gebhart/patrepeval huggingface dataset:
Structures of <i>Saccharomyces cerevisiae</i> <i>N</i>-myristoyltransferase with Bound MyristoylCoA and Peptide Provide Insights about Substrate Recognition and Catalysis (2001)

MyristoylCoA:protein N-myristoyltransferase (Nmt) attaches myristate to the N-terminal Gly residue of proteins involved in a variety of signal transduction cascades, and other critical cellular functions. To gain insight about the structural basis of substrate recognition and catalysis, we determined the structures of a binary complex of Saccharomyces cerevisiae Nmt1p with myristoylCoA to 2.2 A resolution and of a ternary complex of Nmt1p with a nonhydrolyzable myristoylCoA analogue [S-(2-oxo)pentadecylCoA] and an octapeptide substrate (GLYASKLA) to 2.5 A resolution. The binary complex reveals how myristoylCoA alters the conformation of the enzyme to promote binding of both myristoylCoA and peptide and identifies the backbone amides of F170 and L171 as an oxyanion hole which polarizes the reactive thioester carbonyl. The ternary complex structure reveals details of the enzyme's peptide binding specificity and illuminates its mechanism of acyl transfer. The N-terminal Gly ammonium is positioned in close proximity to the C-terminal carboxylate of the protein, where it is poised to undergo the required deprotonation to an amine. In this conformation, the nucleophile is 6.3 A away from the thioester carbonyl. A catalytic mechanism is proposed whereby, once deprotonation is initiated, the N-terminal Gly amine can approximate the thioester carbonyl by rotating along Psi. This motion is facilitated by a H-bond network and leads to reaction between the glycine nitrogen nucleophile and the carbonyl. Loss of CoA from the tetrahedral intermediate may be facilitated by intramolecular H-bonding of the sulfur to the adenylamine of CoA. This affords a compact leaving group and lends a role for the observed bends in the CoA structure. The absolute requirement for Gly at the N-terminus of substrates is explained by the requirement for flexible rotation of its amine.
Reexamining Direct Cache Access to Optimize I/O Intensive Applications for Multi-hundred-gigabit Networks (2020)

Memory access is the major bottleneck in realizing multi-hundred-gigabit networks with commodity hardware, hence it is essential to make good use of cache memory that is a faster, but smaller memory closer to the processor. Our goal is to study the impact of cache management on the performance of I/O intensive applications. Specifically, this paper looks at one of the bottlenecks in packet processing, i.e., direct cache access (DCA). We systematically studied the current implementation of DCA in Intel processors, particularly Data Direct I/O technology (DDIO), which directly transfers data between I/O devices and the processor's cache. Our empirical study enables system designers/developers to optimize DDIO-enabled systems for I/O intensive applications. We demonstrate that optimizing DDIO could reduce the latency of I/O intensive network functions running at 100 Gbps by up to ~30%. Moreover, we show that DDIO causes a 30% increase in tail latencies when processing packets at 200 Gbps, hence it is crucial to selectively inject data into the cache or to explicitly bypass it.
Cell-free production of a functional oligomeric form of a Chlamydia major outer-membrane protein (MOMP) for vaccine development (2017)

Chlamydia is a prevalent sexually transmitted disease that infects more than 100 million people worldwide. Although most individuals infected with <i>Chlamydia trachomatis</i> are initially asymptomatic, symptoms can arise if left undiagnosed. Long-term infection can result in debilitating conditions such as pelvic inflammatory disease, infertility, and blindness. <i>Chlamydia</i> infection, therefore, constitutes a significant public health threat, underscoring the need for a <i>Chlamydia</i>-specific vaccine. <i>Chlamydia</i> strains express a major outer-membrane protein (MOMP) that has been shown to be an effective vaccine antigen. However, approaches to produce a functional recombinant MOMP protein for vaccine development are limited by poor solubility, low yield, and protein misfolding. Here, we used an <i>Escherichia coli</i>-based cell-free system to express a MOMP protein from the mouse-specific species <i>Chlamydia muridarum</i> (MoPn-MOMP or mMOMP). The codon-optimized mMOMP gene was co-translated with Δ49apolipoprotein A1 (Δ49ApoA1), a truncated version of mouse ApoA1 in which the N-terminal 49 amino acids were removed. This co-translation process produced mMOMP supported within a telodendrimer nanolipoprotein particle (mMOMP-tNLP). The cell-free expressed mMOMP-tNLPs contain mMOMP multimers similar to the native MOMP protein. This cell-free process produced on average 1.5 mg of purified, water-soluble mMOMP-tNLP complex in a 1-ml cell-free reaction. The mMOMP-tNLP particle also accommodated the co-localization of CpG oligodeoxynucleotide 1826, a single-stranded synthetic DNA adjuvant, eliciting an enhanced humoral immune response in vaccinated mice. Using our mMOMP-tNLP formulation, we demonstrate a unique approach to solubilizing and administering membrane-bound proteins for future vaccine development. This method can be applied to other previously difficult-to-obtain antigens while maintaining full functionality and immunogenicity.
Sequence-controlled copolymers of 2,3,4,5-pentafluorostyrene: mechanistic insight and application to organocatalysis (2013)

A number of copolymers between styrene (St) or 4-azidomethylstyrene (N3St) and 2,3,4,5,6-pentafluorostyrene (FSt) have been prepared by atom-transfer radical polymerization (ATRP) and conventional free radical polymerization (FRP). The mode of monomer alternation in copolymers has been established unambiguously using heteronuclear multiple bond correlation (HMBC) NMR. The degree and nature of monomer alternation was found to be strongly dependent on both the solvent (or lack thereof) and the polymerization initiator. These results are in contrast to previously published studies, which rely primarily on classic analysis of monomer reactivity ratios. We proceeded to independently functionalize the N3St and FSt moieties using orthogonal “click” chemistries: copper-catalyzed azide–alkyne cycloaddition (CuAAC) and fluoroarene–thiol coupling (FTC). An alternating copolymer bearing –NH2 and –SO3− functional groups was found to be a competent organocatalyst for a Henry reaction between benzaldehyde and nitromethane.
Investigation of hardware transactional memory (2015)

Thesis: M. Eng., Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, 2015.
Suppression of In Vivo Tumorigenicity of Human Lung Cancer Cells by Retrovirus-Mediated Transfer of the Human Tumor Necrosis Factor-α cDNA (1994)

The clinical use of tumor necrosis factor-alpha (TNF) is constrained by tumor cell resistance and systemic toxicity. Based on observations with murine tumors, we hypothesized that induction of local TNF production by the tumor may suppress growth of human cancer cells. To evaluate this, a human TNF cDNA was transferred to human lung cancer cell lines in vitro using a retrovirus vector to produce TNF cDNA-modified cell lines secreting TNF. In vitro cell growth was similar for parental and modified cells. All cells were resistant to TNF. The in vivo tumorigenicity of parental and modified cells was compared in nude mice. Animals injected subcutaneously with parental cells uniformly developed tumors. Tumor growth was markedly less for all modified cells, and this suppression of tumor development was reversed by anti-TNF antibody administration. Animals injected with a mixture of 50% modified and 50% parental cells or parental cell tumors injected with modified cells had decreased tumor growth, demonstrating that modified cells could suppress tumorigenicity. These data suggest that TNF can induce antitumor defenses to suppress in vivo human tumor cell growth and provide a rationale for transferring the human TNF cDNA directly to malignant cells for the therapy of human lung cancer.
Osteoclasts and giant cells: macrophage–macrophage fusion mechanism (2000)

Membrane fusion is a ubiquitous event that occurs in a wide range of biological processes. While intracellular membrane fusion mediating organelle trafficking is well understood, much less is known about cell-cell fusion mediating sperm cell-oocyte, myoblast-myoblast and macrophage-macrophage fusion. In the case of mononuclear phagocytes, their fusion is not only associated with the differentiation of osteoclasts, cells which play a key role in the pathogenesis of osteoporosis, but also of giant cells that are present in chronic inflammatory reactions and in tumours. Despite the biological and pathophysiological importance of intercellular fusion events, the actual molecular mechanism of macrophage fusion is still unclear. One of the main research themes in my laboratory has been to investigate the molecular mechanism of mononuclear phagocyte fusion. Our hypothesis has been that macrophage-macrophage fusion, similar to virus-cell fusion, is mediated by specific cell surface proteins. But, in contrast with myoblasts and sperm cells, macrophage fusion is a rare event that occurs in specific instances. To test our hypothesis, we established an in vitro cell-cell fusion assay as a model system which uses alveolar macrophages. Upon multinucleation, these macrophages acquire the osteoclast phenotype. This indicates that multinucleation of macrophages leads to a specific and novel functional phenotype in macrophages. To identify the components of the fusion machinery, we generated four monoclonal antibodies (mAbs) which block the fusion of alveolar macrophages and purified the unique antigen recognized by these mAbs. This led us to the cloning of MFR (Macrophage Fusion Receptor). MFR was cloned simultaneously as P84/SHPS-1/SIRPalpha/BIT by other laboratories. We subsequently showed that the recombinant extracellular domain of MFR blocks fusion. Most recently, we identified a lower molecular weight form of MFR that is missing two extracellular immunoglobulin (Ig) C domains. Shortly after we cloned MFR, CD47 was reported to be a ligand for P84/SIRPalpha. We have since generated preliminary results which suggest that CD47 interacts with MFR during adhesion/fusion and is a member of the fusion machinery. We also identified CD44 as a plasma membrane protein which, like MFR, is highly expressed at the onset of fusion. The recombinant soluble extracellular domain of CD44 blocks fusion by interacting with a cell-surface binding site. We now propose a model in which both forms of MFR, CD44, and CD47 mediate macrophage adhesion/fusion and therefore the differentiation of osteoclasts and giant cells.
Herpes simplex virus infection is sensed by both Toll-like receptors and retinoic acid-inducible gene- like receptors, which synergize to induce type I interferon production (2008)

The innate antiviral response is initiated by pattern recognition receptors, which recognize viral pathogen-associated molecular patterns. Here we show that retinoic acid-inducible gene (RIG)-I-like receptors (RLRs) in cooperation with Toll-like receptor (TLR) 9 is required for expression of type I interferons (IFNs) after infection with herpes simplex virus (HSV). Our work also identified RNase L as a critical component in IFN induction. Moreover, we found that TLR9 and RLRs activate distinct, as well as overlapping, intracellular signalling pathways. Thus, RLRs are important for recognition of HSV infection, and cooperate with the Toll pathway to induce an antiviral response.
Evaluation of Hemostatic and Fibrinolytic Alterations Associated with Daily Administration of Low-Molecular-Weight Heparin for a 12-Week Period (1995)

The PTCA procedure fails in 30-50% of patients due to late restinosis, meaning that this is a problem of 100,000-150,000 people per year in the USA alone. It has been found that heparin and low-molecular-weight heparin (LMWH) have an inhibitory effect on smooth muscle cell (SMC) proliferation and migration, the major causes of restinosis. However, little is known about the toxicity and side effects of these drugs when used for a long period as may be required for prophylaxis of PTCA restinosis. To investigate possible side effects, non-human primates received daily injections of 1 mg/kg s.c. LMWH (Mono-Embolex) over a 12-week period. The hemostatic system was monitored through measurement of ACT-celite, APTT, Heptest, TT(10U/mL), TFPI, Anti-IIa activity, Anti-Xa activity, ACA-Heparin, AT III, factor VIII R:Ag, fibrinogen, and thrombomodulin levels. Elisa tests for t-PA, PAI-1, u-PA, FgDP, TDP, and D-Di levels were used for measurements of fibrinolytic activity. Increased values of ACT, APTT, Heptest, TT, Anti-IIa, Anti-Xa, ACA-Heparin, and TFPI were observed four hours after LMWH injections. AT III, vWFAg, fibrinogen and thrombomodulin showed no change from the pre-study baseline. An accumulation effect was seen in the APTT and Heptest over the 12 weeks. After the first week the blood levels of Anti-IIa activity remained elevated at 20% inhibition rather than 0% 24 hrs after drug administration. This activity slowly decreased after discontinuation of drug. The Anti-Xa blood level activity remained elevated at 40% inhibition 24 hrs after drug administration 2 weeks into the study, and this activity was detectable even 2 weeks after cessation of drug administration. There was increasing activity of the fibrinolytic system with LMWH treatment. After two weeks t-PA increased two-fold to 6 ng/mL but returned to baseline at six weeks. There was a corresponding increase of the TDP but not a clear increase in D-Di and FgDP. The increase of u-PA was limited to the first days of LMWH treatment only. The PAI-1 activity increased gradually over the entire study period. No bleeding complications occurred throughout the study. The long-term administration of Mono-Embolex as projected for the use in the prophylaxis of restinosis following PTCA appears to be safe for patients.
Molecular First Hyperpolarizability Data for Lanthanate Complexes Containing the Hemicyanine Chromophore (2001)

The molecular nonlinear optical polarizability, or first hyperpolarizability β, of four lanthanate complexes containing the hemicyanine 1-hexadecyl-4-{2-[4-(dimethylamino)phenyl]ethenyl}pyridinium chromophore has been determined with high precision. The experimental measurement of the phase shift and the demodulation between immediate hyper-Rayleigh scattering and time-delayed multiphoton fluorescence as a function of modulation frequency allows for the simultaneous data analysis of phase and demodulation toward precise values for fluorescence-free hyperpolarizability, multiphoton fluorescence contribution, and fluorescence lifetime. One order of magnitude improvement in precision is obtained with respect to the earlier analysis of demodulation data only. This level of precision has been used to show the relative impact of f-orbital filling and ligands on the molecular second-order nonlinear optical response of lanthanate complexes containing a hemicyanine chromophore. Implications for the earlier conclusions about better film formation for lanthanate complexes are discussed.
Multi run ICA and surface EMG based signal processing system for recognising hand gestures (2008)

Hand gesture identification is a complex problem, where more number of muscles will be involved even for a simple hand movement. Surface electromyography (sEMG) is an indicator of muscle activity and related to body movement and posture. In the recent past sEMG had been used with various statistical signal processing technique to identify different hand gestures, but since the hand actions require simultaneous muscle contractions reliability issues exist. Recently Blind source separation (BSS) techniques like Independent Component Analysis (ICA) had been used to tackle this problem. In this paper, a novel method is proposed to enhance the performance of ICA of sEMG by decomposing the signal into components originating from different muscles. First, we use FastICA algorithm to generate random mixing matrix, and the best mixing matrix is chosen based on the highest Signal to interference ratio(SIR) of mixing matrix. Pattern classification of the separated signal is performed in the second step with a back propagation neural network. The proposed model-based approach is able to overcome the ambiguity problems (order and magnitude problem) of BSS methods by selecting an apriori mixing matrix based on known hand muscle anatomy. Testing was conducted using several single shot experiments conducted with seven subjects. The results indicate that the system is able to classify six different hand gestures with 99% accuracy.
Cost Effective Protection Techniques for TCAM Memory Arrays (2011)

This paper presents low cost techniques for error detection and correction in Ternary Content Addressable Memories (TCAMs). The techniques exploit the inherent redundancy of TCAM cells to allow for protection at lower cost. A fault detection technique with the cost of parity but with about the half probability of silent data corruption is proposed. This technique is then applied at both horizontal and vertical dimensions of the TCAM array, and a low cost error correction scheme is derived. Last, another error correction scheme is proposed, which employs a SECDED ECC of the half complexity, by making use of the TCAM redundancy, without compromising single bit error correction. The proposed schemes come with minimal area, power, and critical path overheads, in comparison with standard schemes, and they are good alternatives for TCAM arrays protection.
Optical recording of calcium and voltage transients following impulses in cell bodies and processes of identified leech neurons in culture (1987)

Optical methods were used to examine the spread of electrical potentials and the distribution and time course of calcium transients in individual identified nerve cells isolated from the leech. A photodiode array detected voltage transients by measuring absorbance changes of cells stained with the voltage-sensitive dye RH155 added to the bath. Calcium transients were recorded by measuring absorbance changes of the dye arsenazo III, which had been injected into the cells. In addition, Lucifer yellow was injected to outline the some and processes. Calcium changes resulting from individual action potentials were recorded from N, P, and Retzius cells without averaging. Signals from T cells and anterior pagoda (AP) cells were weaker but could be detected with averaging. These results are in accord with previous studies on calcium contributions to action potentials in these cells. For all cells, larger or wider action potentials gave bigger signals. Calcium changes from each of a train of action potentials were of equal amplitude, showing no sign of facilitation. Calcium transients from Retzius cells that had formed chemical synapses with P cells had properties similar to those of isolated cells. We were also able to detect responses from prolonged subthreshold depolarizations to -40 mV from a hyperpolarized membrane potential (-65 mV). These signals rose throughout the duration of the pulse (1-2 sec). With the photodiode array we mapped the distribution of the calcium signals. The amplitudes from each pixel are proportional to the amount of calcium entering that element in response to the stimulating pulse, if the simplifying assumption is made that the calcium buffering of the cytoplasm is uniform throughout the cell. The largest signals were detected over the axon stump left from the cell isolation procedure. Large signals were also detected from the soma. Weak signals were detected from the processes of some cells. From many Retzius cells, no signals at all were detected from the newly formed processes. Using the photodiode array, we also recorded voltage transients from the cells. Signals were recorded from all over the arborization of the neuron, with no obvious variation in time course, showing that the entire cell, including fine slender processes and broad growth cones, was essentially isopotential. Combining these observations with the measured distribution of calcium transients in the same cell suggests that the density of calcium channels in most cells is less in the outgrowing processes than in the soma or axon stump.
A Downlink Adaptive Transmitting Antenna Method For T/F/Sdma Fdd Systems Avoiding Doa Estimation (1998)

Publication in the conference proceedings of EUSIPCO, Rhodes, Greece, 1998
Solar Photovoltaic Array's Shadow Evaluation Using Neural Network with On-Site Measurement (2007)

This paper proposes a method to accurately predict the maximum output power of the solar photovoltaic arrays under the shadow conditions by using neural network, a combined method using the multilayer perceptrons feed forward network and the backpropagation algorithm. Using the solar irradiation levels, the ambient temperature and the sun's position angles as the input signals, and the maximum output power of the solar photovoltaic array as an output signal, the training data for the neural network is received by measurement on a particular time, when solar panel is shaded. After training, the neural network model's accuracy and generalization are verified by the test data. This model, which is called the shading function, is able to predict the shadow effects on the solar PV arrays for long term with low computational efforts.
Propylene Oxide (2012)

Abstract The article contains sections titled: 1. Introduction 2. Physical Properties 3. Chemical Properties 4. Production and Raw Materials 4.1. Production Route via Propylene Chlorohydrin 4.1.1. Chlorohydrin Process 4.1.2. Other Chlorohydrin Technologies 4.2. Coproduct Routes 4.2.1. Methyl Tert ‐Butyl Ether (MTBE) 4.2.2. Propylene Oxide Styrene Monomer (POSM) 4.2.3. Cumene–PO Route 4.3. Hydrogen Peroxide Routes 4.3.1. Peracetic Acid Route 4.3.2. Hydrogen Peroxide to Propylene Oxide (HPPO) 4.3.3. Hydrogen Peroxide/Hydrogen Peroxide to Propylene Oxide (HP/HPPO) 4.4. Direct Oxidation Route (DOPO) 4.5. Hydro Oxidation Route (HOPO) 4.6. Comparison of the Various Propylene Oxide Routes 5. Environmental Protection and Ecotoxicology 6. Quality Specifications and Analysis 7. Handling, Storage, and Transportation 8. Uses 9. Economic Aspects 10. Toxicology and Occupational Health
A-GAP: An Adaptive Protocol for Continuous Network Monitoring with Accuracy Objectives (2007)

We present A-GAP, a novel protocol for continuous monitoring of network state variables, which aims at achieving a given monitoring accuracy with minimal overhead. Network state variables are computed from device counters using aggregation functions, such as SUM, AVERAGE and MAX. The accuracy objective is expressed as the average estimation error. A-GAP is decentralized and asynchronous to achieve robustness and scalability. It executes on an overlay that interconnects management processes on the devices. On this overlay, the protocol maintains a spanning tree and updates the network state variables through incremental aggregation. Based on a stochastic model, it dynamically configures local filters that control whether an update is sent towards the root of the tree. We evaluate A-GAP through simulation using real traces and two different types of topologies of up to 650 nodes. The results show that we can effectively control the trade-off between accuracy and protocol overhead, and that the overhead can be reduced by almost two orders of magnitude when allowing for small errors. The protocol quickly adapts to a node failure and exhibits short spikes in the estimation error. Lastly, it can provide an accurate estimate of the error distribution in real-time.