gebhart/patrepeval huggingface dataset:
A High-Throughput 1,536-Well Luminescence Assay for Glutathione S-Transferase Activity (2010)

Glutathione S-transferases (GSTs) constitute a family of detoxification enzymes that catalyze the conjugation of glutathione with a variety of hydrophobic compounds, including drugs and their metabolites, to yield water-soluble derivatives that are excreted in urine or bile. Profiling the effect of small molecules on GST activity is an important component in the characterization of drug candidates and compound libraries. Additionally, specific GST isozymes have been implicated in drug resistance, especially in cancer, and thus represent potential targets for intervention. To date, there are no sensitive miniaturized high-throughput assays available for GST activity detection. A series of GST substrates containing a masked luciferin moiety have been described recently, offering the potential for configuring a sensitive screening assay via coupled luciferase reaction and standard luminescence detection. We report on the optimization and miniaturization of this homogeneous method to 1,536-well format using GSTs from 3 different species: mouse isozyme A4-4, human isozymes A1-1, M1-1, and P1-1, and the major GST from the parasitic worm Schistosoma japonicum.
SpeCollate: Deep cross-modal similarity network for mass spectrometry data based peptide deductions (2021)

Historically, the database search algorithms have been the de facto standard for inferring peptides from mass spectrometry (MS) data. Database search algorithms deduce peptides by transforming theoretical peptides into theoretical spectra and matching them to the experimental spectra. Heuristic similarity-scoring functions are used to match an experimental spectrum to a theoretical spectrum. However, the heuristic nature of the scoring functions and the simple transformation of the peptides into theoretical spectra, along with noisy mass spectra for the less abundant peptides, can introduce a cascade of inaccuracies. In this paper, we design and implement a Deep Cross-Modal Similarity Network called SpeCollate, which overcomes these inaccuracies by learning the similarity function between experimental spectra and peptides directly from the labeled MS data. SpeCollate transforms spectra and peptides into a shared Euclidean subspace by learning fixed size embeddings for both. Our proposed deep-learning network trains on sextuplets of positive and negative examples coupled with our custom-designed SNAP-loss function. Online hardest negative mining is used to select the appropriate negative examples for optimal training performance. We use 4.8 million sextuplets obtained from the NIST and MassIVE peptide libraries to train the network and demonstrate that for closed search, SpeCollate is able to perform better than Crux and MSFragger in terms of the number of peptide-spectrum matches (PSMs) and unique peptides identified under 1% FDR for real-world data. SpeCollate also identifies a large number of peptides not reported by either Crux or MSFragger. To the best of our knowledge, our proposed SpeCollate is the first deep-learning network that can determine the cross-modal similarity between peptides and mass-spectra for MS-based proteomics. We believe SpeCollate is significant progress towards developing machine-learning solutions for MS-based omics data analysis. SpeCollate is available at https://deepspecs.github.io/.
Emotive, cognitive and motor rehabilitation post severe traumatic brain injury-A new convergent approach (2011)

Standard of care treats emotive, cognitive and motor rehabilitation needs post severe traumatic brain injury separately. This paper proposes an alternative in the form of convergent rehabilitation, which uses virtual environments to treat the three domains simultaneously. Two clients chronic post severe TBI participated in a feasibility study in which they practiced their affected upper extremity playing custom video games on the Rutgers Arm II. The ABAA protocol consisted of neuro-psychological and motor evaluation pre-, 18 training sessions, then motor and neuro-psychological evaluations post-and at 6 weeks follow up. Training sessions were gradated in duration, difficulty, included dual-tasks, and rewards for good performance. Participants improved in depression, focusing, executive function, shoulder strength and one was faster on the Jebsen test of hand function. Most gains were maintained at follow-up and resulted in improved independence in activities of daily living. Participants liked the technology, giving it a subjective rating of 4.45 out of 5.
Estimation of local subgraph counts (2016)

Graphlets represent small induced subgraphs and are becoming increasingly important for a variety of applications. Despite the importance of the local subgraph (graphlet) counting problem, existing work focuses mainly on counting graphlets globally over the entire graph. These global counts have been used for tasks such as graph classification as well as for understanding and summarizing the fundamental structural patterns in graphs. In contrast, this work proposes an accurate, efficient, and scalable parallel framework for the more challenging problem of counting graphlets locally for a given edge or set of edges. The local graphlet counts provide a topologically rigorous characterization of the local structure surrounding an edge. The aim of this work is to obtain the count of every graphlet of size k for each edge. The framework gives rise to efficient, parallel, and accurate unbiased estimation methods with provable error bounds, as well as exact algorithms for counting graphlets locally. Experiments demonstrate the effectiveness of the proposed exact and estimation methods on various datasets. In particular, the exact methods show strong scaling results (11-16x on 16 cores). Moreover, our estimation framework is accurate with error less than 5% on average.
First report of scaling a normally-off in-situ oxide, GaN interlayer based vertical trench MOSFET (OG-FET) (2017)

GaN lateral transistors (HEMTs) continue to penetrate the power electronics market demonstrating excellent performance in the medium power applications. However, for power applications 10kW and higher, vertical GaN devices are preferred over lateral one, since the former offers higher current and power densities. To date, several different vertical transistor structures have been proposed and reported, such as in-situ oxide based vertical trench MOSFET with an undoped GaN interlayer as a channel (OGFET) [1, 2], current aperture vertical electron transistors (CAVETs) [3, 4], junction field effect transistors (JFETs) [5, 6] and MOSFETs [7, 8]. Gupta et al. have demonstrated the high performance OGFET with low specific on-state resistance (Ron, sp) recently [1]. This study presents the large device scaling of the OGFET to realize high output current.
An intelligent WWW agent for similarity-based searching (1997)

This paper describes the development of a WWW agent that uses similarity-based methods to search the Internet.The Internet Information Agent (IIA) works by analysing a sample of the type of text that is known to be of interest to the user.It then extracts a number of linguistic features and stores these as a feature vector that is used to describe the content of the document.This data is then used as input to a range of similarity metrics that allow the agent to compare new texts with the original and thereby acquire "more of the same".The agent's strengths lie in its use of a range of similarity metrics that are known to perform well over a wide variety of input.The agent has been tested across a range of input data and evaluated against a number of criteria.The results of this evaluation are described and the prospects for the ongoing development of the agent are discussed.
NanoMap (2007)

NATURE is a recently developed hybrid nano/CMOS reconfigurable architecture. It consists of complementary metal-oxide semiconductor (CMOS) reconfigurable logic and interconnect fabric, and carbon nanotube-based non-volatile onchip configuration memory. Compared to existing CMOS-based field-programmable gate arrays (FPGAs), NATURE increases logic density by more than an order of magnitude and offers cycle-by-cycle run-time reconfiguration capability. As opposed to some other recently proposed hybrid nano/CMOS designs, which mostly rely on the not-yet-mature self-assembly fabrication process, NATURE is compatible with mainstream photolithography fabrication techniques. Thus, NATURE offers a commercially feasible technology with high performance, superior integration density, and excellent run-time flexibility.
A Hand-Held, Intra-Operative Positron Imaging Probe for Surgical Applications (2015)

We have developed a prototype intra-operative β <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> imaging probe to help tumor removal and malignant tissue resection. The probe can be used during surgery to provide clear delineation of malignant tissues. Our probe consists of a hybrid scintillator coupled to a silicon photomultiplier (SiPM) array with associated front-end electronics encapsulated in an ergonomic aluminum housing. Pulse shape discrimination electronics has been implemented and integrated into the downstream data acquisition system. The field of view of the probe is 10 ×10 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> realized by a 0.4 mm thick CsI:Tl scintillator coupled to a 1 mm thick LYSO. While CsI:Tl layer acts as β <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> sensitive detector, LYSO detects gamma radiation where the gamma response can be subtracted from the total signal to improve SNR and contrast. The thickness of the LYSO scintillator is optimized such that it acts as light diffuser to spread the scintillation light generated in CsI:Tl over multiple SiPM pixels for accurate estimation of the β <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> interaction location. The probe shows FWHM spatial resolution in the presence of large background radiation. The probe was used to study rabbits with tongue tumors. The experimental results show that the probe can successfully locate the tongue tumors in its active imaging area.
Volumetric Photoacoustic Endoscopy (2012)

Photoacoustic endoscopy provides unique functional information through its broad spectroscopic imaging capability. The imaging results presented here suggest its potential for use as a comprehensive endoscopic tool in various medical applications.
SrB<sub>5</sub>O<sub>7</sub>F<sub>3</sub> Functionalized with [B<sub>5</sub>O<sub>9</sub>F<sub>3</sub>]<sup>6−</sup> Chromophores: Accelerating the Rational Design of Deep‐Ultraviolet Nonlinear Optical Materials (2018)

Fluorooxoborates, benefiting from the large optical band gap, high anisotropy, and ever-greater possibility to form non-centrosymmetric structures activated by the large polarization of [BO<sub>x</sub> F<sub>4-x</sub> ]<sup>(x+1)-</sup> building blocks, have been considered as the new fertile fields for searching the ultraviolet (UV) and deep-UV nonlinear optical (NLO) materials. Herein, we report the first asymmetric alkaline-earth metal fluorooxoborate SrB<sub>5</sub> O<sub>7</sub> F<sub>3</sub> , which is rationally designed by taking the classic Sr<sub>2</sub> Be<sub>2</sub> B<sub>2</sub> O<sub>7</sub> (SBBO) as a maternal structure. Its [B<sub>5</sub> O<sub>9</sub> F<sub>3</sub> ]<sup>6-</sup> fundamental building block with near-planar configuration composed by two edge-sharing [B<sub>3</sub> O<sub>6</sub> F<sub>2</sub> ]<sup>5-</sup> rings in SrB<sub>5</sub> O<sub>7</sub> F<sub>3</sub> has not been reported in any other borates. Solid state <sup>19</sup> F and <sup>11</sup> B magic-angle spinning NMR spectroscopy verifies the presence of covalent B-F bonds in SrB<sub>5</sub> O<sub>7</sub> F<sub>3</sub> . Property characterizations reveal that SrB<sub>5</sub> O<sub>7</sub> F<sub>3</sub> possesses the optical properties required for deep-UV NLO applications, which make SrB<sub>5</sub> O<sub>7</sub> F<sub>3</sub> a promising crystal that could produce deep-UV coherent light by the direct SHG process.
Effects of overexpression of jasmonic acid biosynthesis genes on nicotine accumulation in tobacco (2018)

Nicotine is naturally synthesized in tobacco roots and accumulates in leaves as a defense compound against herbivory attack. Nicotine biosynthesis pathway has been extensively studied with major genes and enzymes being isolated and functionally characterized. However, the molecular regulation of nicotine synthesis has not been fully understood. The phytohormone jasmonic acid (JA) mediates many aspects of plant defense responses including nicotine biosynthesis. In this study, five key genes (<i>AtLOX2</i>, <i>AtAOS</i>, <i>AtAOC2</i>, <i>AtOPR3</i>, <i>AtJAR1</i>) involved in JA biosynthesis from <i>Arabidopsis</i> were individually overexpressed, and a JA-Ile hydrolysis-related gene, <i>NtJIH1</i>, was suppressed by RNAi approach, to understand their effects on nicotine accumulation in tobacco. Interestingly, while transgene expression was high, levels of JA-Ile (the biologically active form of JA) were often significantly reduced. Meanwhile, nicotine content in these transgenic plants did not increase. The research revealed a tightly controlled JA signaling pathway and a complicated regulatory network for nicotine biosynthesis by JA signaling.
A Systematic Study of Nitrated Indenoisoquinolines Reveals a Potent Topoisomerase I Inhibitor (2006)

The biological activity of indenoisoquinoline topoisomerase I inhibitors is significantly enhanced by nitration of the isoquinoline ring. In the present study, nitrated analogues were synthesized with the indenone ring substituted with methoxy groups to further explore a previously identified structure-activity relationship between the nitrated isoquinoline ring and a methylenedioxy-substituted indenone ring. The results indicate that a single methoxy group at the 9-position of an indenoisoquinoline affords superior biological activity. Hypothetical binding models have been developed to rationalize these results, and they indicate that pi-stacking between the indenoisoquinolines and the DNA base pairs, as visualized by electrostatic complementarity, is important for the intercalation and biological activity of the indenoisoquinoline analogues. Collectively, the analysis of methoxy groups on the indenone ring also illustrates a strict steric requirement for substituents extending toward the nonscissile DNA backbone and emphasizes a need for planarity to afford potent biological activity.
Automating resource optimisation in reconfigurable design (abstract only) (2013)

A design approach is proposed to automatically identify and exploit run-time reconfiguration opportunities while optimising resource utilisation. We introduce Configuration Data Flow Graph, a hierarchical graph structure enabling reconfigurable designs to be synthesised in three steps: function analysis, configuration organisation, and run-time solution generation. Three applications, based on barrier option pricing, particle filter, and reverse time migration are used in evaluating the proposed approach. The run-time solutions approximate the theoretical performance by eliminating idle functions, and are 1.61 to 2.19 times faster than optimised static designs. FPGA designs developed with the proposed approach are up to 28.8 times faster than optimised CPU reference designs and 1.55 times faster than optimised GPU designs.
“Clicked” Bivalent Ligands Containing Curcumin and Cholesterol As Multifunctional Aβ Oligomerization Inhibitors: Design, Synthesis, and Biological Characterization (2010)

In our effort to develop multifunctional compounds that cotarget beta-amyloid oligomers (AbetaOs), cell membrane/lipid rafts (CM/LR), and oxidative stress, a series of bivalent multifunctional Abeta oligomerization inhibitors (BMAOIs) containing cholesterol and curcumin were designed, synthesized, and biologically characterized as potential treatments for Alzheimer's disease (AD). The in vitro assay results established that the length of spacer that links cholesterol and curcumin and the attaching position of the spacer on curcumin are important structural determinants for their biological activities. Among the BMAOIs tested, 14 with a 21-atom-spacer was identified to localize to the CM/LR of human neuroblastoma MC65 cells, to inhibit the formation of AbetaOs in MC65 cells, to protect cells from AbetaOs-induced cytotoxicity, and to retain antioxidant properties of curcumin. Furthermore, 14 was confirmed to have the potential to cross the blood-brain barrier (BBB) as demonstrated in a Caco-2 cell model. Collectively, these results strongly encourage further optimization of 14 as a new hit to develop more potent BMAOIs.
The chemotactic and mitogenic effects of platelet-derived growth factor-BB on rat aorta smooth muscle cells are inhibited by basic fibroblast growth factor (2000)

In response to endovascular injury, platelet-derived growth factor-BB (PDGF-BB) and basic fibroblast growth factor (bFGF) are released locally and modulate vascular smooth muscle cells (SMC) proliferation and migration within the vascular wall. The aim of the present in vitro study was to determine how rat aorta SMC respond to the simultaneous exposure to PDGF-BB and bFGF. In a modified Boyden chamber assay bFGF exhibited a dose-dependent effect to inhibit the chemotactic action of PDGF-BB. A comparable result was observed in proliferation assays. In contrast, MIP-1 beta, epidermal growth factor (EGF), fibronectin and acidic FGF (aFGF) did not inhibit the chemotactic effect of PDGF-BB. Denatured bFGF did not exert an inhibitory effect and neutralizing antibodies either to bFGF or to bFGF-receptor abolished the inhibition observed in the presence of bFGF. The role played by PDGF receptor alpha (PDGF-Ralpha) was investigated in PDGF-Ralpha-dominant negative-transfected SMC, by selectively blocking PDGF-BB-binding to PDGF-Ralpha with neomycin, by neutralizing PDGF-Ralpha with a monoclonal antibody and by selectively stimulating PDGF-Ralpha with PDGF-AA; in all cases the effect of bFGF to inhibit PDGF-BB-directed SMC migration was abolished. These in vitro studies show that bFGF significantly inhibits PDGF-BB-induced SMC migration and proliferation and that this effect is mediated by both PDGF-Ralpha and bFGF receptor.
High-Performance Silver Alloy Bonding Wire for Memory Devices (2017)

For memory devices, focus has been on Ag alloy bonding wire as a low-cost alternative to Au bonding wire. However, Ag bonding wire has lower long-term bond reliability than Au bonding wire under high temperature and humidity conditions. Past research has mainly been concerned with enhancing the bond reliability by Pd doping into the Ag bonding wire. On the other hand, Ag-Pd alloy bonding wire has practical issues such as high electrical resistance and high free-air-ball (FAB) hardness. A new type of Ag alloy wire (2N Ag alloy) was developed to achieve enhanced bond reliability, low electrical resistance and low FAB hardness compared to conventional one. Moreover, the 2N Ag alloy wire has good FAB formability and bond properties. This new Ag alloy wire is considered to be preferable for advanced memory devices.
ChemInform Abstract: Reactivity of Hypervalent Species: Reactions of Anionic Penta‐Coordinated Silicon Complexes Towards Nucleophiles. (1988)

Abstract The title compounds (I) can be reduced by different procedures to yield silanes (II).
Phosphorus-containing imide resins - Modification by elastomers (1984)

The syntheses and general features of addition-type maleimide resins based on bis(m-aminophenyl)phosphine oxide and tris(m-aminophenyl)phosphine oxide have been reported previously. These resins have been used to fabricate graphite cloth laminates having excellent flame resistance. These composites did not burn even in pure oxygen. However, these resins were somewhat brittle. This paper reports the modification of these phosphorus-containing resins by an amine-terminated butadiene-acrylonitrile copolymer (ATBN) and a perfluoroalkylene diaromatic amine elastomer (3F). An approximately two-fold increase in short beam shear strength and flexural strength was observed at 7 percent ATBN concentration. The tensile, flexural, and shear strengths were reduced when 18 percent ATBN was used. Anaerobic char yields of the resins at 800 C and the limiting oxygen indexes of the laminates decreased with increasing ATBN concentration. The perfluorodiamine (3F) was used with both imide resins at 6.4 percent concentration. The shear strength was doubled in the case of the bisimide with no loss of flammability characteristics. The modified trisimide laminate also had improved properties over the unmodified one. The dynamic mechanical analysis of a four-ply laminate indicated a glass transition temperature above 300 C. Scanning electron micrographs of the ATBN modified imide resins were also recorded.
Future Prospects for Regenerated Heart Using Induced Pluripotent Stem Cells (2014)

Induced pluripotent stem cell (iPSC) generation is an epoch-making technology. The potential applications for iPSCs are wide-ranging from in vitro disease models to drug discovery. For regenerative medicine in particular, the technology provides great hope for patients with incurable diseases or potentially fatal disorders such as heart failure (HF). However, the true realization of that promise for HF remains uncertain and moving toward the clinical application of iPSCs needs to be stepwise and careful. The establishment of "safe" iPSCs must be a major premise, while genome integration-free and oncogene-free reprogramming is also necessary. Teratoma formation also remains a risk with undifferentiated iPSCs, but it must not happen in patients' bodies. Thus, regardless of the target organ, the differentiated cells from iPSCs must be purified to exclude any possibility of tumorigenicity. The transplantation strategies used for iPSC-derived cells are very important for the recovery of lost cardiac function. Longer engraftment of transplanted iPSCs-derived cardiomyocytes is essential particularly because their survival could be hampered by ischemia, inflammation, apoptosis, immunological rejection, and other cardiac phenomena. Providing these multistep solutions will open the new frontier of regenerative therapies with iPSCs for patients with severe HF.