. This work proposes a method to build a 3D point cloud classification using random walk Kalman filters. The method enables retention of prior classification information and additionally provides a framework to include additional sensor classifications contributing to a single, final 3D segmentation result. The method is demonstrated using a simulated environment intended to emulate the inside of a human bladder.
New era for personalized medicine: the diagnosis and management of age‐related macular degeneration (2009)

It can be argued that age-related macular degeneration is one of the best characterized complex trait diseases. Extensive information related to genetic and environmental risk factors exists, and a number of different biological pathways are strongly implicated in its aetiology. Along with recent improvements in high throughput and relatively inexpensive genetic technologies, we are now in a position to consider developing a presymptomatic, personalized approach towards the assessment, management and treatment of this disease. We explore the applicability and challenges of this approach if it is to become commonplace for guiding treatment decisions for individuals with pre-existing disease or for those at high risk of developing it.