gebhart/patrepeval huggingface dataset:
Design, Synthesis, and Biological Evaluation of Novel Bifunctional C-Terminal-Modified Peptides for δ/μ Opioid Receptor Agonists and Neurokinin-1 Receptor Antagonists (2007)

A series of bifunctional peptides that act as agonists for delta and mu opioid receptors with delta selectivity and as antagonist for neurokinin-1 (NK1) receptors were designed and synthesized for potential application as analgesics in various pain states. The peptides were characterized using radioligand binding assays and functional assays using cell membrane and animal tissue. Optimization was performed on the fifth residue which serves as an address moiety for both receptor recognitions. It had critical effects on both activities at delta/mu opioid receptors and NK1 receptors. Among the synthesized peptides, H-Tyr-D-Ala-Gly-Phe-Met-Pro-Leu-Trp-O-3,5-Bzl(CF3) 2 (5) and H-Tyr-D-Ala-Gly-Phe-Nle-Pro-Leu-Trp-O-3,5-Bzl(CF3)2 (7) had excellent agonist activity for both delta opioid and mu opioid receptors and excellent antagonist activity for NK1 receptors. These results indicate that the rational design of multifunctional ligands with opioid agonist and neurokinin-1 antagonist activities can be accomplished and may provide a new tool for treatment of chronic and several pain states.
Near-field scanning microwave microscopy: measuring local microwave properties and electric field distributions (2002)

We describe the near-field scanning microwave microscopy of microwave devices on a length scale much smaller than the wavelength used for imaging. Our microscope can be operated in two possible configurations, allowing a quantitative study of either material properties or local electric fields.
Zinc-aminomethylenephosphonate for control of oxygen corrosion (1970)

Aminomethylenephosphonates will provide protection against oxygen corrosion. This action is markedly enhanced when these phosphonates are used in conjunction with zinc salts. Inhibition is somewhat analogous to that by the polyphosphates, but differs in several significant respects. The pronounced hydrolytic stability of the aminomethylenephosphonates renders them particularily attractive for applications where prolonged exposure to high water temperatures are involved. It practically eliminates the problem of calcium phosphate deposition. Protective film formation with the aminomethylenephosphonates also is more tolerant of pH levels in the alkaline range than is the case with the polyphosphates. pH levels in the range of 7 to 8.5 or above commonly are maintained in aminomethylenephosphonate-zinc treated systems. Laboratory data illustrative of the inhibitive action of several of the aminomethylenephosphonates and the influence thereon of zinc salts are considered. The influence of pH, dissimilar metal couples, differential aeration, etc. are included. Test with copper and admiralty metal, as well as steel, are discussed.
Gremlins, glomeruli and diabetic nephropathy (2000)

There have been major advances in our understanding of the pathogenetic mechanisms of diabetic nephropathy in recent years. Of particular interest is the emerging paradigm of the role that developmentally important genes may play in this process, representing recapitulation of the ontogenic process. This review examines the potential pathophysiological involvement of one such developmental gene gremlin in diabetic nephropathy.
Design and Preparation of Potent, Nonpeptidic, Bioavailable Renin Inhibitors (2009)

Starting from known piperidine renin inhibitors, a new series of 3,9-diazabicyclo[3.3.1]nonene derivatives was rationally designed and prepared. Optimization of the positions 3, 6, and 7 of the diazabicyclonene template led to potent renin inhibitors. The substituents attached at the positions 6 and 7 were essential for the binding affinity of these compounds for renin. The introduction of a substituent attached at the position 3 did not modify the binding affinity but allowed the modulation of the ADME properties. Our efforts led to the discovery of compound (+)-26g that inhibits renin with an IC(50) of 0.20 nM in buffer and 19 nM in plasma. The pharmacokinetics properties of this and other similar compounds are discussed. Compound (+)-26g is well absorbed in rats and efficacious at 10 mg/kg in vivo.
Genetic-Algorithm-Based Computational Models for Optimizing the Process Parameters of A-TIG Welding to Achieve Target Bead Geometry in Type 304 L(N) and 316 L(N) Stainless Steels (2007)

Abstract The weld-bead geometry in 304LN and 316LN stainless steels produced by A-TIG welding plays an important role in determining the mechanical properties of the weld and its quality. Its shape parameters such as bead width, depth of penetration, and reinforcement height are decided according to the A-TIG welding process parameters such as current, voltage, torch speed, and arc gap. Identification of a suitable combination of A-TIG process parameters to produce the desired weld-bead geometry required many experiments, and the experimental optimization of the A-TIG process was indeed time consuming and costly. Therefore it becomes necessary to develop a methodology for optimizing the A-TIG process parameters to achieve the target weld-bead geometry. In the present work, genetic algorithm (GA)-based computational models have been developed to determine the optimum/near optimum process parameters to achieve the target weld-bead geometry in 304LN and 316LN stainless steel welds produced by A-TIG welding. Keywords: A-TIG weldingAustenitic stainless steelsGenetic algorithmWeld bead geometry
A murine neonatal model of necrotizing enterocolitis caused by anemia and red blood cell transfusions (2019)

Necrotizing enterocolitis (NEC) is an idiopathic, inflammatory bowel necrosis of premature infants. Clinical studies have linked NEC with antecedent red blood cell (RBC) transfusions, but the underlying mechanisms are unclear. Here we report a neonatal murine model to investigate this association. C57BL/6 mouse pups rendered anemic by timed phlebotomy and then given RBC transfusions develop NEC-like intestinal injury with prominent necrosis, inflammation, and submucosal edema/separation of the lamina propria in the ileocecal region and colon within 12-24 h. The anemic intestine is infiltrated by inflammatory macrophages, which are activated in situ by RBC transfusions via a Toll-like receptor (TLR)-4-mediated mechanism and cause bowel injury. Chelation of RBC degradation products with haptoglobin, absence of TLR4, macrophage depletion, and inhibition of macrophage activation is protective. Intestinal injury worsens with increasing severity and the duration of anemia prior to transfusion, indicating a need for the re-evaluation of current transfusion guidelines for premature infants.
Query Performance Prediction using Passage Information (2018)

We focus on the post-retrieval query performance prediction (QPP) task. Specifically, we make a new use of passage information for this task. Using such information we derive a new mean score calibration predictor that provides a more accurate prediction. Using an empirical evaluation over several common TREC benchmarks, we show that, QPP methods that only make use of document-level features are mostly suited for short query prediction tasks; while such methods perform significantly worse in verbose query prediction settings. We further demonstrate that, QPP methods that utilize passage-information are much better suited for verbose settings. Moreover, our proposed predictor, which utilizes both document-level and passage-level features provides a more accurate and consistent prediction for both types of queries. Finally, we show a connection between our predictor and a recently proposed supervised QPP method, which results in an enhanced prediction.
An Efficient Technique for Searching Very Large Files with Fuzzy Criteria Using the Pigeonhole Principle (2014)

Big Data is the new term of the exponential growth of data in the Internet. The importance of Big Data is not about how large it is, but about what information you can get from analyzing these data. Such analysis would help many businesses on making smarter decisions, and provide time and cost reduction. Therefore, to make such analysis, you will definitely need to search the large files on Big Data. Big Data is such a construction where sequential search is prohibitively inefficient, in terms of time and energy. Therefore, any new technique that allows very efficient search in very large files is highly demanded. The paper presents an innovative approach for efficient searching with fuzzy criteria in very large information systems(Big Data). Organization of efficient access to a large amount of information by an "approximate" or "fuzzy" indication is a rather complicated Computer Science problem. Usually, the solution of this problem relies on a brute force approach, which results in sequential look-up of the file. In many cases, this substantially undermines system performance. The suggested technique in this paper uses different approach based on the Pigeonhole Principle. It searches binary strings that match the given request approximately. It substantially reduces the sequential search operations and works extremely efficiently from several orders of magnitude including speed, cost and energy. This paper presents a complex developed scheme for the suggested approach using a new data structure, called FuzzyFind Dictionary. The developed scheme provides more accuracy than the basic utilization of the suggested method. It also, works much faster than the sequential search.
Thermally Stable Perovskite Solar Cells by Systematic Molecular Design of the Hole-Transport Layer (2019)

With metal halide perovskite solar cells (PSCs) now reaching device efficiencies >23%, more emphasis must now shift toward addressing their device stability. Recently, a triarylamine-based organic hole-transport material (HTM) doped with its oxidized salt analogue (EH44/EH44-ox) led to unencapsulated PSCs with high stability in ambient conditions. Here we report criteria for triarylamine-based organic HTMs formulated with stable oxidized salts as hole-transport layer (HTL) for increased PSC thermal stability. The triarylamine-based dopants must contain at least two para-electron-donating groups for radical cation stabilization to prevent impurity formation that leads to reduced PSC performance. The stability of unencapsulated devices prepared using these new HTMs stressed under constant load and illumination far outperforms that of both EH44/EH44-ox and Li+-doped spiro-OMeTAD controls at 50 °C. Furthermore, the ability to mix and match these dopants with a nonidentical small-molecule-based HTL matrix broadens the design scope for highly stable and cost-effective PSCs without sacrificing performance.
Genesis of the novel human-infecting influenza A(H10N8) virus and potential genetic diversity of the virus in poultry, China (2014)

Human infection with a novel influenza A(H10N8) virus was first described in China in December 2013. However, the origin and genetic diversity of this virus is still poorly understood. We performed a phylogenetic analysis and coalescent analysis of two viruses from the first case of influenza A(H10N8) (A/Jiangxi-Donghu/346-1/2013 and A/Jiangxi-Donghu/346-2/2013 and a novel A(H10N8) virus (A/chicken/Jiangxi/102/2013) isolated from a live poultry market that the patient had visited. The haemagglutinin (HA), neuraminidase (NA), PA subunit of the virus polymerase complex, nucleoprotein (NP), M and nonstructural protein (NS) genes of the three virus strains shared the same genetic origins. The origins of their HA and NA genes were similar: originally from wild birds to ducks, and then to chickens. The PA, NP, M, and NS genes were similar to those of chicken influenza A(H9N2) viruses. Coalescent analyses showed that the reassortment of these genes from A(H9N2) to A(H10N8) might have occurred at least twice. However, the PB1 and PB2 genes of the chicken A(H10N8) virus most likely originated from H7-like viruses of ducks, while those of the viruses from the case most likely stemmed from A(H9N2) viruses circulating in chickens. The oseltamivir-resistance mutation, R292K (R291K in A(H10N8) numbering) in the NA protein, occurred after four days of oseltamivir treatment. It seems that A(H10N8) viruses might have become established among poultry and their genetic diversity might be much higher than what we have observed.
Hypervariable Region 1 Deletion and Required Adaptive Envelope Mutations Confer Decreased Dependency on Scavenger Receptor Class B Type I and Low-Density Lipoprotein Receptor for Hepatitis C Virus (2013)

Hypervariable region 1 (HVR1) of envelope protein 2 (E2) of hepatitis C virus (HCV) serves important yet undefined roles in the viral life cycle. We previously showed that the viability of HVR1-deleted JFH1-based recombinants with Core-NS2 of H77 (H77(ΔHVR1), genotype 1a) and S52 (S52(ΔHVR1), genotype 3a) in Huh7.5 cells was rescued by E2 substitutions N476D/S733F and an E1 substitution, A369V, respectively; HVR1-deleted J6 (J6(ΔHVR1), genotype 2a) was fully viable. In single-cycle production assays, where HCV RNA was transfected into entry-deficient Huh7-derived S29 cells with low CD81 expression, we found no effect of HVR1 deletion on replication or particle release for H77 and S52. HCV pseudoparticle assays in Huh7.5 cells showed that HVR1 deletion decreased entry by 20- to 100-fold for H77, J6, and S52; N476D/S733F restored entry for H77(ΔHVR1), while A369V further impaired S52(ΔHVR1) entry. We investigated receptor usage by antibody blocking and receptor silencing in Huh7.5 cells, followed by inoculation of parental and HVR1-deleted HCV recombinants. Compared to parental viruses, scavenger receptor class B type I (SR-BI) dependency was decreased for H77(ΔHVR1/N476D/S733F), H77(N476D/S733F), S52(ΔHVR1/A369V), and S52(A369V), but not for J6(ΔHVR1). Low-density lipoprotein receptor (LDLr) dependency was decreased for HVR1-deleted viruses, but not for H77(N476D/S733F) and S52(A369V). Soluble LDLr neutralization revealed strong inhibition of parental HCV but limited effect against HVR1-deleted viruses. Apolipoprotein E (ApoE)-specific HCV neutralization was similar for H77, J6, and S52 viruses with and without HVR1. In conclusion, HVR1 and HVR1-related adaptive envelope mutations appeared to be involved in LDLr and SR-BI dependency, respectively. Also, LDLr served ApoE-independent but HVR1-dependent functions in HCV entry.
A 16-bit 16-MS/s SAR ADC With On-Chip Calibration in 55-nm CMOS (2018)

This paper presents a successive approximation register (SAR) analog-to-digital converter (ADC) that is much smaller and faster than other recently reported precision (16-bit and beyond) SAR ADCs. In addition, it features low input capacitance and an efficient on-chip foreground calibration algorithm to fix bit weight errors. Several other enabling techniques are also used, including signal independent reference using reservoir capacitors to improve speed and reduce area, plus LSB repeats and statistical residue measurement to improve efficiency. The prototype achieves 97.5-dB spurious-free dynamic range at 100-kHz input while operating at 16 MS/s and consumes 16.3 mW. It was fabricated in a 55-nm CMOS process and occupies 0.55 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> .
Field intercomparison of channel master ADCP with riversonde radar for measuring river discharge (2005)

The RiverSonde radar makes non-contact measurement of a horizontal swath of surface velocity across a river section. This radar, which has worked successfully at several rivers in the western USA, has shown encouraging correlation with simultaneous measurements of average currents at one level recorded by an acoustic travel-time system. This work reports a field study intercomparing data sets from a 600 kHz Channel Master ADCP with the RiverSonde radar. The primary goal was to begin to explore the robustness of the radar data as a reliable index of discharge. This site is at Three Mile Slough in northern California, USA. The larger intent of the work is to examine variability in space and time of the radar's surface currents compared with subsurface flows across the river section. Here we examine data from a couple of periods with strong winds.
Spectinomycin modification. V. The synthesis and biological activity of spectinomycin analogs with ring-expanded sugars. (1988)

Tiffeneau-Demjanov rearrangement of 3'-(R)-N,N'-dibenzyloxycarbonyl-3'-aminomethyl-dihydrospectinom ycin results in ring expansion affording the homologous analog with a seven-membered sugar ring. In stark contrast, attempted rearrangement of the 3'-S-isomer leads only to epoxide formation. Deprotection of the ring-expanded homolog gives homospectinomycin. The synthesis and biological activity of this interesting new member of the spectinomycin series and the derived dihydrohomospectinomycin is detailed in this paper.
All-optical regeneration at the receiver of 10-Gb/s RZ data transmitted over 30 000 km using an electroabsorption modulator (2000)

We have demonstrated all-optical regeneration (reshape and reamplify) at the receiver of 10-Gb/s return-to-zero (RZ) data transmitted over 30 000 km in a dispersion-managed system using cross-absorption modulation in an electroabsorption modulator at the receiver. The nonlinear optical transmission characteristic of the modulator increases the signal-to-noise ratio by preferentially suppressing the accumulated amplified spontaneous emission noise of the propagated signal. Fast recovery of the optical absorption under reverse bias allows high data-rate operation without bit-patterning effect. The error-free propagation distance of the dispersion-managed system and its performance is increased as a result of the regeneration.
Consistent Weighted Sampling Made Fast, Small, and Easy (2014)

Document sketching using Jaccard similarity has been a workable effective technique in reducing near-duplicates in Web page and image search results, and has also proven useful in file system synchronization, compression and learning applications. Min-wise sampling can be used to derive an unbiased estimator for Jaccard similarity and taking a few hundred independent consistent samples leads to compact sketches which provide good estimates of pairwise-similarity. Subsequent works extended this technique to weighted sets and show how to produce samples with only a constant number of hash evaluations for any element, independent of its weight. Another improvement by Li et al. shows how to speedup sketch computations by computing many (near-)independent samples in one shot. Unfortunately this latter improvement works only for the unweighted case. In this paper we give a simple, fast and accurate procedure which reduces weighted sets to unweighted sets with small impact on the Jaccard similarity. This leads to compact sketches consisting of many (near-)independent weighted samples which can be computed with just a small constant number of hash function evaluations per weighted element. The size of the produced unweighted set is furthermore a tunable parameter which enables us to run the unweighted scheme of Li et al. in the regime where it is most efficient. Even when the sets involved are unweighted, our approach gives a simple solution to the densification problem that other works attempted to address. Unlike previously known schemes, ours does not result in an unbiased estimator. However, we prove that the bias introduced by our reduction is negligible and that the standard deviation is comparable to the unweighted case. We also empirically evaluate our scheme and show that it gives significant gains in computational efficiency, without any measurable loss in accuracy.
XIVE: External interrupt virtualization for the cloud infrastructure (2018)

In today's microprocessors, external interrupts are the only processor resource that has no full virtualization hardware support. Therefore, they create significant overhead in the form of virtual machine (VM) context switches, especially in cloud and hyperscale datacenter systems, in which the physical processors are shared by a large number of virtual processors allocated to the VMs running on the system. The IBM POWER9 processor closes this gap in the processor hardware virtualization support by introducing an eXternal Interrupt Virtualization Engine (XIVE) architecture. XIVE defines a holistic interrupt delivery mechanism that supports multiple layers of interrupt coalescing and hardware-based routing of interrupts to the correct physical thread and target level. As required, individual interrupts can thus be routed directly to a user process, to a specific supervisor or an operating system, or to the hypervisor, thereby eliminating the need for interrupt rerouting in software and minimizing the number of context switches. In addition, XIVE provides the means to automatically trigger escalation interrupts to the next higher privilege level in case the target of an interrupt is not dispatched. In this paper, we discuss the fundamental concepts of the XIVE architecture and provide an overview of the XIVE-based interrupt controller implementation of the IBM POWER9 processor.
92 Single chain urokinase-type plasminogen activator bound to its receptor is relatively resistant to plasminogen activator inhibitor type 1 (1996)

Urokinase-type plasminogen activator (uPA) is synthesized as single-chain protein (scuPA) with little intrinsic activity. scuPA is activated when it is converted to two-chain urokinase (tcuPA) by plasmin or when it binds as a single-chain molecule to its cellular receptor (uPAR). Previous data indicate that complexes between scuPA and its receptor have somewhat higher affinity for plasminogen than does tcuPA. The current study indicates that plasminogen activator activity of scuPA bound to recombinant, soluble uPAR (suPAR) is also fivefold less sensitive to inhibition by plasminogen activator type 1 (PAI-1) than is soluble or receptor-bound tcuPA. Binding of PaI-1 to suPAR/scuPA complexes is totally reversible and can be overcome by increasing the concentration of plasminogen, suggesting a competitive mechanism of inhibition (Ki = 18 nmol/L). Binding of scuPA to suPAR also retards its cleavage by plasmin. These results indicates that binding of single-chain urokinase to its receptor promotes its activity, retards its inhibition, and protects it from conversion to a two-chain form of the enzyme, a step that may precede its inactivation and clearance from cell surfaces. These results are consistent with a physiologic role for receptor-bound single-chain urokinase as a cellular plasminogen activator.
Single-shot two-dimensional infrared spectroscopy (2007)

Multidimensional infrared spectroscopy is a robust tool for studying the structural dynamics of molecules. In particular, twodimensional infrared (2DIR) spectroscopy can reveal vibrational coupling among the internal modes of molecules, uncovering the transient structure of complex systems. While spectroscopically very powerful, current experimental techniques are time consuming to perform, requiring ~10(6) laser shots for a single 2DIR spectrum. In this work, we demonstrate a new technique that can acquire a full 2DIR correlation spectrum using a single ultrafast laser pulse. This apparatus will allow 2DIR spectroscopy to be extended to systems that were unattainable with previous technology, including, irreversible chemical reactions, rapid flow experiments, or with low repetition rate laser systems.