gebhart/patrepeval huggingface dataset:
The immunocytochemical localization of enkephalin in the central nervous system of the rat (1981)

The immunocytochemical localization of enkephalin-like immunoreactivity (ELI) throughout the rat central nervous system (CNS) was investigated. The detection of ELI-containing structures was facilitated through the use of (1) brains from colchicine-treated rats, (2) the proteolytic pretreatment of sections with pronase and (3) the "double-bridge" staining technique. Our findings confirm the presence of ELI in perikarya, neuronal processes and terminals in many areas of the CNS. In addition, the localization of ELI-containing perikarya is reported for the first time in the following areas: the olfactory bulb, the olfactory tubercle, the lateral preoptic nucleus, several nuclei within the amygdaloid nuclear complex, the hippocampus, the neocortex, the cingulate cortex, the posterior mammillary nucleus, the medial nucleus of the optic tract, the brachium of the inferior colliculus, the ventral tegmental nucleus, the locus ceruleus, the sub-ceruleal region, the lateral trapezoid nucleus, the nucleus reticularis lateralis, and lamina VII of the cervical spinal cord. Our results demonstrate ELI in neurons which are heterogeneous in size, some probably functioning as interneurons and others as projection neurons in different areas of the CNS. The location of these neurons within the brain suggests that these pentapeptides serve diverse functions which include, in addition to nociception, the regulation of neuroendocrine, respiratory, auditory, vestibular, and olfactory functions.
Transient retroviral transfection for single patient cancer immunotherapy (2015)

Kriley, Isaac R. MD; Feldman, Steve A.; Tran, Eric; Black, Mary; Xu, Hui; Rosenberg, Steven A. MD, PhD; Goff, Stephanie MD Author Information
Mechanism-Based Post-Translational Modification and Inactivation in Terpene Synthases (2015)

Terpenes are ubiquitous natural chemicals with diverse biological functions spanning all three domains of life. In specialized metabolism, the active sites of terpene synthases (TPSs) evolve in shape and reactivity to direct the biosynthesis of a myriad of chemotypes for organismal fitness. As most terpene biosynthesis mechanistically involves highly reactive carbocationic intermediates, the protein surfaces catalyzing these cascade reactions possess reactive regions possibly prone to premature carbocation capture and potentially enzyme inactivation. Here, we show using proteomic and X-ray crystallographic analyses that cationic intermediates undergo capture by conserved active site residues leading to inhibitory self-alkylation. Moreover, the level of cation-mediated inactivation increases with mutation of the active site, upon changes in the size and structure of isoprenoid diphosphate substrates, and alongside increases in reaction temperatures. TPSs that individually synthesize multiple products are less prone to self-alkylation then TPSs possessing relatively high product specificity. In total, the results presented suggest that mechanism-based alkylation represents an overlooked mechanistic pressure during the evolution of cation-derived terpene biosynthesis.
Simplified Dynamic SC-Flip Polar Decoding (2020)

SC-Flip (SCF) decoding is a low-complexity polar code decoding algorithm alternative to SC-List (SCL) algorithm with small list sizes. To achieve the performance of the SCL algorithm with large list sizes, the Dynamic SC-Flip (DSCF) algorithm was proposed. However, DSCF involves logarithmic and exponential computations that are not suitable for practical hardware implementations. In this work, we propose a simple approximation that replaces the transcendental computations of DSCF decoding. Moreover, we show how to incorporate fast decoding techniques with the DSCF algorithm. With proposed approaches, the computational complexity of DSCF decoding is remarkably reduced while maintaining equivalent decoding performance.
Mapping the Active Site of the Bacterial Enzyme LpxC Using Novel Carbohydrate‐Based Hydroxamic Acid Inhibitors* (2005)

LpxC (UDP-3-O-(R-3-hydroxymyristoyl)-GlcNAc deacetylase), an enzyme involved in the biosynthesis of lipid A, is crucial for the growth of Gram-negative bacteria. This enzyme has accordingly been identified as a potential target for the development of novel antibiotics against Gram-negative bacteria. The carbohydrate-derived hydroxamic acid 1 (1,5-anhydro-2-C- (carboxymethyl N-hydroxyamide)-2-deoxy-3-O-myristoyl-D-glucitol) was previously shown to exhibit a wide spectrum of inhibitory activity against LpxC enzymes. Here we describe the preparation of seven analogs of 1 and their enzymatic evaluation. Two of the hydroxyl groups (OH-3 and 6) of the GlcNAc residue were found to be involved in the binding interaction, and there is an important hydrophobic interaction in the vicinity O-3 position with the enzyme that recognizes aromatic as well as aliphatic substituents. Copyright © Taylor &amp; Francis, Inc.
Design and optimisation of dendrimer-conjugated Bcl-2/xL inhibitor, AZD0466, with improved therapeutic index for cancer therapy (2021)

Dual Bcl-2/Bcl-x<sub>L</sub> inhibitors are expected to deliver therapeutic benefit in many haematological and solid malignancies, however, their use is limited by tolerability issues. AZD4320, a potent dual Bcl-2/Bcl-x<sub>L</sub> inhibitor, has shown good efficacy however had dose limiting cardiovascular toxicity in preclinical species, coupled with challenging physicochemical properties, which prevented its clinical development. Here, we describe the design and development of AZD0466, a drug-dendrimer conjugate, where AZD4320 is chemically conjugated to a PEGylated poly-lysine dendrimer. Mathematical modelling was employed to determine the optimal release rate of the drug from the dendrimer for maximal therapeutic index in terms of preclinical anti-tumour efficacy and cardiovascular tolerability. The optimised candidate is shown to be efficacious and better tolerated in preclinical models compared with AZD4320 alone. The AZD4320-dendrimer conjugate (AZD0466) identified, through mathematical modelling, has resulted in an improved therapeutic index and thus enabled progression of this promising dual Bcl-2/Bcl-x<sub>L</sub> inhibitor into clinical development.
Dopant Concentration Dependence of Luminescence in Cu-doped Lithium Aluminophosphate Glasses (2019)

We have prepared glasses with the composition of Cu-doped 30Li 3 PO 4 -70Al(PO 3 ) 3 and investigated their luminescence characteristics. The glass samples were synthesized by the melt quenching method, and the Cu concentrations of the prepared samples were 0.1, 0.2, 0.5, and 1.0%. In the absorption spectrum, the absorptions due to Cu + and Cu 2+ around 290 and 850 nm were observed, respectively. The absorption due to Cu 2+ increased in proportion to the amount of Cu. In the photoluminescence (PL) decay curve, the PL decay time was a typical value of the 3d 9 4s 1 -3d 10 transition of Cu + (~30 s). The scintillation spectra showed a broad emission band from 400 to 600 nm, and the emission intensities were proportional to the Cu concentration.
Sensing Nerve Activity with Scalable and Robust Nerve Interfaces (2019)

Sensing the electrical activity of peripheral nerves with high spatial resolution is needed to accurately capture dynamic and detailed movement intent of amputees and could be helpful to adapt the treatment of other disease states through closed-loop neuromodulation of bioelectronic medicines. However, existing nerve interfaces have designs that significantly limit their recording performance. To overcome these limitations, we have combined micromachined neural interfaces with tissue- engineered hydrogel-based scaffolds. These tissue-engineered electronic nerve interfaces (TEENI) enable highly scalable nerve interfaces that provide significant interface-design freedom. To speed the development of a robust microfabrication processes, a high-temperature reactive-accelerated-aging (RAA) soak test is used. Chronic electrophysiological experiments demonstrate high- SNR recording performance for implanted TEENI devices.
Correction: Biofunctional Janus particles promote phagocytosis of tumor cells by macrophages (2022)

[This corrects the article DOI: 10.1039/D0SC01146K.].
Bursting Scientific Filter Bubbles: Boosting Innovation via Novel Author Discovery (2022)

Isolated silos of scientific research and the growing challenge of information overload limit awareness across the literature and hinder innovation. Algorithmic curation and recommendation, which often prioritize relevance, can further reinforce these informational “filter bubbles.” In response, we describe Bridger, a system for facilitating discovery of scholars and their work. We construct a faceted representation of authors with information gleaned from their papers and inferred author personas, and use it to develop an approach that locates commonalities and contrasts between scientists to balance relevance and novelty. In studies with computer science researchers, this approach helps users discover authors considered useful for generating novel research directions. We also demonstrate an approach for displaying information about authors, boosting the ability to understand the work of new, unfamiliar scholars. Our analysis reveals that Bridger connects authors who have different citation profiles and publish in different venues, raising the prospect of bridging diverse scientific communities.
Tentacular Artificial Intelligence, and the Architecture Thereof, Introduced (2018)

We briefly introduce herein a new form of distributed, multi-agent artificial intelligence, which we refer to as "tentacular." Tentacular AI is distinguished by six attributes, which among other things entail a capacity for reasoning and planning based in highly expressive calculi (logics), and which enlists subsidiary agents across distances circumscribed only by the reach of one or more given networks.
Intra-cavity patterning for mode control in 13μm coupled VCSEL arrays (2011)

We report coupled VCSEL arrays, emitting at 1.3 μm wavelength, in which both the optical gain/loss and refractive index distributions were defined on different vertical layers. The arrays were electrically pumped through a patterned tunnel junction, whereas the array pixels were realized by intra-cavity patterning using sub-wavelength air gaps. Stable oscillations in coupled modes were evidenced for 2x2 array structures, from threshold current up to thermal roll-over, using spectrally resolved field pattern analysis.
Intramolecular Charge-Transfer Tuning of Perylenes:  Spectroscopic Features and Performance in Dye-Sensitized Solar Cells (2007)

Five novel perylene molecules with different intramolecular charge-transfer (ICT) characters have been synthesized. The relation between the ICT character for different donating groups and the results for their electro- and photochemical properties as well as their performance in nanostructured dye-sensitized solar cells (nDSC) are reported. With the stronger donors, we obtain a shift of the lowest unoccupied molecular orbital (LUMO) to more negative potential versus normal hydrogen electrode (NHE) as well as an increase the charge separation in the dye upon excitation. Ab initio calculations were used to analyze the effects on orbital energies and electron distribution with the different donors. Incorporating the dyes in nDSCs, we see a drastical improvement in the performance for the more polar dyes. In particular, we find a much improved photovoltage because of higher LUMO levels, allowing conduction band tuning in the TiO2 as well as a contribution from the permanent dipoles in the dyes. The photocurrent improves remarkably with increasing ICT character of the dyes. The external quantum efficiency reached over 70%, and the overall solar-to-electrical energy conversion efficiency was improved to almost 4% for the dye with highest ICT character, which can be compared with devices with the standard N719 dye (Ru(dcbpy)2(NCS)2) showing 6% under similar conditions. The performance is a significant improvement compared to previous reports for perylenes and lifts the performance from modest to promising. Initial stability tests show that the dye with the highest performance was spectrally stable after more than 2000 h of irradiation in a solar-cell device.
Protein Hal: Partial Deletion of a “γ” Immunoglobulin Gene(s) and Apparent Reinitiation at an Internal AUG Codon (1973)

Protein Hal is a human gamma4 heavy-chain disease protein whose molecular weight is reduced from 55,000 to 25,000 in 6 M guanidine due to the lack of disulfide bonds between heavy chains. Studies of aminoacid sequence indicate that it contains a gap of about 240 residues, starting 10 residues from the N-terminal end and including the rest of the Fd fragment, as well as the hinge region. Normal sequence apparently resumes at a methionine residue (position 252) in the second constant domain (C(H)2) and seems normal from there to the carboxyl end of the molecule. These results imply that reinitiation of translation at an internal AUG codon occurs in protein Hal.
Physical map of a Plutella xylostella granulovirus genome. (2000)

A plasmid library of restriction DNA fragments of a Plutella xylostella granulovirus (PxGV) was constructed, which covered all 9 EcoRI and all 19 HindIII fragments, and 18 of 20 PstI fragments. Restriction endonuclease analysis and DNA-DNA hybridization analysis of the cloned viral DNA fragments in the library and the restricted viral DNA fragments were carried out for construction of a physical map of PxGV DNA for ApaI, BamHI, BglII, EcoRI, HindIII, KpnI, PstI, SacII, XbaI and XhoI. The size of PxGV genome was estimated to be 102.2 kb. Location of the left-most DNA fragment on the physical map that contained granulin gene was determined by hybridization using a DNA probe of granulin gene of Trichoplusia ni granulovirus. Four homologous regions interspersed on the genome were also determined by DNA-DNA hybridization analysis.
Injectorless quantum cascade lasers for room-temperature short-wavelength emission by efficient second-harmonic generation (2010)

In this paper we demonstrate RT second-harmonic generation around 2.7 μm with peak output powers close to 10 μW at current densities of around 2 kA/cm2. We also discuss possible device structures for wavelengths around 3.5 μm and a future development strategy for single-mode, two-color tunable laser sources.
Selective Hartmann-Hahn Transfer in Liquids (2011)

Magnetization can be transferred selectively between chosen pairs of spins in liquids by suitable radio-frequency irradiation schemes.
Neurally dissociable cognitive components of reading deficits in subacute stroke (2015)

According to cognitive models of reading, words are processed by interacting orthographic (spelling), phonological (sound), and semantic (meaning) information. Despite extensive study of the neural basis of reading in healthy participants, little group data exist on patients with reading deficits from focal brain damage pointing to critical neural systems for reading. Here, we report on one such study. We have performed neuropsychological testing and magnetic resonance imaging on 11 patients with left-hemisphere stroke (<=5 weeks post-stroke). Patients completed tasks assessing cognitive components of reading such as semantics (matching picture or word choices to a target based on meaning), phonology (matching word choices to a target based on rhyming), and orthography (a two-alternative forced choice of the most plausible non-word). They also read aloud pseudowords and words with high or low levels of usage frequency, imageability, and spelling-sound consistency. As predicted by the cognitive model, when averaged across patients, the influence of semantics was most salient for low-frequency, low-consistency words, when phonological decoding is especially difficult. Qualitative subtraction analyses revealed lesion sites specific to phonological processing. These areas were consistent with those shown previously to activate for phonology in healthy participants, including supramarginal, posterior superior temporal, middle temporal, inferior frontal gyri, and underlying white matter. Notable divergence between this analysis and previous functional imaging is the association of lesions in the mid-fusiform gyrus and anterior temporal lobe with phonological reading deficits. This study represents progress toward identifying brain lesion-deficit relationships in the cognitive components of reading. Such correspondences are expected to help not only better understand the neural mechanisms of reading, but may also help tailor reading therapy to individual neurocognitive deficit profiles.
Fast and Scalable Expansion of Natural Language Understanding Functionality for Intelligent Agents (2018)

Anuj Kumar Goyal, Angeliki Metallinou, Spyros Matsoukas. Proceedings of the 2018 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, Volume 3 (Industry Papers). 2018.
Contrasting responses within a single neuron class enable sex-specific attraction in Caenorhabditis elegans (2016)

Animals find mates and food, and avoid predators, by navigating to regions within a favorable range of available sensory cues. How are these ranges set and recognized? Here we show that male Caenorhabditis elegans exhibit strong concentration preferences for sex-specific small molecule cues secreted by hermaphrodites, and that these preferences emerge from the collective dynamics of a single male-specific class of neurons, the cephalic sensory neurons (CEMs). Within a single worm, CEM responses are dissimilar, not determined by anatomical classification and can be excitatory or inhibitory. Response kinetics vary by concentration, suggesting a mechanism for establishing preferences. CEM responses are enhanced in the absence of synaptic transmission, and worms with only one intact CEM show nonpreferential attraction to all concentrations of ascaroside for which CEM is the primary sensor, suggesting that synaptic modulation of CEM responses is necessary for establishing preferences. A heterogeneous concentration-dependent sensory representation thus appears to allow a single neural class to set behavioral preferences and recognize ranges of sensory cues.
Root causing flaky tests in a large-scale industrial setting (2019)

In today’s agile world, developers often rely on continuous integration pipelines to help build and validate their changes by executing tests in an efficient manner. One of the significant factors that hinder developers’ productivity is flaky tests—tests that may pass and fail with the same version of code. Since flaky test failures are not deterministically reproducible, developers often have to spend hours only to discover that the occasional failures have nothing to do with their changes. However, ignoring failures of flaky tests can be dangerous, since those failures may represent real faults in the production code. Furthermore, identifying the root cause of flakiness is tedious and cumbersome, since they are often a consequence of unexpected and non-deterministic behavior due to various factors, such as concurrency and external dependencies.
Mutant p53 proteins bind DNA abnormally in vitro. (1991)

The p53 gene encodes a phosphoprotein which binds DNA. Many types of tumors contain mutant p53 genes, but the effects of these mutations on the intrinsic properties of p53 are largely unknown. In the present study, we tested the effect of p53 mutations on DNA-binding. Each of 15 different mutant p53 gene products derived from human tumors or mouse transformants bound calf thymus DNA more weakly than did wild-type products. A significant subset of mutant proteins were also found to be underphosphorylated compared to the wild-type protein when produced in a reticulocyte lysate system, but this did not appear to explain the pattern of alterations of DNA-binding. The tested mutations were dispersed over several regions of the p53 gene and included representatives of all four of the evolutionarily conserved domains that are the known 'hot spots' for p53 mutation. The results suggest common pathways by which these various mutations affect the normal function of p53.
Dicarboxylic acids may compete with standard vulcanisation processes for crosslinking expoxidised natural rubber (2013)

International audience
Overhead-Free Channel Estimation using Implicit Training for Polarization-Multiplexed Coherent Optical Systems (2013)

Implicit training is successfully demonstrated for the first time in a 40-Gb/s QPSK experiment and 224-Gb/s 16-QAM simulation. Overhead-free transmission can be achieved with less than 0.5 dB Q-penalty compared to traditional explicit training scheme.
Propagation, detection and containment of mobile malware (2008)

Today's enterprise systems and networks are frequent targets of malicious attacks, such as worms, viruses, spyware and intrusions that can disrupt, or even disable critical services. Recent trends suggest that by combining spyware as a malicious payload with worms as a delivery mechanism, malicious programs can potentially be used for industrial espionage and identity theft. The problem is compounded further by the increasing convergence of wired, wireless and cellular networks, since virus writers can now write malware that can crossover from one network segment to another, exploiting services and vulnerabilities specific to each network. This dissertation makes four primary contributions. First, it builds more accurate malware propagation models for emerging hybrid malware (i.e., malware that use multiple propagation vectors such as Bluetooth, Email, Peer-to-Peer, Instant Messaging, etc.), addressing key propagation factors such as heterogeneity of nodes, services and user mobility within the network. Second, it develops a proactive containment framework based on group-behavior of hosts against such malicious agents in an enterprise setting. The majority of today's anti-virus solutions are reactive, i.e., these are activated only after a malicious activity has been detected at a node in the network. In contrast, proactive containment has the potential of closing the vulnerable services ahead of infection, and thereby halting the spread of the malware. Third, we study (1) the current-generation mobile viruses and worms that target SMS/MMS messaging and Bluetooth on handsets, and the corresponding exploits, and (2) their potential impact in a large SMS provider network using real-life SMS network data. Finally, we propose a new behavioral approach for detecting emerging malware targeting mobile handsets. Our approach is based on the concept of generalized behavioral patterns instead of traditional signature-based detection. The signature-based methods are not scalable for deployment in mobile devices due to limited resources available on today's typical handsets. Further, we demonstrate that the behavioral approach not only has a compact footprint, but also can detect new classes of malware that combine some features from existing classes of malware.