gebhart/patrepeval huggingface dataset:
Design of anti-allergic inhibitors for human hematopoietic prostaglandin D synthase (2008)

Choline kinase (ChoK) catalyzes the ATP-dependent phosphorylation of choline, the first committed step in the CDP-choline pathway for the biosynthesis of phosphatidylcholine. Overexpression and increased activity of one of the human ChoK isoforms, ChoK alpha have been constitutively reported in malignant cells and tumour tissues. This suggests that the enzyme plays a relevant role in tumorigenesis. Some sets of in vitro and in vivo experiments confirmed that ChoK inhibition is one of the potential novel strateges for the development of new antiproliferative and anticancer drugs. The importance of ChoK for the regulation of cell proliferation has been studied by using an inhibitor hemicholinium-3 (HC-3), which was initially characterized as a lethal, respiratory paralytic agent. Most of the ChoK inhibitors introduced so far are the chemically modified derivatives based on the structure of HC-3. Crystal structures of HC-3 bound human ChoK alpha were determinded with and without ADP. In the crystal structures, HC-3 molecule was well accommodated between the N and C-terminal lobes of ChoK protein, and its one end was placed on the same binding site as a substrate choline, while the other end partially exposed to the solvent. The inhibitor molecule was stabilized mainly through the hydrophobic interactions contributed by the C-terminal lobe. These 3D information provides the first molecular detailed view concerning the mode of inhibitory action and expand our understanding of the factors governing selectivity.
Incorporating prior knowledge improves detection of differences in bacterial growth rate (2015)

We have demonstrated that by making use of existing experimental knowledge, it is possible to significantly improve detection of differences in bacterial growth rate.
A Generative Adversarial Network for Climate Tipping Point Discovery (TIP-GAN) (2023)

We propose a new Tipping Point Generative Adversarial Network (TIP-GAN) for better characterizing potential climate tipping points in Earth system models. We describe an adversarial game to explore the parameter space of these models, detect upcoming tipping points, and discover the drivers of tipping points. In this setup, a set of generators learn to construct model configurations that will invoke a climate tipping point. The discriminator learns to identify which generators are generating each model configuration and whether a given configuration will lead to a tipping point. The discriminator is trained using an oracle (a surrogate climate model) to test if a generated model configuration leads to a tipping point or not. We demonstrate the application of this GAN to invoke the collapse of the Atlantic Meridional Overturning Circulation (AMOC). We share experimental results of modifying the loss functions and the number of generators to exploit the area of uncertainty in model state space near a climate tipping point. In addition, we show that our trained discriminator can predict AMOC collapse with a high degree of accuracy without the use of the oracle. This approach could generalize to other tipping points, and could augment climate modeling research by directing users interested in studying tipping points to parameter sets likely to induce said tipping points in their computationally intensive climate models.
Urine and serum analysis of consumed curcuminoids using an IkappaB-luciferase surrogate marker assay. (2011)

the GEM assay is a very sensitive and accurate non-invasive assay that could be utilized to detect metabolites in body fluids. It could also serve as a tool to determine participants' compliance during clinical research studies.
Objective biomarkers of depression: A study of Granger causality and wavelet coherence in resting‐state fMRI (2023)

Based on abnormal functional dynamics between brain networks, we were able to identify subjects with depression with high accuracy. The findings of this study contribute to the understanding of the impaired emotional and attention processing associated with depression, as well as decreased motor activity.
ChemInform Abstract: Magnesium‐Assisted Imidazole Formation from Unreactive Ureas. (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
A Comparison of SC-FDE and UW DFT-s-OFDM for Millimeter Wave Communications (2018)

In this study, we compare the single-carrier (SC) waveform adopted in IEEE 802.11ad and unique word discrete Fourier transform spread orthogonal frequency division multiplexing (UW DFT-s-OFDM) waveform. We provide equivalent representations of up-sampling and down-sampling operations of the SC waveform by using discrete Fourier transform (DFT) and inverse DFT to enable explicit comparison of these two similar waveforms. By using this representation, we discuss why the IEEE 802.11ad SC waveform can cause suboptimal performance in multipath channel and discuss how to improve it with UW DFT-s-OFDM. With comprehensive link-level simulations, we show that replacing the 802.11ad SC waveform with UW DFT-spread OFDM can result in 1 dB gain in peak throughput without affecting the IEEE 802.11ad packet structure. We also evaluate the cross links where the transmitter is UW-DFT-s- OFDM and the receiver is traditional SC-FDE or vice versa. We demonstrate that UW DFT-s-OFDM receiver can decode an IEEE 802.11ad SC waveform with a slight SNR loss while IEEE 802.11ad SC receiver can decode a UW DFT-spread OFDM waveform with an interference floor.
ChemInform Abstract: Pentacarbonyl(aminocarbene)chromium(0) Complexes (I): Reductive Cleavage of the Chromium‐Carbon Double Bond to Secondary and Tertiary Amines (II). (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Characterization of Glycosaminoglycan (GAG) Sulfatases from the Human Gut Symbiont Bacteroides thetaiotaomicron Reveals the First GAG-specific Bacterial Endosulfatase (2014)

Despite the importance of the microbiota in human physiology, the molecular bases that govern the interactions between these commensal bacteria and their host remain poorly understood. We recently reported that sulfatases play a key role in the adaptation of a major human commensal bacterium, Bacteroides thetaiotaomicron, to its host (Benjdia, A., Martens, E. C., Gordon, J. I., and Berteau, O. (2011) J. Biol. Chem. 286, 25973-25982). We hypothesized that sulfatases are instrumental for this bacterium, and related Bacteroides species, to metabolize highly sulfated glycans (i.e. mucins and glycosaminoglycans (GAGs)) and to colonize the intestinal mucosal layer. Based on our previous study, we investigated 10 sulfatase genes induced in the presence of host glycans. Biochemical characterization of these potential sulfatases allowed the identification of GAG-specific sulfatases selective for the type of saccharide residue and the attachment position of the sulfate group. Although some GAG-specific bacterial sulfatase activities have been described in the literature, we report here for the first time the identity and the biochemical characterization of four GAG-specific sulfatases. Furthermore, contrary to the current paradigm, we discovered that B. thetaiotaomicron possesses an authentic GAG endosulfatase that is active at the polymer level. This type of sulfatase is the first one to be identified in a bacterium. Our study thus demonstrates that bacteria have evolved more sophisticated and diverse GAG sulfatases than anticipated and establishes how B. thetaiotaomicron, and other major human commensal bacteria, can metabolize and potentially tailor complex host glycans.
16.6 A Calibration-Free Triple-Loop Bang-Bang PLL Achieving 131fs<inf>rms</inf> Jitter and-70dBc Fractional Spurs (2019)

To deliver a good EVM performance, modern communication standards, such as WiFi 802.11ax with a 1024-QAM mode, require RF clocks with extremely low integrated phase error and low spurs. Because of their good scalability, digital phase-locked loops (DPLLs) have been widely studied [1]–[3]. However, they face two problems: nonlinearity and quantization noise of time-to-digital converters (TDCs). High-performance DPLLs require complicated TDC structures and calibrations. By contrast, a bang-bang phase detector (PD), i.e., a one-bit TDC, can be linear and low noise [4]. However, in the fractional mode, the PD gain is lowered by the significant phase fluctuations from the fractional divider. The gain can be restored by calibration, but the nonlinearity of the calibration circuit creates large spurs in an otherwise good integrated rms noise [5]. A sub-sampling PLL [6] avoids amplifying the PD noise and eliminates the loop divider, but still needs calibration for fractional operation. This work describes a calibration-free fractional BBDPLL. With the assistance of two auxiliary PLLs, this triple-loop PLL architecture combines the advantages of the sub-sampling PLL and bang-bang PD to achieve $131fs_{\mathrm{rms}}$ jitter and lower than-70dBc fractional spurs.
Synthetic Control of Kinetic Reaction Pathway and Cationic Ordering in High‐Ni Layered Oxide Cathodes (2017)

Nickel-rich layered transition metal oxides, LiNi<sub>1-</sub><sub>x</sub> (MnCo)<sub>x</sub> O<sub>2</sub> (1-x ≥ 0.5), are appealing candidates for cathodes in next-generation lithium-ion batteries (LIBs) for electric vehicles and other large-scale applications, due to their high capacity and low cost. However, synthetic control of the structural ordering in such a complex quaternary system has been a great challenge, especially in the presence of high Ni content. Herein, synthesis reactions for preparing layered LiNi<sub>0.7</sub> Mn<sub>0.15</sub> Co<sub>0.15</sub> O<sub>2</sub> (NMC71515) by solid-state methods are investigated through a combination of time-resolved in situ high-energy X-ray diffraction and absorption spectroscopy measurements. The real-time observation reveals a strong temperature dependence of the kinetics of cationic ordering in NMC71515 as a result of thermal-driven oxidation of transition metals and lithium/oxygen loss that concomitantly occur during heat treatment. Through synthetic control of the kinetic reaction pathway, a layered NMC71515 with low cationic disordering and a high reversible capacity is prepared in air. The findings may help to pave the way for designing high-Ni layered oxide cathodes for LIBs.
Multi-objective Optimization of Meta-atoms (2019)

Metasurfaces are thin structures that can control electromagnetic propagation in a variety of ways. This is done by designing discrete elements (meta-atoms) with desired properties that form the building blocks of the metasurface. In the past, these meta-atoms have often been comprised of simple shapes (e.g., rectangles, ellipses, split-rings). However, greater throughput and multiple functionalities can be achieved by more complex shapes. In the present work, a single method to represent most shapes is demonstrated. By combining this shape generation method with a multi-objective optimizer, the best meta-atom designs can be found that achieve good performance for multiple objectives. This method is demonstrated by designing a polarization-selective, beam steering application where transmitted electromagnetic radiation deflects into the +1 or -1 diffraction order depending on the incident wave polarization.
Functional Genomic Assessment of Phosgene-Induced Acute Lung Injury in Mice (2013)

In this study, a genetically diverse panel of 43 mouse strains was exposed to phosgene and genome-wide association mapping performed using a high-density single nucleotide polymorphism (SNP) assembly. Transcriptomic analysis was also used to improve the genetic resolution in the identification of genetic determinants of phosgene-induced acute lung injury (ALI). We prioritized the identified genes based on whether the encoded protein was previously associated with lung injury or contained a nonsynonymous SNP within a functional domain. Candidates were selected that contained a promoter SNP that could alter a putative transcription factor binding site and had variable expression by transcriptomic analyses. The latter two criteria also required that ≥10% of mice carried the minor allele and that this allele could account for ≥10% of the phenotypic difference noted between the strains at the phenotypic extremes. This integrative, functional approach revealed 14 candidate genes that included Atp1a1, Alox5, Galnt11, Hrh1, Mbd4, Phactr2, Plxnd1, Ptprt, Reln, and Zfand4, which had significant SNP associations, and Itga9, Man1a2, Mapk14, and Vwf, which had suggestive SNP associations. Of the genes with significant SNP associations, Atp1a1, Alox5, Plxnd1, Ptprt, and Zfand4 could be associated with ALI in several ways. Using a competitive electrophoretic mobility shift analysis, Atp1a1 promoter (rs215053185) oligonucleotide containing the minor G allele formed a major distinct faster-migrating complex. In addition, a gene with a suggestive SNP association, Itga9, is linked to transforming growth factor β1 signaling, which previously has been associated with the susceptibility to ALI in mice.
Intraocular Pressure and Big Bubble Diameter in Deep Anterior Lamellar Keratoplasty: An Ex-Vivo Microscope-Integrated OCT With Heads-Up Display Study (2017)

Purpose: To investigate the relationship between intraocular pressure (IOP) and big bubble (BB) formation in a model of deep anterior lamellar keratoplasty (DALK). Design: Ex-vivo. Methods: Corneoscleral buttons from human donors were loaded onto an artificial anterior chamber connected to a column of balanced salt solution. A surgeon-in-training learned to perform DALK via the BB technique using swept-source microscope-integrated optical coherence tomography (SS-MIOCT) with heads-up display (HUD). DALK procedures were performed at 6 different IOPs (5, 10, 15, 20, 30, or 40 mm Hg; n = 6 per group) in a randomized fashion, with the surgeon-in-training masked to the pressure and guided by SS-MIOCT with HUD. For a subset of corneas within each pressure group, DALK was performed on matching donor tissue at a control IOP. BB diameter was recorded, and a diameter exceeding the trephine diameter was considered optimal. Results: Wilcoxon rank sum test showed a difference in BB diameter among the different pressure groups (mean ± SD of 7.75 ± 1.60, 8.33 ± 1.99, 10.9 ± 0.92, 9.08 ± 1.07, 6.67 ± 3.33, and 3.42 ± 3.77 mm in the 5, 10, 15, 20, 30, and 40 mm Hg groups, respectively; P = 0.0014). Per Tukey test, this difference was attributable to comparisons between the 40 mm Hg group and the 5, 10, 15, or 20 mm Hg groups (P = 0.04, 0.02, 0.0001, 0.004, respectively). Conclusions: In this ex-vivo model of DALK, the BB technique guided by SS-MIOCT with HUD yielded bubbles of optimal diameters only at physiologic pressures (10-20 mm Hg). Extremely high IOP (40 mm Hg) resulted in BBs of significantly smaller diameter than BBs obtained at physiologic and low (5 mm Hg) IOPs.
Current status of robotic surgery for hepato-pancreato-biliary malignancies (2022)

Robotic-assisted surgery for oncological indications is promising, in part, an established technique that has already shown its advantages in the last decade, although high-quality studies are missing. Upcoming experience must consider the oncological benefit and putative new indications in a rapidly changing field of anti-neoplastic regimens. Also, robotic surgery may possess the ability to accelerate digitalization and AI-based augmentation in this context.
Familial spinal neurofibromatosis (1991)

We studied two families with an unusual variant of neurofibromatosis (NF). The first family had spinal neurofibromas and café au lait spots (CLS), the second spinal neurofibromas without CLS. Other signs of NF1 or NF2, such as cutaneous tumors, Lisch nodules, or acoustic tumors, were absent. The inheritance pattern in both pedigrees was consistent with autosomal dominant inheritance. Using genetic linkage analysis with DNA markers tightly linked to the NF1 and NF2 loci, we determined that the likely location for the mutation in the first family was in the NF1 gene with odds of 97:1, whereas the mutation in the second family was excluded from the NF1 locus with odds greater than 100,000:1. Families such as these, in which a defined subset of the NF phenotype is passed on, are important for understanding the functional consequences of particular mutations in the NF genes.
STUDY OF ELECTROMAGNETIC SPECTRUM FROM A FOCUS SCIENCE, TECHNOLOGY AND SOCIETY (2016)

Appears in: EDULEARN16 Proceedings Publication year: 2016Pages: 2942-2947ISBN: 978-84-608-8860-4ISSN: 2340-1117doi: 10.21125/edulearn.2016.1647Conference name: 8th International Conference on Education and New Learning TechnologiesDates: 4-6 July, 2016Location: Barcelona, Spain
Surface Engineering with Poly(ethylene glycol) Photolithography to Create High-Density Cell Arrays on Glass (2003)

This manuscript presents a microfabrication-derived approach for controlling mammalian cell−surface interactions. Poly(ethylene glycol)-diacrylate (PEG-DA) was patterned, in a process analogous to photolithography, to manufacture high-density arrays of micrometer-scale PEG hydrogel wells on glass. Individual wells consisted of PEG walls and glass attachment pads; thus, as a result of the biological inertness of PEG, microwell patterning created a highly ordered biointerface with modulating-cell or protein-repellent properties. Fabricated hydrogel microstrucures proved very effective in guiding and confining adhesion of transformed 3T3 fibroblasts and primary rat hepatocytes to defined regions on the glass substrate. PEG-patterned glass surfaces were selectively modified with collagen (type I) to induce hepatocyte attachment. Localization of the fluorescein-conjugated collagen within the glass attachment pads of PEG hydrogel microwells was visualized by fluorescence microscopy. Further surface analysis was performed by tapping mode atomic force microscopy conducted within individual PEG wells. Protein-modified regions inside the wells had a root-mean-square roughness of 1.13 ± 0.03 nm compared to 0.7 ± 0.04 nm for alkylsilane-treated regions lacking protein. The cell occupancy of 96.7 ± 1.9% within the arrays of 30 × 30 μm individual wells was demonstrated for 3T3 fibroblasts. At the same time, cells remained effectively isolated in the individual PEG microwells. Primary hepatocytes attached and became fully confluent within the collagen-coated PEG after 24 h of incubation. Each 30 × 30 μm well contained one to three hepatocytes. Cells patterned on the surface remained viable after 24 h of incubation.
Quantum State Detector Design: Optimal Worst-Case a posteriori Performance (2004)

The problem addressed is to design a detector which is maximally sensitive to specific quantum states. Here we concentrate on quantum state detection using the worst-case a posteriori probability of detection as the design criterion. This objective is equivalent to asking the question: if the detector declares that a specific state is present, what is the probability of that state actually being present? We show that maximizing this worst-case probability (maximizing the smallest possible value of this probability) is a quasiconvex optimization over the matrices of the POVM (positive operator valued measure) which characterize the measurement apparatus. We also show that with a given POVM, the optimization is quasiconvex in the matrix which characterizes the Kraus operator sum representation (OSR) in a fixed basis. We use Lagrange Duality Theory to establish the optimality conditions for both deterministic and randomized detection. We also examine the special case of detecting a single pure state. Numerical aspects of using convex optimization for quantum state detection are also discussed.
Cyclic Prefix (CP) Jamming Against Eavesdropping Relays in OFDM Systems (2022)

Cooperative communication has been widely used to provide spatial diversity benefits for low-end user equipments, especially in ad hoc and wireless sensor networks. However, the lack of strong authentication mechanisms in these networks leaves them prone to eavesdropping relays. In this paper, we propose a secure orthogonal frequency division multiplexing (OFDM) transmission scheme, where the destination node transmits a jamming signal over the cyclic prefix (CP) duration of the received signal. Simulation results verify that as long as at least a part of the jamming signal falls to the actual data portion of the eavesdropping relay, it spreads through all the data symbols due to the fast Fourier transformation (FFT) operation, resulting in degraded interception at the eavesdropper.
Weaknesses in some recent key agreement protocols (1994)

B. Arazi recently proposed a way to integrate the DSS (digital signature standard) to the Diffie-Hellman key exchange system to obtain an authenticated key establishment mechanism for secret session keys. This Letter poins out the following weakness in the Arazi system: if one key is compromised then the others will be disclosed as well. A similar weakness appears also in another recently presented key distribution system.
Probing Heme Coordination States of Inducible Nitric Oxide Synthase with a Re(I)(imidazole-alkyl-nitroarginine) Sensitizer-Wire (2007)

Mammalian inducible nitric oxide synthase (iNOS) catalyzes the production of l-citrulline and nitric oxide (NO) from L-arginine and O2. The Soret peak in the spectrum of the iNOS heme domain (iNOSoxy) shifts from 423 to 390 nm upon addition of a sensitizer-wire, [ReI-imidazole-(CH2)8-nitroarginine]+, or [ReC8argNO2]+, owing to partial displacement of the water ligand in the active site. From analysis of competitive binding experiments with imidazole, the dissociation constant (Kd) for [ReC8argNO2]+-iNOSoxy was determined to be 3.0+/-0.1 microM, confirming that the sensitizer-wire binds with higher affinity than both L-arginine (Kd=22+/-5 microM) and imidazole (Kd=14+/-3 microM). Laser excitation (355 nm) of [ReC8argNO2]+-iNOSoxy triggers electron transfer to the active site of the enzyme, producing a ferroheme in less than approximately 1 micros.
FACE AND CONSTRUCT VALIDATION OF A NOVEL VIRTUAL REALITY ROBOTIC SIMULATOR (2008)

You have accessJournal of Urology1 Apr 2008FACE AND CONSTRUCT VALIDATION OF A NOVEL VIRTUAL REALITY ROBOTIC SIMULATOR Amanjot S Sethi, William J Peine, Yousef Mohammadi, Thomas A Gardner, Michael O Koch, and Chandru P Sundaram Amanjot S SethiAmanjot S Sethi More articles by this author , William J PeineWilliam J Peine More articles by this author , Yousef MohammadiYousef Mohammadi More articles by this author , Thomas A GardnerThomas A Gardner More articles by this author , Michael O KochMichael O Koch More articles by this author , and Chandru P SundaramChandru P Sundaram More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(08)61928-XAboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "FACE AND CONSTRUCT VALIDATION OF A NOVEL VIRTUAL REALITY ROBOTIC SIMULATOR." The Journal of Urology, 179(4S), p. 660 © 2008 by American Urological AssociationFiguresReferencesRelatedDetails Volume 179Issue 4SApril 2008Page: 660 Advertisement Copyright & Permissions© 2008 by American Urological AssociationMetricsAuthor Information Amanjot S Sethi More articles by this author William J Peine More articles by this author Yousef Mohammadi More articles by this author Thomas A Gardner More articles by this author Michael O Koch More articles by this author Chandru P Sundaram More articles by this author Expand All Advertisement PDF downloadLoading ...