gebhart/patrepeval huggingface dataset:
Inhibition of HIV-1 Replication Using a Mutated tRNALys-3 Primer (1997)

Cellular tRNALys-3 serves as the primer for reverse transcription of human immunodeficiency virus, type 1 (HIV-1). tRNALys-3 interacts directly with HIV-1 reverse transcriptase, is packaged into viral particles and anneals to the primer-binding site (PBS) of the HIV-1 genome to initiate reverse transcription. Therefore, the priming step of reverse transcription is a potential target for antiviral strategies. We have developed a mutant tRNALys-3 derivative with mutations in the PBS-binding region such that priming specificity was re-directed to the highly conserved TAR stem-loop region. This mutant tRNA retains high-affinity binding to HIV-1 reverse transcriptase, viral encapsidation, and is able to prime at both the targeted TAR sequence and at the viral PBS. Constitutive expression of mutant tRNA in T-cells results in marked inhibition of HIV-1 replication, as determined by measurements of viral infectivity, syncytium formation, and p24 production. Inhibition of retroviral replication through interference with the normal process of priming constitutes a new anti-retroviral approach and also provides a novel tool for dissecting molecular aspects of priming.
A CACNA1A variant associated with trigeminal neuralgia alters the gating of Cav2.1 channels (2021)

A novel missense mutation in the CACNA1A gene that encodes the pore forming α<sub>1</sub> subunit of the Ca<sub>V</sub>2.1 voltage-gated calcium channel was identified in a patient with trigeminal neuralgia. This mutation leads to a substitution of proline 2455 by histidine (P2455H) in the distal C-terminus region of the channel. Due to the well characterized role of this channel in neurotransmitter release, our aim was to characterize the biophysical properties of the P2455H variant in heterologously expressed Ca<sub>V</sub>2.1 channels. Whole-cell patch clamp recordings of wild type and mutant Ca<sub>V</sub>2.1 channels expressed in tsA-201 cells reveal that the mutation mediates a depolarizing shift in the voltage-dependence of activation and inactivation. Moreover, the P2455H mutant strongly reduced calcium-dependent inactivation of the channel that is consistent with an overall gain of function. Hence, the P2455H Ca<sub>V</sub>2.1 missense mutation alters the gating properties of the channel, suggesting that associated changes in Ca<sub>V</sub>2.1-dependent synaptic communication in the trigeminal system may contribute to the development of trigeminal neuralgia.
Multipath variability due to the Gulf Stream (1981)

A phase-coded signal with 64-ms resolution was transmitted at 10-min intervals for a 19-day period over two -300-km ranges. The acoustic source was moored at 2000-m depth northwest of Bermuda. One receiver was moored at 2000-m depth to the northeast of the source and the other receiver was bottom mounted at -1000m depth near Bermuda. The large ( -0.6 s) travel time change at the Bermuda receiver is probably due in large part to motion of the source mooring in the presence of currents. The multipath arrival pattern at the moored receiver undergoes significant modification due to the presence of a southern meander of the Gulf Stream which intersects this transmission path.
Braid: Weaving Symbolic and Statistical Knowledge into Coherent Logical Explanations. (2020)

Traditional symbolic reasoning engines, while attractive for their precision and explicability, have a few major drawbacks: the use of brittle inference procedures that rely on exact matching (unification) of logical terms, an inability to deal with uncertainty, and the need for a precompiled rule-base of (the knowledge acquisition problem). These issues are particularly severe for the Natural Language Understanding (NLU) task, where we often use implicit background to understand and reason about text, resort to fuzzy alignment of concepts and relations during reasoning, and constantly deal with ambiguity in representations. To address these issues, we devise a novel FOL-based reasoner, called Braid, that supports probabilistic rules, and uses the notion of custom unification functions and dynamic rule generation to overcome the brittle matching and knowledge-gap problem prevalent in traditional reasoners. In this paper, we describe the reasoning algorithms used in Braid-BC (the backchaining component of Braid), and their implementation in a distributed task-based framework that builds proof/explanation graphs for an input query in a scalable manner. We use a simple QA example from a children's story to motivate Braid-BC's design and explain how the various components work together to produce a coherent logical explanation.
Optical cavities and waveguides in hyperuniform disordered photonic solids (2013)

Using finite-difference time domain and band structure computer simulations, we show that it is possible to construct optical cavities and waveguide architectures in hyperuniform disordered photonic solids that are unattainable in photonic crystals. The cavity modes can be classified according to the symmetry (monopole, dipole, quadrupole, etc.) of the confined electromagnetic wave pattern. Owing to the isotropy of the band-gap characteristics of hyperuniform disordered solids, high-quality waveguides with free-form geometries (e.g., arbitrary bending angles) can be constructed that are unprecedented in periodic or quasiperiodic solids. These capabilities have implications for many photonic applications.
Single-Molecule Charge-Transport Measurements that Reveal Technique-Dependent Perturbations (2006)

We compare scanning tunneling microscopy (STM) imaging with single-molecule conductive atomic force microscopy (C-AFM) measurements by probing a series of structurally related thiol-terminated oligo(phenylenevinylene)s (OPVs) designed to have unique charge-transport signatures. When one or two methylene spacers are inserted between the thiol points of attachment and the OPV core, a systematic reduction in the imaged molecular transconductance and the current transmitted through a metal-molecule-metal junction containing the molecule is observed, indicating good agreement between STM and C-AFM measurements. However, a structure where the OPV backbone is interrupted by a [2.2]paracyclophane core has a low molecular transconductance, as determined from STM images, and a high measured single-molecule conductance. This apparent disconnect can be understood by comparing the calculated molecular orbital topology of the OPV with one thiol bound to a gold surface (the geometry in the STM experiment) with the topology of the molecule with both thiol termini bound to gold (relevant to C-AFM). In the former case, a single contact splits low-lying molecular orbitals into two discrete fragments, and in the latter case, molecular orbitals that span the entire molecule are observed. Although the difference in observed conductance between the two different measurements is resolved, the overall set of observations highlights the importance of using combined techniques to better characterize charge-transport properties relevant to molecular electronics.
LAVA: An Open-Source Approach To Designing LAMP (Loop-Mediated Isothermal Amplification) DNA Signatures (2011)

We have designed and demonstrated new software for identifying signature candidates appropriate for LAMP assays. The software is available for download at http://lava-dna.googlecode.com/.
Frontispiece: Chemo‐ and Regioselective Ethynylation of Tryptophan‐Containing Peptides and Proteins (2016)

A gold Tr(i)p! In their Communication on page 1572 ff., M. B. Hansen and co-workers functionalized (poly)-peptides with TIPS-ethynyl moieties at their tryptophan residues using Waser's reagent, 1-[(triisopropylsilyl)ethynyl]-1,2-benziodoxol-3(1 H)-one (TIPS-EBX), under gold(I) catalysis. The reaction proceeded in a regio- and chemoselective manner leading to C2 substitution at the tryptophan residues only. Subsequently, the terminal alkyne was used to label one of the model peptides with a fluorophore by means of copper-catalyzed click chemistry.
Nano Ellagic Acid Counteracts Cisplatin-Induced Upregulation in OAT1 and OAT3: A Possible Nephroprotection Mechanism (2020)

Cisplatin is an anticancer drug commonly used for solid tumors. However, it causes nephrotoxicity. OAT1 and OAT3 are organic anion transporters known to contribute to the uptake of cisplatin into renal tubular cells. The present study was designed to examine the protective role of ellagic acid nanoformulation (ellagic acid nano) on cisplatin-induced nephrotoxicity in rats, and the role of OAT1/OAT3 in this effect. Four groups of male Wistar rats were used (n = 6): (1) control, (2) cisplatin (7.5 mg/kg single dose, intraperitoneal), (3) cisplatin + ellagic acid nano (1 mg/kg), and (4) cisplatin + ellagic acid nano (2 mg/kg). Nephrotoxic rats treated with ellagic acid nano exhibited a significant reduction in elevated serum creatinine, urea, and oxidative stress marker, malondialdehyde (MDA). Additionally, ellagic acid nano restored renal glutathione (GSH), superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GPx). Ellagic acid nano improved the histopathological changes induced by cisplatin, such as tubular dilatation, necrosis, and degeneration. Interestingly, OAT1 and OAT3 showed significantly lower expression at both mRNA and protein levels following ellagic acid nano treatment relative to the cisplatin-exposed group. These findings reveal a potential inhibitory role of ellagic acid antioxidant on OAT1 and OAT3 expression and thus explains its nephroprotective effect against cisplatin nephrotoxicity.
Large-scale whole-genome sequencing of three diverse Asian populations in Singapore (2018)

Abstract Asian populations are currently underrepresented in human genetics research. Here we present whole-genome sequencing data of 4,810 Singaporeans from three diverse ethnic groups: 2,780 Chinese, 903 Malays, and 1,127 Indians. Despite a medium depth of 13.7×, we achieved essentially perfect (&gt;99.8%) sensitivity and accuracy for detecting common variants and good sensitivity (&gt;89%) for detecting extremely rare variants with &lt;0.1% allele frequency. We found 89.2 million single-nucleotide polymorphisms (SNPs) and 9.1 million small insertions and deletions (INDELs), more than half of which have not been cataloged in dbSNP. In particular, we found 126 common deleterious mutations (MAF&gt;0.01) that were absent in the existing public databases, highlighting the importance of local population reference for genetic diagnosis. We describe fine-scale genetic structure of Singapore populations and their relationship to worldwide populations from the 1000 Genomes Project. In addition to revealing noticeable amounts of admixture among three Singapore populations and a Malay-related novel ancestry component that has not been captured by the 1000 Genomes Project, our analysis also identified some fine-scale features of genetic structure consistent with two waves of prehistoric migration from south China to Southeast Asia. Finally, we demonstrate that our data can substantially improve genotype imputation not only for Singapore populations, but also for populations across Asia and Oceania. These results highlight the genetic diversity in Singapore and the potential impacts of our data as a resource to empower human genetics discovery in a broad geographic region.
Au nanoparticle clusters from deposition of a coalescing emulsion (2015)

Clusters are observed to contain as few as 8 to as many as 24 Au nanoparticles. The clusters are anisotropic and can also be formed from larger nanoparticles. Hydrophobic and hydrophilic interactions are implicated in the formation of these clusters within the interfacial tension gradients of a coalescing emulsion. The clusters can be re-suspended in ethanol and water, maximizing the utility of these clusters with an extinction band in the near-Infrared region of the electromagnetic spectrum.
A Data-Driven Framework for the Accelerated Discovery of CO2 Reduction Electrocatalysts (2021)

Searching for next-generation electrocatalyst materials for electrochemical energy technologies is a time-consuming and expensive process, even if it is enabled by high-throughput experimentation and extensive first-principle calculations. In particular, the development of more active, selective and stable electrocatalysts for the CO 2 reduction reaction remains tedious and challenging. Here, we introduce a material recommendation and screening framework, and demonstrate its capabilities for certain classes of electrocatalyst materials for low or high-temperature CO 2 reduction. The framework utilizes high-level technical targets, advanced data extraction, and categorization paths, and it recommends the most viable materials identified using data analytics and property-matching algorithms. Results reveal relevant correlations that govern catalyst performance under low and high-temperature conditions.
Downregulated miR-15b-5p induces suppressor of cytokine signaling 6 (SOCS6) expression during viral hemorrhagic septicemia virus infection in olive flounder (2022)

Abstract MicroRNAs (miRNAs) are endogenous small non-coding RNAs consisted of 21–25 nucleotides that modulate the gene expression by binding to 3′ untranslated region (3′ UTR) of target messenger RNA (mRNA) at the post-transcriptional level. The miRNAs are well known to participate in various physiological processes including cellular differentiation, apoptosis, angiogenesis and immune responses. In particular, during a viral infection, the virus regulates host miRNA expression to evade host immunity. In this study, we investigated whether viral hemorrhagic septicemia virus (VHSV) infection affects the expression of miR-15b-5p and its target gene, suppressor of cytokine signaling ( SOCS6 ) in olive flounder ( Paralichthys olivaceus ). The relative expression of miR-15b-5p and SOCS6 was analyzed in VHSV-infected olive flounder at different time points: 1, 3, and 7 days post infection (dpi). The expression of miR-15b-5p was decreased in the infected group but that of SOCS6 was increased. These alterations in miR-15b-5p and SOCS6 expression suggest that they could be important factors regulated by VHSV during infection.
d-Amino Acid Scan of Two Small Proteins (2016)

A "D-scan" of two small proteins, the disulfide-rich Ecballium elaterium trypsin inhibitor II (EETI-II) and a minimized Z domain of protein A (Z33), is reported. For each protein, the stereochemistry of one amino acid at a time was inverted to generate a series of diastereomers. In much the same way an alanine scan determines necessary residues for protein function, the D-scan elucidated the critical stereocenters of the 30-residue EETI-II and the 33-residue Z33. The folding properties and activity of each variant were investigated. A total of 24 out of 30 EETI-II D-scan analogues folded to give a three-disulfide product. Of the 24 variants that folded, half were high-affinity trypsin inhibitors, and three were as active as the wild type (WT). Of these 12 active variants, most were substantially less stable to reduction than WT EETI-II (WT first reduction potential -270.0 ± 1.5 mV, WT second reduction potential -307.2 ± 1.1 mV). Similarly, ten Z33 analogues retained high binding affinity to IgG (KD < 250 nM, WT: 24 ± 1 nM) and 12 additional analogues had reduced but appreciable IgG binding affinity (KD between 250 nM and 2.5 μM). As with EETI-II, most Z33 analogues were substantially less stable than the WT (ΔG(H2O, 263 K) = 2.4 ± 1.2 kcal/mol). Collectively, our findings show that the D-scan is powerful new strategy for studying how the stereochemistry of amino acids affects the structure and function of proteins.
Feature-Based Molecular Networking for the Targeted Identification of Gq-Inhibiting FR900359 Derivatives (2021)

Both the soil bacterium <i>Chromobacterium vaccinii</i> and the bacterial endosymbiont <i>Candidatus</i> Burkholderia crenata of the plant <i>Ardisia crenata</i> are producers of FR900359 (FR). This cyclic depsipeptide is a potent and selective G<sub>q</sub> protein inhibitor used extensively to investigate the intracellular signaling of G protein coupled receptors (GPCRs). In this study, the metabolomes of both FR producers were investigated and compared using feature-based molecular networking (FBMN). As a result, 30 previously unknown FR derivatives were identified, one-third being unique to <i>C. vaccinii</i>. Guided by MS, a novel FR derivative, FR-6 (compound <b>1</b>), was isolated, and its structure unambiguously established. In a whole-cell biosensing assay based on detection of dynamic mass redistribution (DMR) as readout for G<sub>q</sub> inhibition, FR-6 suppressed G<sub>q</sub> signaling with micromolar potency (pIC<sub>50</sub> = 5.56). This functional activity was confirmed in radioligand binding assays (p<i>K</i><sub>i</sub> = 7.50). This work demonstrates the power of molecular networking, guiding the way to a novel G<sub>q</sub>-inhibiting FR derivative and underlining the potency of FR as a G<sub>q</sub> inhibitor.
Micro‐reactors to Study Alite Hydration (2015)

A new approach to study the early hydration reaction of alite is presented. It relies on milling micron‐sized gaps into alite grains using a Focused Ion Beam. This provides for a “micro‐reactor” in which hydration in confined conditions can be followed after introducing aqueous solutions of any desired composition. Hydration is followed by stopping the reaction at desired ages using solvent exchange and imaging the gaps using a Scanning Electron Microscope. These micro‐reactors offer several advantages over conventional methods to monitor alite hydration. In particular, we can study the time evolution of dissolution in a reproducible manner using a setup that mimics particles in close contact. This paper presents this new methodology and applies it to studying the effects of solution composition and selected chemical admixtures on the dissolution of alite. New insights into the role of these factors are obtained and discussed.
GPS Cycle Slip Detection and Correction at Measurement Level (2014)

Carrier phase measurements are much more precise than pseudorange measurements and can be used to achieve very accurate positioning solutions. However, carrier phase measurements require resolution of integer ambiguities before precise positioning can be achieved. The GPS receiver can keep track of the integer number of cycles as long as the receiver maintains lock to the satellite signal. However, in reality, the GPS signal could be interrupted momentary by some disturbing factors leading to a discontinuity of an integer number of cycles in the measured carrier phase. This interruption in the counting of cycles in the carrier phase measurements is known as a cycle slip. When a cycle slip occurs, the Doppler counter would restart causing a jump in the instantaneous accumulated phase by an integer number of cycles. Thus, the integer counter is reinitialized meaning that ambiguities are unknown again. In this event, either the ambiguities need to be resolved again or cycle slips need to be corrected to resume the precise positioning/navigation process. These cycle slips can, to some extent, be detected and fixed to avoid delay and computation complexity attributed to integer ambiguity resolution. Researchers have been addressing the problem of cycle slip detection and correction for the last two decades. This paper provides a detailed survey for available techniques to tackle the problem showing their pros and cons.
Crossover scale of the fixed point with replica symmetry breaking in the random Potts model (1997)

We study the scaling properties of the renormalization group (RG) flows in the two-dimensional random Potts model, assuming a general type of replica symmetry breaking (RSB) in the renormalized coupling matrix. It is shown that in the asymptotic regime the RG flows approach the non-trivial RSB fixed point algebraically slowly, which reflects the fact that this type of the fixed point is marginally stable. As a consequence, the crossover spatial scale corresponding to the critical regime described by this fixed point turns out to be exponentially large.
Solitary current-density patterns in thin ZnS:Mn films (2000)

We experimentally investigate pattern formation phenomena in the electroluminescence of ac-driven ZnS:Mn thin films. Under suitable driving conditions, certain samples show a broad spectrum of patterns, which ranges from stationary filamentary distributions to traveling fronts and pulses. We present a survey of the bifurcation scenarios, choosing the frequency and amplitude of the driving voltage as bifurcation parameters. Moreover, we investigate the influence of the temperature on the dissipative current and pattern formation. The experimental results are used to identify activating and inhibiting processes, and a pattern formation mechanism based on autocatalysis and lateral inhibition is suggested.
Blood Concentration of Food-Derived Peptides follwing Oral Intake of Chicken Collagen Hydrolysate and its Angiotensin-Converting Enzyme Inhibitory Activity in Healthy Volunteers (2009)

降圧作用を有する鶏コラーゲン加水分解物（C-COP）を健常人に摂取させ，C-COPの血中動態およびアンジオテンシン変換酵素（ACE）阻害活性との関連性について検討した．体重60kgあたり25gのC-COPをヒトに単回摂取させた場合，血中に遊離ヒドロキプロリン（Hyp）とともに，ペプチド型のHypも確認された．血中のペプチド型Hyp量は，2時間後（91.1μmol/L）に最大となった．摂取2時間後の血中からPro-Hyp, Leu-Hyp, Pro-Hyp-Gly, Phe-Hyp, Ala-Hyp, Hyp-Gly, Glu-Hyp-Gly, Ala-Hyp-Gly, Ser-Hyp-GlyのHyp含むペプチドが確認された．血中ペプチドは，ACEに対する阻害活性を有しており，Ala-Hyp（IC50 : 0.177mmol/L）の活性がもっとも高かった．以上より，C-COPの降圧作用は，血中ペプチドによるACE阻害が作用機序であると考えられた．
Breakthroughs in Photonics 2013: A Microwatt-Threshold Raman Silicon Laser (2014)

A continuous-wave Raman silicon laser using a photonic-crystal high- Q nanocavity was developed in 2013, with a cavity size of less than 10 μm and an unprecedented ultralow threshold of 1 μW. This report describes how this breakthrough was accomplished by adopting a unique nanocavity design.
Polyelectrolyte Complex Coacervation across a Broad Range of Charge Densities (2021)

Polyelectrolyte complex coacervates of homologous (co)polyelectrolytes with a near-ideally random distribution of a charged and neutral ethylene oxide comonomer were synthesized. The unique platform provided by these building blocks enabled an investigation of the phase behavior across charge fractions 0.10 ≤ <i>f</i> ≤ 1.0. Experimental phase diagrams for <i>f</i> = 0.30-1.0 were obtained from thermogravimetric analysis of complex and supernatant phases and contrasted with molecular dynamics simulations and theoretical scaling laws. At intermediate to high <i>f</i>, a dependence of polymer weight fraction in the salt-free coacervate phase (<i>w</i> <sub>P,c</sub>) of <i>w</i> <sub>P,c</sub> ∼ <i>f</i> <sup>0.37±0.01</sup> was extracted; this trend was in good agreement with accompanying simulation predictions. Below <i>f</i> = 0.50, <i>w</i> <sub>P,c</sub> was found to decrease more dramatically, qualitatively in line with theory and simulations predicting an exponent of 2/3 at <i>f</i> ≤ 0.25. Preferential salt partitioning to either coacervate or supernatant was found to be dictated by the chemistry of the constituent (co)polyelectrolytes.