gebhart/patrepeval huggingface dataset:
Single and multiple channel estimation using the time-updated recursive least squares algorithm (2007)

A time-updated recursive least squares algorithm (TURLS) is presented, analyzed, and applied to the problem of estimating the time-varying impulse response in both single and multiple channel cases. The TURLS algorithm may be viewed as a least squares extension of the EM channel estimation algorithm [W. Li and J. C. Preisig, ICASSP, IV 313IV, 316 (2005)], in the sense that it jointly estimates the channel impulse response and its dynamic parameters by minimizing a least squares error instead of maximizing the likelihood function. Based on the intuition that the sequence of channel estimates contains information regarding the true channel dynamics, the algorithm estimates the parameters from the sequence of channel estimates. Analysis of the algorithm based on a first-order AR channel model shows that the resulting channel estimate is a second-order approximation whose poles converge as the parameter estimate improves. In addition, it is shown that with exponential weighting, the resulting parameter estimate may be biased at low SNR level. The algorithm is applied to experimental data and results with both single channel and multiple channels are demonstrated. [Work supported by ONR Ocean Acoustics.]
ChemInform Abstract: Highly Functionalized and Potent Antiviral Cyclopentane Derivatives Formed by a Tandem Process Consisting of Organometallic, Transition‐Metal‐Catalyzed, and Radical Reaction Steps. (2015)

Abstract An one‐pot reaction sequence is used for the preparation of tetrasubstituted cyclopentanes (V)/(VI).
WaterWOLF: Water Watch on Load Flow (2014)

We have developed WaterWOLF, a new electronic system and signal processing algorithm for evaluating flow components in pipes. These techniques nonintrusively convert an existing flow meter into a high resolution wireless meter for determining flow rates in real-time. These techniques exploit new tunneling magneto-resistive materials (TMR) for detecting very small magnetic fields generated by certain types of flow meters. The sensors are nonintrusive, requiring no new access to the flow stream. A pipe distribution network, e.g., for water or oil production or potentially even gas utilities, can not only deliver a commodity like water but can also serve as its own sensor for monitoring water flow and the operation of individual water consuming appliances. Continuous measurements of water consumption can be fed back to the user to help find opportunities for conservation. Additionally, high resolution flow sensing can improve leak detection accuracy. This is important for countries with significant water challenges like Kuwait.
Long-term survival and long-lived immune memory in patients with metastatic melanoma vaccinated with melanoma-antigen loaded dendritic cells. (2010)

e19018
Immunization with Th-CTL Fusion Peptide and Cytosine-Phosphate-Guanine DNA in Transgenic HLA-A2 Mice Induces Recognition of HIV-Infected T Cells and Clears Vaccinia Virus Challenge (2003)

We evaluated immunogenicity of a novel Th-CTL fusion peptide composed of the pan DR Th epitope and a CTL epitope derived from HIV-pol in two transgenic HLA-A*0201/K(b) mouse models. The immunogenicity of peptides of this structure is highly dependent on coadministered cytosine-phosphate-guanine DNA. Initial evaluations of peptide-specific immunity are based on results of chromium release assay, intracellular cytokine, and tetramer staining. Significant cytotoxic T cell responses are found upon a single immunization with as low as 0.1 nmol both peptide and cytosine-phosphate-guanine DNA. Splenocytes from immunized mice recognize naturally processed HIV-pol expressed from vaccinia virus (pol-VV). Translation of immunologic criteria into more relevant assays was pursued using systemic challenge of immunized mice with pol-VV. Only mice receiving both peptide and DNA together successfully cleared upward of 6 logs of virus from ovaries, compared with controls. Challenge with pol-VV by intranasal route of intranasal immunized mice showed a significant reduction in the levels of VV in lung compared with naive mice. A convincing demonstration of the relevance of these vaccines is the robust lysis of HIV-infected Jurkat T cells (JA2/R7/Hyg) by immune splenocytes from peptide- and DNA-immunized mice. This surprisingly effective immunization merits consideration for clinical evaluation, because it succeeded in causing immune recognition and lysis of cells infected with its target virus and reduction in titer of highly pathogenic VV.
A Chromium Hydroxide/MIL‐101(Cr) MOF Composite Catalyst and Its Use for the Selective Isomerization of Glucose to Fructose (2018)

Abstract A metal–organic framework (MOF)‐based catalyst, chromium hydroxide/MIL‐101(Cr), was prepared by a one‐pot synthesis method. The combination of chromium hydroxide particles on and within Lewis acidic MIL‐101 accomplishes highly selective conversion of glucose to fructose in the presence of ethanol, matching the performance of optimized Sn‐containing Lewis acidic zeolites. Differently from zeolites, NMR spectroscopy studies with isotopically labeled molecules demonstrate that isomerization of glucose to fructose on this catalyst, proceeds predominantly via a proton transfer mechanism.
Data for microbe resistant engineered recombinant spider silk protein based 2D and 3D materials (2020)

Data presented in this article describe bacterial and fungal repellent properties of 2D-films and 3D-hydrogels made of different recombinantly produced spider silk proteins based on consensus sequences of Araneus diadematus dragline silk proteins (fibroin 3 and 4). Here, the attachment, growth, and microbial colonization of Streptococcus mutans (S. mutans) as well as Candida albicans (C. albicans) on plane and micro-patterned films were visualized by scanning electron microscopy (SEM). Also, microbial viability data are provided of Escherichia coli (E. coli) and Pichia pastoris (P. pastoris) on hydrogels made of eADF4(C16) and eADF4(C16)-RGD, quantified using the Alamar blue assay. Experimental results, design of a post-operative contamination model of microbes with mammalian cells, and methods in the data article refer to the research paper "Engineered spider silk-based 2D and 3D materials prevent microbial infestation" published recently [1].
Analysis of the Carbohydrate Components of Glycosylphosphatidylinositol Structures Using Fluorescent Labeling (2003)

Glycosylphosphatidylinositols (GPIs) are a family of structures that contain the structural motif: Mana1-4GlcNH2a1-6myo-Inositol-1-PO4-lipid. This common substructure suggests that this family of molecules is biosynthetically related, and it differentiates them from other glycosylated phosphoinositides, such as the glycosylated phosphatidylinositols of mycobacteria and the glycosylated inositol phosphoceramides of yeasts and plants. The GPI family can be conveniently divided into two groups, based on structural homology and function. The first group (1–34) is the membrane protein anchors (Fig. 1) which are found covalently linked to the C-termini of a wide variety of externally disposed plasma-membrane proteins throughout the eukaryotes. These GPI anchors afford a stable attachment of proteins to the membrane, and can be viewed as an alternative mechanism of membrane attachment to a singlepass hydrophobic transmembrane peptide domain. For recent reviews of GPI anchor structure, biosynthesis, and function, see refs. 35–40. The second group of GPI structures have only been found in protozoan organisms. These molecules exist as free glycophospholipids, such as the glycoinositol phospholipids (GIPLs) of the Leishmania, Trypanosoma cruzi, Leptomonas, Herpetomonas, Phytomonas, and Toxoplasma (35,41–45), or are attached to phosphorylated repeating units, as in the lipophosphoglycans (LPGs) of the Leishmania (35,46). This chapter describes protocols specifically designed to analyze the carbohydrate components of protein-linked GPI anchors, although they are also applicable to the GIPLs and, to some extent, the LPGs.
Optimal Load Sharing for Serial Compressors via Modifier Adaptation (2018)

This paper investigates the optimal load-sharing problem of serial gas compressors in the presence of plant- model mismatch. The problem is formulated as a static real- time optimization task that is solved via modifier adaptation for interconnected systems. The proposed approach guarantees optimal operation of the plant upon convergence. Furthermore, it is shown how the specific problem structure can be exploited during process operation for the efficient estimation of plant gradients with respect to local inputs. A simulated case study demonstrates the effectiveness of the proposed real-time optimization approach.
High Spatial Resolution T1-Weighted MR Imaging of Liver and Biliary Tract During Uptake Phase of a Hepatocyte-Specific Contrast Medium (2008)

T1-weighted respiratory triggered high spatial resolution images obtained in the hepatobiliary phase are technically feasible and significantly improve the image quality compared with breath-hold images.
Heavy End Analysis by Ultrahigh Resolution Mass Spectrometry in Oils and Tar in Two Adjacent Reservoirs (2022)

Two adjacent reservoirs in the North Sea contain very different crude oils. One reservoir contains a disequilibrium distribution of black and heavy oil with asphaltene content approaching 35% at the oil-water contact (OWC). The other reservoir contains an equilibrated light oil and also has a tar mat at the OWC. The same reservoir fluid geodynamic (RFG) processes have been proposed to account for both oil columns, with the differences ascribed to different phases of this process. These RFG processes involve gas/condensate diffusion down into the black oil from initially density stacked, separate charge fluids, destabilization of asphaltenes and their subsequent migration down to the base of the reservoir. Ultimately, bulk phase transition of asphaltenes form a tar mat at the base of the oil column. One reservoir is thought to be in the middle of this process while the adjacent reservoir is thought to have completed this process yielding an equilibrated light oil column with an underlying tar mat. Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI FT ICR MS) has been employed to evaluate heavy ends in oils and in core deposits to determine consistency of the proposed RFG process to account for the different crude oils and tar deposits in the reservoirs. Thousands of peaks are resolved in terms of elemental composition. Broad compositional consistency is obtained across all samples. Dominant chemical species measured include larger aromatic compounds with a single nitrogen atom, smaller aromatics with a single oxygen atom, and highly saturated organic acids (with corresponding high cross section of detection). Two-dimensional gas chromatography results on the crude oils are consistent with conclusions from mass spectrometry. The detailed chemical analyses are consistent with the previously proposed RFG processes in these two reservoirs. These analyses are particularly useful to understand production rates and aquifer sweep in these reservoirs.
The direct interaction between Amphiregulin(AR), Epiregulin(EPR)-CTF and PLZF using surface plasmon resonance(SPR) spectroscopy. (2015)

&lt;p&gt;A direct interaction between EGFR-ligand-CTF and PLZF (GST-tagged-ZnF5-8) with the SPR system. Rate constants (ka) and dissociation constants (kd) for GST-ZnF5-8 binding to biotin-AR-CTF or biotin-EPR-CTF are performed. KD = kd/ka.&lt;/p&gt;
Peroxisome Proliferator‐Activated Receptor α Agonists Regulate Cholesterol Ester Transfer Protein (2008)

Peroxisome proliferator-activated receptor alpha (PPARalpha) belongs to the nuclear receptor superfamily that regulates multiple target genes involved in lipid metabolism. Cholesterol ester transfer protein (CETP) is a secreted glycoprotein that modifies high-density lipoprotein (HDL) particles. In humans, plasma CETP activity is inversely correlated with HDL cholesterol levels. We report here that PPARalpha agonists increase CETP mRNA, protein and accordingly its activity. In a human CETP transgenic animal model harboring the natural flanking regions (Jiang et al. in J Clin Investigat 90:1290-1295, 1992), both fenofibrate and a specific synthetic PPARalpha agonist LY970 elevated human CETP mRNA in liver, serum protein and CETP activity. In hamsters, the endogenous liver CETP mRNA level and the serum CETP activity were dose-dependently upregulated by fenofibrate. In addition Wy14643, a PPARalpha agonist, also significantly elevated CETP mRNA and activity. In a carcinoma cell line of hepatic origin, HepG2 cells, overexpression of PPARalpha resulted in increased CETP mRNA and agonist treatment further elevated CETP mRNA levels. We conclude that PPARalpha agonists upregulate CETP expression and activity and may play an important role in PPARalpha (agonist mediated HDL cholesterol homeostasis in humans.
RAFT Polymerization of Phenyl Vinyl Sulfide Using Trithiocarbonate Mediating Agents and Synthesis of Block Copolymers (2015)

Summary Reversible addition‐fragmentation chain transfer (RAFT) polymerization of phenyl vinyl sulfide (PVS), in which the thioether moiety is directly connected to the vinyl group, was investigated using trithiocarbonates as chain transfer agents (CTAs). A trithiocarbonate with a 2‐cyano‐2‐propyl group in the R moiety was found to be effective in achieving controlled radical polymerization of the S ‐vinyl monomer. Reasonable control of the polymerization of PVS was indicated by the formation of a narrow dispersity polymer, molecular weight controlled by the monomer/CTA molar ratio, a linear increase in molecular weight with the conversion, and preserved chain end structure (determined by 1 H NMR). Well‐defined block copolymers were synthesized by RAFT polymerization of PVS using polystyrene macro‐CTA.
Inhibitory Activity of Alternative Splice Variants of the Bullfrog GnRH Receptor-3 on Wild-Type Receptor Signaling (2001)

Recently we characterized three distinct GnRH receptors in the bullfrog (bfGnRHR-1, bfGnRHR-2, and bfGnRHR-3). In the present study, we further investigated the expression and function of splice variants, generated from the primary bfGnRHR-3 transcript by exon skipping (splice variant 1), intron retention (splice variants 2 and 3), and/or transcriptional slippage (splice variant 4), apart from the constitutively spliced form (wild-type). Cellular expression and function of the splice variants were examined using a transient expression system. Immunoblot analysis revealed that the wild-type receptor and all splice variant proteins were expressed in transfected HeLa cells with no significant differences in expression levels. These splice variants showed a very low binding affinity to ligand and did not induce signal transduction in response to GnRH treatment. Interestingly, cotransfection of the wild-type with splice variants 2--4, but not with splice variant 1, significantly inhibited wild-type receptor-mediated signaling. Subcellular localization analysis of green fluorescent protein-tagged wild-type and splice variant proteins revealed that the wild-type receptor protein was mainly localized in the cell membrane, whereas the splice variant 1 protein was exclusively detected in the cytoplasm. The splice variant 2--4 proteins, however, were found in both the cell membrane and cytoplasm. The inhibition of wild-type receptor signaling by splice variants 2--4 and the subcellular localization of splice variants 2-4 suggest a possible physical interaction of splice variants 2--4 with the wild-type receptor protein. In addition, the ratio of mRNA levels of the wild-type to splice variants 2--4 significantly varied from hibernation (wild-type < splice variants 2--4) to the prebreeding season (wild-type > splice variants 2--4). Collectively, these results suggest that alternative splicing of the bfGnRHR-3 primary transcript plays a role in fine-tuning GnRH receptor function in amphibians.
Bacterial clogging of porous media: A new modelling approach (1995)

A comparison is made between existing mathematical models and experimental data that relate the reduction of the saturated hydraulic conductivity (K) of a porous medium to the porosity reduction caused by microbial growth. The models yielded a realistic prediction of a data set obtained with a model porous medium consisting of millimeter‐size glass spheres, but failed to predict the clogging behaviour observed in smaller‐than‐1‐mm sand. A new modelling approach, semi‐mechanistic in nature, is proposed that gives good predictions of fine sand media as well. It relaxes the assumption about uniformly‐thick biofilms by allowing a second arrangement to occur, i.e. discrete plugs filling the pore lumen. The new model requires input data on two intrinsic properties of the system, which renders it sufficiently flexible as to fit very different data sets. The two model parameters are Kmin, the minimum K value when all porosity is filled with microorganisms, and Bc, the biovolume fraction at which most cell detachment from biofilm occurs.
P3H-4 Formation of Desired Waveform and Focus Structure by Time Reversal Acoustic Focusing System (2006)

The ultrasound focusing systems based on time reversal acoustic (TRA) principles are capable of delivering ultrasound energy to the specific region in a highly inhomogeneous medium with focusing efficacy virtually unachievable using conventional phased array transmitters. Furthermore, numerous reflections from various boundaries, which distort focusing in conventional ultrasound focusing systems and are viewed as a significant technical hurdle, lead to improvement of the focusing ability of the TRA system. We present a novel approach to TRA focusing of ultrasound that allows: (i) calculation of the TRA focused ultrasound waveform and spatial distribution and (ii) formation of the TRA focused signal with desired waveforms. This approach is based on the measurements of impulse responses of the TRA focusing system (TRA FS) transducers. The proposed method requires creating a library of impulse responses recorded for each transducer of the TRA FS to short pulses radiated from a grid of points in the projected focal area. The developed approach for TRA waveform prediction was tested on a 5 channel TRA FS based on aluminum resonator with attached piezotransducers. The TRA FS provided focusing of ultrasound in the frequency band of 100-1000 kHz. The calculated and experimentally measured waveforms and spatial distributions were practically identical. The formation of ultrasonic signals with various predefined envelopes was demonstrated experimentally. We formed triangular, rectangular, and amplitude modulated tone burst signals with different frequencies in the focal region. Experiments were conducted for focusing of ultrasound to several points simultaneously and formation of focal area with the shape of an elongated ellipse was demonstrated
Security Mandates are Pervasive: An Inter-School Study on Analyzing User Authentication Behavior (2019)

Two-factor authentication (2FA) technologies are designed to increase the security and usability of authentica-tion. Adoption of 2FA hardware devices that generate one-time passwords has proven to be effective as a risk mitigating strategy. Despite 2FA addressing user data security concerns, individuals appear either disinterested or unable to adopt 2FA tools. Many institutions are now mandating 2FA to better secure their network and user data. Some have more rigid requirements than others (e.g., offering only one 2FA method vs. offering multiple 2FA options). To better understand the impact of mandatory 2FA policies, we conducted a study of the usability, adoption, and acceptability of 2FA at three different universities. In our study, using the Yubico FIDO U2F security token, we found that mandating the use of 2FA without complementary risk communication is often inadequate. In our interviews, we found that mandatory 2FA did not necessarily increase security, instead leading to less secure user behavior, such as sharing 2FA tokens, storing credentials for a longer time in public devices, and other security avoidance behaviors.
2441. Automated, Rapid Detection of Potential Healthcare-Acquired Infection Clusters Based on Microbiology And Patient Geotemporal Data (2019)

Abstract Background Whole-genome sequencing (WGS) has shown promise in identifying transmissions of healthcare-associated infections (HAIs), but it may be costly to sequence all potential HAIs. By automatically identifying samples likely to be HAIs, WGS can be focused on specific samples. We describe an algorithm that quickly identifies potential HAI clusters by analyzing patient geotemporal and pathogen microbiology data. This approach systematically triages potential HAI investigations to aid infection control professionals (ICPs) in their workflow. Methods This novel algorithm within Philips IntelliSpace Epidemiology scores the potential of transmission for pairs of infections. Inputs include microbiology (MB) data (genus- or species-level identification and antimicrobial susceptibility test results) and geotemporal (GT) data (timing of sample collection and shared location stays). From the resulting pairwise scores, clusters of potential HAIs are identified. Leveraging 9 months (June, 2018 – March, 2019) of data from a 900-bed US hospital (i.e., 2825 samples, 1814 patients and 13 organisms—of which a subset of 404 samples had WGS performed concomitantly with MB studies), we evaluated the extent to which this algorithm captures genetically similar sample pairs. Results Pairwise scores enrich for genetically similar samples when considering MB data only (odds ratio: 17.3), GT only (odds ratio: 6.1) and a combination of both (odds ratio: 19.8), with highly significant P-values for all (P &lt; 10−16). Considering MB only, 91% of samples group together in potential transmission clusters. With MB and GT data, this fraction drops to 24.6% (694 samples) forming 178 possible clusters, 173 of which contain fewer than ten samples each. The 5 larger clusters contain 40–64 samples each and span multiple units in the hospital. Conclusion The proposed system automatically suggests potential HAI clusters. By combining MB and GT data, the number of samples to review is reduced, enabling ICPs to focus their attention and sequencing efforts. By focusing on a targeted group of higher probability clusters, ICPs may be able to increase their efficiency and effectiveness in controlling the spread of HAIs—thus boosting potential for patient safety and amelioration of cost of care. Disclosures All authors: No reported disclosures.
Molecular Profiling Associated with Calcium/Calmodulin-Dependent Protein Kinase Kinase 2 (CAMKK2)-Mediated Carcinogenesis in Gastric Cancer (2021)

Gastric cancer is the fifth most common cancer and the third leading cause of cancer-related death worldwide. We showed previously that calcium/calmodulin-dependent protein kinase kinase 2 (CAMKK2), a serine-threonine kinase, is highly expressed in gastric cancer and leads to progression. In the present study, we identified the molecular networks involved in CAMKK2-mediated progression of gastric adenocarcinoma. Treatment of gastric cancer cell lines with a CAMKK2 inhibitor, STO-609, resulted in decreased cell migration, invasion, and colony-forming ability and a G1/S-phase arrest. In addition, tandem mass tag (TMT)-based quantitative proteomic analysis resulted in the identification of 7609 proteins, of which 219 proteins were found to be overexpressed and 718 downregulated (1.5-fold). Our data identified several key downregulated proteins involved in cell division and cell proliferation, which included DNA replication licensing factors, replication factor C, origin recognition complex, replication protein A and GINS, and mesenchymal markers, upon CAMKK2 inhibition. Immunoblotting and immunofluorescence results showed concordance with our mass spectroscopy data. Taken together, our study supports CAMKK2 as a novel therapeutic target in gastric cancer.