gebhart/patrepeval huggingface dataset:
G‐protein‐coupled receptor oligomers: two or more for what? Lessons from mGlu and GABAB receptors (2009)

G-protein-coupled receptors (GPCRs) are key players in the precise tuning of intercellullar communication. In the brain, both major neurotransmitters, glutamate and GABA, act on specific GPCRs [the metabotropic glutamate (mGlu) and GABA(B) receptors] to modulate synaptic transmission. These receptors are encoded by the largest gene family, and have been found to associate into both homo- and hetero-oligomers, which increases the complexity of this cell communication system. Here we show that dimerization is required for mGlu and GABA(B) receptors to function, since the activation process requires a relative movement between the subunits to occur. We will also show that, in contrast to the mGlu receptors, which form strict dimers, the GABA(B) receptors assemble into larger complexes, both in transfected cells and in the brain, resulting in a decreased G-protein coupling efficacy. We propose that GABA(B) receptor oligomerization offers a way to increase the possibility of modulating receptor signalling and activity, allowing the same receptor protein to have specific properties in neurons at different locations.
Improvements in estimating the spectra of random PWM waveforms (1993)

Accurate estimates of the power spectral density of random-pulse-width-modulated waveforms (RPWM) are essential in reducing the perceived acoustic emissions from modern motor control drives. It is shown that by refining the estimate of the autocorrelation function of the phase of the RPWM waveform about the origin the resulting power spectral density is greatly improved, giving excellent agreement with the observed spectrum.
Evaluating the Mobility of Nanorods in Electric Fields (2013)

The mobility of a nonspherical particle is a function of both particle shape and orientation. In turn, the higher magnitude of electric field causes nonspherical particles to align more along the field direction, increasing their mobility or decreasing their mobility diameter. In previous works, Li et al. developed a general theory for the orientation-averaged mobility and the dynamic shape factor applicable to any axially symmetric particles in an electric field, and applied it to the specific cases of nanowires and doublets of spheres. In this work, the theory for a nanowire is compared with experimental results of gold nanorods with known shape determined by TEM images. We compare the experimental measured mobility sizes with the theoretical predicted mobility in the continuum, free molecular, and the transition regime. The mobility size shift trends in the electric fields based on our model, expressed both in the free molecular regime and in the transition regime, are in good agreement with the experimental results. For rods of dimension: width dr = 17 nm and length Lr = 270 nm, where one length scale is smaller than the mean free path and one larger, the results clearly show that the flow regime of a slender rod is mostly controlled by the diameter of the rod (i.e., the smallest dimension). In this case, the free molecule transport properties best represented our nanorod. Combining both theory and experiment we show how, by evaluating the mobility as a function of applied electric field, we can extract both rod length and diameter. Copyright 2013 American Association for Aerosol Research
SDCG: Silhouette-based Deep Clustering with GNN for Improved Graph Node Clustering (2023)

Graph Neural Networks (GNNs) are powerful tools for analyzing graph-structured data in various fields because of their great expressive power for graph data. They use a message-passing mechanism to update node embeddings, which are then used for tasks such as node classification and link prediction. Recently, node embeddings have also been used in research on graph node clustering, which aims to group similar nodes based on their features and graph topology. However, traditional methods for node clustering have a limitation in that GNNs only focus on generating node embeddings without considering the ultimate objective of clustering. To address this issue, a novel technique called "Deep Clustering" has been proposed, which integrates both node embedding and clustering stages. This requires defining a new loss function by simultaneously minimizing the GNN loss and the clustering loss. Our proposed loss function incorporates not only the distance within clusters but also the distance between clusters by applying the Silhouette coefficient, which enables us to achieve better clustering results. In this paper, we propose a Silhouette-based Deep Clustering with GNN (SDCG) to more effectively cluster nodes in a graph by iteratively training the embedding model to produce embedding vectors with improved clustering results. Through extensive experiments, we demonstrate that SDCG outperforms the conventional approach of performing embedding and clustering independently.
Designing high-performance electrochemical energy-storage nanoarchitectures to balance rate and capacity (2013)

The impressive specific capacitance and high-rate performance reported for many nanometric charge-storing films on planar substrates cannot impact a technology space beyond microdevices unless such performance translates into a macroscale form factor. In this report, we explore how the nanoscale-to-macroscale properties of the electrode architecture (pore size/distribution, void volume, thickness) define energy and power performance when scaled to technologically relevant dimensions. Our test bed is a device-ready electrode architecture in which scalable, manufacturable carbon nanofoam papers with tunable pore sizes (5-200 nm) and thickness (100-300 μm) are painted with ~10 nm coatings of manganese oxide (MnOx). The quantity of capacitance and the rate at which it is delivered for four different MnOx-C variants was assessed by fabricating symmetric electrochemical capacitors using a concentrated aqueous electrolyte. Carbon nanofoam papers containing primarily 10-20 nm mesopores support high MnOx loadings (60 wt%) and device-level capacitance (30 F g(-1)), but the small mesoporous network hinders electrolyte transport and the low void volume restricts the quantity of charge-compensating ions within the electrode, making the full capacitance only accessible at slow rates (5 mV s(-1)). Carbon nanofoam papers with macropores (100-200 nm) facilitate high rate operation (50 mV s(-1)), but deliver significantly lower device capacitance (13 F g(-1)) as a result of lower MnOx loadings (41 wt%). Devices comprising MnOx-carbon nanofoams with interconnecting networks of meso- and macropores balance capacitance and rate performance, delivering 33 F g(-1) at 5 mV s(-1) and 23 F g(-1) at 50 mV s(-1). The use of carbon nanofoam papers with size-tunable pore structures and thickness provides the opportunity to engineer the electrode architecture to deliver scalable quantities of capacitance (F cm(-2)) in tens of seconds with a single device.
Synthesis of Tripeptide Mimetics Based on Dihydroquinolinone and Benzoxazinone Scaffolds (2011)

In the image: The design and synthesis of peptidomimetics that maintain the configuration of the triad Asp-Thr-Gly found in the catalytic site of the HIV-1 protease (see scheme) are described. By using regioselective nitration and reductive lactamisation, the bicyclic mimetics were constructed in a simple fashion and further equipped with appropriate protecting groups suitable for application in solid-phase peptide synthesis.
ChemInform Abstract: SYNTHETIC APPLICATIONS OF 2‐PHENYLSELENENYL ENONES. SELECTIVE FORMATION OF EXOCYCLIC OR ENDOCYCLIC ENONES FROM A COMMON INTERMEDIATE (1980)

Abstract Aus den Z‐Phenylselenenyl‐enonen (I) entstehen mit den Ii‐cupraten (II) die Enolate (III), die über (IV) zu (V) bzw. (VI) weiter umgesetzt werden können.
PSVII-14 Effects of Feeding High Level of Crystalline L-Lysine on Performance of Nursery Pigs (2022)

Abstract A total of 408 weaned pigs (19 d of age; 6.59 kg initial BW) were used in a 3-phase feeding program to evaluate effects of increasing levels of crystalline L- Lysine on performance of nursery pigs. Pigs were blocked by weaning BW and allotted to 44 pens which were assigned to one of 4 dietary treatments (9-10 pigs/pen; 11 pens/treatment), including the control diet supplemented with one of the four L-Lysine levels: 0.3% (L1), 0.5% (L2), 0.6% (L3), or 0.7% (L4). Diets were formulated to be isocaloric and contained 1.40, 1.32, and 1.25% Sid Lys for phase 1, 2, and 3, respectively. L-Val, L-His and L-Arg were included in the L2, L3, and L4 treatments in addition to DL-Met, L-Thr, L-Trp, and L-Ile which were offered in all diets. In Phase 1 (d 0-9), no effects of L-Lys levels on performance were observed (P &amp;gt; 0.10). In Phase 2 (d 9-21), increasing L-Lys from L2 to L4 Lys reduced ADG (Linear, P &amp;lt; 0.001), while L4 also reduced ADFI (Linear, P = 0.01) and feed efficiency (Linear, P &amp;lt; 0.001). In Phase 3 (d 21-42), L3 and L4 significantly improved feed efficiency (Linear, P = 0.001). Overall (d 0-42), feeding L-Lys at L4 tended to reduce ADG (Linear, P &amp;lt; 0.10) and ADFI (Linear, P &amp;lt; 0.10), while feeding L-Lys at L3 improved feed efficiency (Cubic, P &amp;lt; 0.05). Data of this study suggest that responses to high levels of L-Lys are more profound on feed efficiency during phase 2 and 3. Inclusion level of L-Lys at 0.3% is best for gain but 0.6% is the best for optimal feed efficiency. Increasing L-Lys level to 0.7% enhanced feed efficiency in phase 3, but reduced all performance measures in Ph1, 2, and overall.
Terahertz phase modulation in a slab waveguide metasurface (2017)

We describe experimental measurements and simulations of a switchable THz metasurface device in a slab waveguide geometry. The device exhibits giant phase modulation of the TE <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> mode at particular frequencies determined by the metamaterial geometry. Simulations predict that a 2π phase shift can be realized in an interaction length of only a few millimeters.
Novel magnetostrictive memory device (2000)

A stress-operated memory device consisting of an ellipsoidal magnetic particle array and an electrostrictive grid is proposed. In the device, the magnetic state of the particle can be controlled only by the magnetostriction effect. Each particle is located at the intersection of the grid and has an in-plane uniaxial anisotropy. A pair of electric contacts is connected to the end of each wire. In the writing process, the driving voltages are simultaneously applied to two pairs of the selected contacts. This allows to apply a local electric field whose direction and amplitude can be regulated by varying the voltage intensity and polarity. The exerting stress on the magnetic particle results in the linear magnetostriction and hence an additional anisotropy energy in the particle. The in-plane total energy minimum, corresponding to the magnetization direction, follows the local electric field. Consequently the magnetization of the single magnetic particle located at the intersection can therefore be selectively switched.
MID-TERM OUTCOME OF COMBINED OXFORD UNICOMPARTMENTAL KNEE REPLACEMENT AND ANTERIOR CRUCIATE LIGAMENT RECONSTRUCTION (2012)

Introduction The options for the treatment of the young active patient with unicompartmental symptomatic osteoarthritis and pre-existing Anterior Cruciate Ligament (ACL) deficiency are limited. Patients with ACL deficiency and end-stage medial compartment osteoarthritis are usually young and active. The Oxford Unicompartmental Knee Replacement (UKA) is a well established treatment option in the management of symptomatic end-stage medial compartmental osteoarthritis, but a functionally intact ACL is a pre-requisite for its satisfactory outcome. If absent, high failure rates have been reported, primarily due to tibial loosening. Previously, we have reported results on a consecutive series of 15 such patients in whom the ACL was reconstructed and patients underwent a staged or simultaneous UKA. The aim of the current study is to provide an update on the clinical and radiological outcomes of a large, consecutive cohort of patients with ACL reconstruction and UKA for the treatment of end-stage medial compartment osteoarthritis and to evaluate, particularly, the outcome of those patients under 50. Methods This study presents a consecutive series of 52 patients with ACL reconstruction and Oxford UKA performed over the past 10 years (mean follow-up 3.4 years). The mean age was 51 years (range: 36–67). Procedures were either carried out as Simultaneous (n=34) or Staged (n=18). Changes in clinical outcomes were measured using the Oxford Knee Score (OKS), the change in OKS (OKS=Post-op − Pre-op) and the American Knee Society Score (AKSS). Fluoroscopy assisted radiographs were taken at each review to assess for evidence of loosening, radiolucency progression, (if present), and component subsidence. Results Five year survival was 90%. At last follow-up, the mean outcome scores for the group were: OKS 40 (SD: 8.3), objective AKSS 77 (SD: 16.1), functional AKSS 93 (SD: 13.7) and OKS of 11. Complications were recorded in three patients, (one early infection requiring a two-stage revision, a bearing dislocation and progression of OA in the lateral compartment). 25 patients, whose procedure occurred under the age of 50, had mean outcome scores of: OKS 38 (SD: 7.7), objective AKSS 73 (SD: 20.2), functional AKSS 93 (SD: 11.9) and OKS 12. No patients had radiological evidence of component loosening. Discussion and Conclusion This study has demonstrated that combined ACL reconstruction and Oxford UKA provide good medium-term clinical and radiological results. The mobile bearing used in the Oxford knee minimises wear and our radiographic study has seen no suggestions of loosening.
Extensible indexing: a framework for integrating domain-specific indexing schemes into Oracle8i (2002)

Extensible indexing is a SQL-based framework that allows users to define domain-specific indexing schemes, and integrate them into the Oracle8i server. Users register a new indexing scheme, the set of related operators, and additional properties through SQL data definition language extensions. The implementation for an indexing scheme is provided as a set of Oracle Data Cartridge Interface (ODCIIndex) routines for index-definition, index-maintenance, and index-scan operations. An index created using the new indexing scheme, referred to as domain index, behaves and performs analogous to those built natively by the database system. The Oracle8i server implicitly invokes user-supplied index implementation code when domain index operations are performed, and executes user-supplied index scan routines for efficient evaluation of domain-specific operators. This paper provides an overview of the framework and describes the steps needed to implement an indexing scheme. The paper also presents a case study of Oracle Cartridges (intermedia text, spatial, and visual information retrieval), and Daylight (Chemical compound searching) Cartridge, which have implemented new indexing schemes using this framework and discusses the benefits and limitations.
Interactive Webtool for Tempospatial Data and Visual Audio Analysis : VAST Challenge 2018: Honorable Mention for Interactive Analytic Tool (2018)

To solve VAST Mini Challenge 1, we build an interactive visualization tool that allows hypothesis testing and exploratory analysis of the data. The tool contains different visualizations for metadata and audio data analysis. To analyze the recorded bird calls, we trained a Gradient Boosting-classifier to distinguish different bird species. Our tool integrates these results and visualizes them in combination with additional data allowing the user to get context information and confirm the results.
Observations outside the light cone: Algorithms for nonequilibrium and thermal states (2008)

We apply algorithms based on Lieb-Robinson bounds to simulate time-dependent and thermal quantities in quantum systems. For time-dependent systems, we modify a previous mapping to quantum circuits to significantly reduce the computer resources required. This modification is based on a principle of ``observing'' the system outside the light cone. We apply this method to study spin relaxation in systems started out of equilibrium with initial conditions that give rise to a very rapid entanglement growth. We also show that it is possible to approximate time evolution under a local Hamiltonian by a quantum circuit whose light cone naturally matches the Lieb-Robinson velocity. Asymptotically, these modified methods allow a doubling of the system size that one can obtain as compared to a direct simulation. We then consider a different problem of thermal properties of disordered spin chains and use quantum belief propagation to average over different configurations. We test this algorithm on one-dimensional systems with mixed ferromagnetic and antiferromagnetic bonds, where we can compare to quantum Monte Carlo, and then we apply it to the study of disordered, frustrated spin systems.
Unraveling the macromolecules formation mechanism during bio-oil catalytic hydroconversion (2016)

SSCI-VIDE+ECI2D+DLA:CGE
Metabolic and immunologic features of Chinese patients with atypical diabetes mellitus. (2000)

ADM, which was first described in African-Americans, is seen also in Chinese subjects. These patients have significant residual C-peptide secretory capacity and should not be misdiagnosed and treated as patients with type 1 diabetes with life-long insulin therapy.
Idle and busy periods in stable M/M/k queues (1998)

This paper finds the first and second moments of the number of arrivals in a stable M / M / k queue during an idle period , i.e. in a period when at least one server is idle. These and similar results are used along with renewal theory asymptotics to find the first and second moments of the proportion of arrivals occurring while there are at least ξ customers waiting for service. The asymptotics of the second moment for large ξ are established.
Host–microbiota interaction induces bi-phasic inflammation and glucose intolerance in mice (2017)

Our results provide new insights on host-microbiota interaction during colonization of GF mice and the resulting effects on adiposity and glucose metabolism in a time resolved fashion.
IL12 polarization of mouse and human T‐cells: implications for adoptive immunotherapy (2008)

Adoptive immunotherapy with TCR transduced autologous PBL can mediate objective clinical responses in patients with advanced metastatic melanoma. Different factors affecting adoptively transferred cells include avidity and affinity of the TCR, TCR expression, differentiation state, and immunological phenotype of the transferred cells. In vitro, naïve murine splenocytes can be polarized into Type 1, 2 or 3 (Treg) cells by TCR activation in the presence of specific cytokines. Here we show both TCR‐specific murine and human T‐cells can be polarized into a Type 1 phenotype by TCR stimulation in presence of IL12, using whole PBL or naïve T‐cells. In both models, IL12 polarized T‐cells produced the most IFNg in response to tumor antigen stimulation, and had the highest lytic capabilities against cognate antigen‐bearing tumor targets in vitro. Unexpectedly, IL12 programmed human T‐cells demonstrated a reduction in FoxP3+CD4+ cells, suggesting reduced Tregs, while maintaining similar expansion. We found that IL12 polarization of TCR‐specific T‐cells from both mouse and human donors resulted in similar in vitro anti‐tumor phenotypes. These results, combined with our finding that IL12 polarized cells demonstrated superior tumor regression on established tumors in an animal model, suggest the potential to utilize IL12 polarization of TCR transduced human PBL in the clinic to treat patients with cancer.
Antileukemic Activity of Shepherdin, a Novel Targeted Inhibitor of the Survivin-Hsp90 Complex. (2005)

Abstract Cancer therapy now aims at disabling critical signaling pathways essential for tumor cell maintenance without affecting normal cellular functions. The molecular interaction between heat shock protein 90 (Hsp90) and survivin functions as a crossroad to preserve cell viability and cell proliferation in malignant cells, and offers tangible therapeutic prospects. We recently used structure-based rational design to identify Shepherdin, a cell permeable peptidomimetic from the survivin sequence Lys79-Leu87, which inhibits the complex between survivin and Hsp90 in tumor cells (Kd~80 nM). Here, we tested the activity of Shepherdin against a panel of acute leukemia cell lines (AML). We identified a shorter cell-permeable Shepherdin variant Lys79-Gly83 that docked in the Hsp90 ATP pocket by molecular dynamics simulations, bound recombinant Hsp90 in vitro, and competitively inhibited the survivin-Hsp90 complex. When administered in cell culture, Shepherdin rapidly (&amp;lt;30 min) accumulated intracellularly in all AML cells tested, as well as in quiescent or phytohemagglutinin (PHA)-stimulated normal mononuclear cells. A brief, 30-min exposure of AML cells to Shepherdin was sufficient to induce complete cell killing by apoptotic and non-apoptotic mechanisms, with associated mitochondrial dysfunction and effector caspase activity. Conversely, Shepherdin did not affect colony formation of isolated CD34+ hematopoietic progenitors or viability of resting or proliferating normal mononuclear cells. When compared with known Hsp90 antagonists currently in the clinic, i.e. 17-AAG, Shepherdin was superior for rapidity and efficacy of antileukemic activity. Shepherdin induced collapse of Hsp90 chaperone functions in solid tumor cell types with destabilization of multiple Hsp90 client proteins, but did not affect the levels of pro-survival Hsp70 in AML cells, which is typically upregulated following Hsp90 inhibition by 17-AAG. In conclusion, Shepherdin provides a novel approach for rational therapy of acute leukemia.
Data-Driven Discovery of New Materials for Solid-State Batteries (2020)

All-solid-state Li-ion battery based on solid electrolytes is a promising next-generation battery technology with high energy density, intrinsic safety, long cycle life, and wide operational temperatures. However, the lack of solid electrolyte materials that satisfy multiple requirements, such as high ionic conductivity, good stability, and interfacial compatibility with the electrode, are impeding the development of this new battery technology. To resolve these materials challenges, we develop and leverage an array of data-driven computation techniques including machine learning to discover and design novel solid-state Li-ion conductors as solid electrolytes for all-solid-state batteries. The data-driven approach enables rapid searching over a large materials space of tens of thousands of materials with highly diverse structures and chemistries. Dozens of novel solid-state conductors are discovered through our data-driven materials search. Our data-driven analyses provide unique insights into the fundamental understanding about solid-state Li-ion conductors beyond traditional physical mechanistic studies. Our study demonstrates a new paradigm of using machine learning techniques for materials discovery that overcome the data-scarcity challenges. Zhang et al., “Unsupervised Discovery of Solid-State Lithium Ion Conductors”, Nature Communications, 10, 5260 (2019) DOI: 10.1038/s41467-019-13214-1 He et al., “Crystal Structural Framework of Lithium Super-Ionic Conductors”, Advanced Energy Materials 9, 1902078 (2019) DOI: 10.1002/aenm.201902078 Nolan et al., “Computation-Accelerated Design of Materials and Interfaces for All-Solid-State Lithium-Ion Batteries”, Joule, 2, 2016-2046 (2018) DOI: 10.1016/j.joule.2018.08.017