gebhart/patrepeval huggingface dataset:
An Immunocompetent Mouse Model of Zika Virus Infection (2020)

Progress toward understanding Zika virus (ZIKV) pathogenesis is hindered by lack of immunocompetent small animal models, in part because ZIKV fails to effectively antagonize Stat2-dependent interferon (IFN) responses in mice. To address this limitation, we first passaged an African ZIKV strain (ZIKV-Dak-41525) through Rag1-/- mice to obtain a mouse-adapted virus (ZIKV-Dak-MA) that was more virulent than ZIKV-Dak-41525 in mice treated with an anti-Ifnar1 antibody. A G18R substitution in NS4B was the genetic basis for the increased replication, and resulted in decreased IFN-β production, diminished IFN-stimulated gene expression, and the greater brain infection observed with ZIKV-Dak-MA. To generate a fully immunocompetent mouse model of ZIKV infection, human STAT2 was introduced into the mouse Stat2 locus (hSTAT2 KI). Subcutaneous inoculation of pregnant hSTAT2 KI mice with ZIKV-Dak-MA resulted in spread to the placenta and fetal brain. An immunocompetent mouse model of ZIKV infection may prove valuable for evaluating countermeasures to limit disease.
Tree pyramidal adaptive importance sampling (2019)

This paper introduces Tree-Pyramidal Adaptive Importance Sampling (TP-AIS), a novel iterated sampling method that outperforms state-of-the-art approaches like deterministic mixture population Monte Carlo (DM-PMC), mixture population Monte Carlo (M-PMC) and layered adaptive importance sampling (LAIS). TP-AIS iteratively builds a proposal distribution parameterized by a tree pyramid, where each tree leaf spans a subspace that represents its importance density. After each new sample operation, a set of tree leaves are subdivided for improving the approximation of the proposal distribution to the target density. Unlike the rest of the methods in the literature, TP-AIS is parameter free and requires no tuning to achieve its best performance. We evaluate TP-AIS with different complexity randomized target probability density functions (PDF) and also analyze its application to different dimensions. The results are compared to state-of-the-art iterative importance sampling approaches and other baseline MCMC approaches using Normalized Effective Sample Size (N-ESS), Jensen-Shannon Divergence, and time complexity.
Intelligent Reflecting Surfaces in UAV-Assisted 6G Networks: An Approach for Enhanced Propagation and Spectral Characteristics (2022)

Intelligent reflecting surfaces (IRSs) with the ability to reconfigure inherent electromagnetic reflection and absorption characteristics in real-time provide unparalleled prospects to improve wireless connectivity in adverse circumstances. Unmanned aerial vehicles (UAV)-assisted wireless networks are evolved as a reliable solution to combat non-line of sight (NLoS) scenarios. Thereby, the IRS-empowered UAV-assisted cellular networks will be a significant role-player to improve the coverage and user experiences. The paper aimed to minimize the path loss and maximize the achievable data rate in IRS-UAV-assisted networks. In this context, the work analyzed path loss and achievable rate utilizing millimeter wave (mmWave) carrier considering the conventional UAV model and IRS-empowered UAV communication model. The research obtained that the IRS-empowered UAV communications model can significantly minimize path loss and maximize the achievable data rate compared to the conventional UAV-assisted model.
RE: Acetabular paralabral cysts and perineural propagation (2023)

We read with great interest the recent article ' Acetabular paralabral cysts demonstrating perineural propagation' by Hynes et al. 1 Over the years, our group has been excited to see additional examples of intraneural cysts being recognized at all para-articular sites and reported by others.We were surprised, however, that this paper concluded that it was "the first description of (such) a series of patients with acetabular paralabral cysts." It did not include other related case series of intraneural ganglion cysts, which arose from the hip joint and spread along the affected articular branch into parent nerves published over the past decade. 2-4It also did not discuss the unified articular (synovial) theory 5 ; this explanation put forth more than 20 years ago and substantiated by many authors across the world, 6,7 not only describes the underlying mechanism of intraneural (and extraneural) cysts but also provides implications for their treatment.We call the readership's attention to the long history and growing body of clinicoradiological work related to these cysts, characterizing their predictable articular formation and perineural propagation patterns.
Analysis of Spectral Parameters of Audio Signals for the Identification of Spam Over IP Telephony. (2008)

Introduction of single amino acid substitutions into the C-terminal Arg-Gly-Asp-Ser (RGDS) site of von Willebrand Factor, referred to as RGD mutant vWF, selectively abrogated vWF binding to platelet glycoprotein IIb/IIIa (GpIIb/IIIa alpha IIb beta 3) and abolished human umbilical vein endothelial cell (HUVEC) spreading, but not attachment, to RGD mutant vWF (Beacham, D.A., Wise, R.J., Turci, S.M. and Handin, R. I. 1992. J. Biol. Chem. 167, 3409-3415). These results suggested that in addition to the vitronectin receptor (VNR, alpha V beta 3), a second endothelial membrane glycoprotein can mediate HUVEC adhesion to vWF. HUVEC attachment to wild-type (WT) and RGD-mutant vWF was reduced by two proteins known to block the vWF-platelet glycoprotein Ib/IX (GpIb/IX) interaction, the monoclonal antibody AS-7 and the recombinant polypeptide, vWF-A1. The addition of cytochalasin B or DNase I to disrupt potential GPIb alpha-cytoskeletal interactions enhanced the immunoprecipitation of endothelial GPIB alpha, caused HUVEC to round up, and increased HUVEC adhesion to RGD mutant vWF. These results indicate that while the VNR is the primary adhesion receptor for vWF, endothelial GPIb alpha can mediate HUVEC attachment to vWF. GpIb-dependent attachment could contribute to HUVEC adhesion under conditions when cell surface expression of the VNR is downregulated, and VNR-dependent adhesion is reduced.
Resveratrol inhibits cell proliferation and induces apoptosis of human breast carcinoma MCF-7 cells (2004)

Resveratrol, which is found in grapes and wine, has been reported to have a variety of important pharmacological effects including anti-inflammatory, anti-platelet, and anti-carcinogenetic properties. In this study, using the human breast cancer cell line MCF-7, we have analyzed a possible mechanism by which resveratrol could interfere with cell cycle control and induce cell death. Resveratrol treatment of MCF-7 cells resulted in a dose-dependent inhibition of the cell growth and the cells accumulated at the S phase transition of the cell cycle at low concentrations, but high concentrations do not induce S phase accumulation. The anti-proliferative effects of resveratrol were associated with a marked inhibition of cyclin D and cyclin-dependent kinase (Cdk) 4 proteins, and induction of p53 and Cdk inhibitor p21WAF1/CIP. Growth suppression by resveratrol was also due to apoptosis, as seen by the appearance of a sub-G1 fraction and chromatin condensation. In addition, the apoptotic process involves activation of caspase-9, a decrease of Bcl-2 as well as Bcl-XL levels, and an increase of Bax levels.
Electrochemical Detection of Surface Hybridization of Oligodeoxynucleotides Bearing Anthraquinone Tags at Gold Electrodes (2000)

Gold electrodes modified with a DNA 20-mer via a thiol linkage were shown to efficiently capture the complementary 20-mer that was tagged with anthraquinone (AQ) reporter groups. Treatment of the electrodes with 2-mercaptoethanol was required for both efficient surface hybridization and for reversible electron transfer between the gold electrode and the tethered anthraquinone tag. In addition, slow thermal annealing through the melting temperature of the duplex increased the efficiency of the process. Electrodes that had been modified with a ds-DNA bearing AQ tags gave slightly greater voltammetric signals, but after dissociation of the duplex were not as effective as the ss-DNA in capturing the complementary 20-mer from the buffer solutions.
Use of cinacalcet and sunitinib to treat hypercalcaemia due to a pancreatic neuroendocrine tumor (2017)

Neuroendocrine tumors (NETs) can secrete hormones, including ectopic secretions, but they have been rarely associated with malignant hypercalcemia. A 52-year-old man with a history of diabetes mellitus was diagnosed with a pancreatic tumor. A pancreatic biopsy confirmed a well-differentiated pancreatic NET (pNET). The patient subsequently developed liver metastasis and hypercalcemia with high 1,25 OH vitamin D and suppressed parathyroid hormone (PTH) levels. Hypercalcemia was refractory to chemotherapy, intravenous saline fluids, diuretics, calcitonin and zoledronate. Cinacalcet administration (120 mg/day) resulted in a significant calcium reduction. Hypocalcemia was observed when sunitinib was added three months later and cinacalcet was stopped. Subsequently, the calcium and PTH levels normalized. After six months, we observed 20% shrinkage of the pancreatic tumor and necrosis of a liver metastasis. Cinacalcet is an allosteric activator of the calcium receptor agonist, and it is used for severe hypercalcemia in patients with primary (benign and malignant) hyperparathyroidism. In this patient, cinacalcet demonstrated a calcium lowering effect, normalized hypophosphatemia, and improved the clinical condition of the patient. The mechanism through which cinacalcet improved PTH-rp mediated hypercalcemia is still unclear, but studies have suggested that a potential mechanism is the activation of calcitonin secretion. Sunitinib is an oral multi-targeted tyrosine kinase inhibitor used to treat advanced pNETs. The hypocalcemic effects of sunitinib have not been previously described in a patient with pNET. Here, we report for the first time the successful combination of cinacalcet and sunitinib in the treatment of a pNET patient presenting with malignant hypercalcemia.
Structure-Based Design with Tag-Based Purification and In-Process Biotinylation Enable Streamlined Development of SARS-CoV-2 Spike Molecular Probes (2020)

Biotin-labeled molecular probes, comprising specific regions of the SARS-CoV-2 spike, would be helpful in the isolation and characterization of antibodies targeting this recently emerged pathogen. To develop such probes, we designed constructs incorporating an N-terminal purification tag, a site-specific protease-cleavage site, the probe region of interest, and a C-terminal sequence targeted by biotin ligase. Probe regions included full-length spike ectodomain as well as various subregions, and we also designed mutants to eliminate recognition of the ACE2 receptor. Yields of biotin-labeled probes from transient transfection ranged from ~0.5 mg/L for the complete ectodomain to >5 mg/L for several subregions. Probes were characterized for antigenicity and ACE2 recognition, and the structure of the spike ectodomain probe was determined by cryo-electron microscopy. We also characterized antibody-binding specificities and cell-sorting capabilities of the biotinylated probes. Altogether, structure-based design coupled to efficient purification and biotinylation processes can thus enable streamlined development of SARS-CoV-2 spike-ectodomain probes.
Conventional and living carbocationic polymerizations united. II. The conversion of conventional to living isobutylene polymerization by proton trap and a comprehensive closed-loop mechanism of proton trap mediated living polymerization (1996)

The effect of the proton trap, 2,6hyphen;di-tert-butylpyridine (DtBP), on the polymerization of isobutylene (IB) induced by the “HX”/TiCl4 (“HX” = protoic impurity) intiating system has been studied. Significantly, in the presence of a large (∼ 40 molar) excess of DtBP relative to “HX”, free proton-induced chain transfer-dominated conventional IB polymerization is converted to living polymerization. In the absence of the proton trap the kinetics are dominated by rapid proton-induced processs which overwhelm the relatively slower living polymerization. These investigations also led to a quantitative assessment of the concentration of initiating species: [“HX”] = 1.46 × 10−4 mol/L. The polymerizations are first-order in monomer and the apparent rate constants of propagation drop precipituously with increasing DtBP concentration until a constant low value is reached. The rate of formation of propagating living chains has been expressed quantitatively. Chain transfer is bimolecular and first order in monomer, and kinetic investigations led to a quantitative description of the effect of proton trap concentration on the apparent first order chain transfer constant. The results have been explained in terms of a simple mechanistic scheme. © 1996 John Wiley & Sons, Inc.
Organotypic systems in drug metabolism and toxicity: challenges and opportunities (2012)

Decisions from translational systems that bridge basic drug efficacy and toxicity with clinical outcome must be benchmarked against human-relevant endpoints and clinical data for early meaningful pre-clinical decisions. The use of human primary cells coupled with emerging technologies that allow precise control of the culture environment and analysis of meaningful endpoints paves the way for human organotypic systems as a major initiative in de-risking the drug discovery and development process.
Resonant Rayleigh scattering from an anisotropic organic single-crystal microcavity (2008)

Resonant Rayleigh scattering (RRS) is observed upon excitation of a microcavity containing a single crystal of the organic molecule anthracene. The RRS profile is obtained for a range of excitation energies and angles. In contrast to the circular profile observed for inorganic microcavities, the scattered light pattern is elliptical when projected normal to the sample surface. The profile shape provides a direct visual representation of the anisotropic microcavity polariton dispersion characteristic of organic crystals.
The Influence of Some Axial Ligands on Ruthenium–Phthalocyanine Complexes: Chemical, Photochemical, and Photobiological Properties (2021)

This work presents a new procedure to synthesize ruthenium-phthalocyanine complexes and uses diverse spectroscopic techniques to characterize <i>trans-</i>[RuCl(Pc)DMSO] <b>(I)</b> (Pc = phthalocyanine) and <i>trans</i>-[Ru(Pc)(4-ampy)<sub>2</sub>] <b>(II)</b> (4-ampy = 4-aminopyridine). The triplet excited-state lifetimes of <b>(I)</b> measured by nanosecond transient absorption showed that two processes occurred, one around 15 ns and the other around 3.8 μs. Axial ligands seemed to affect the singlet oxygen quantum yield. Yields of 0.62 and 0.14 were achieved for <b>(I)</b> and <b>(II)</b>, respectively. The lower value obtained for <b>(II)</b> probably resulted from secondary reactions of singlet oxygen in the presence of the ruthenium complex. We also investigate how axial ligands in the ruthenium-phthalocyanine complexes affect their photo-bioactivity in B16F10 murine melanoma cells. In the case of <b>(I)</b> at 1 μmol/L, photosensitization with 5.95 J/cm<sup>2</sup> provided B16F10 cell viability of 6%, showing that <b>(I)</b> was more active than <b>(II)</b> at the same concentration. Furthermore, <b>(II)</b> was detected intracellularly in B16F10 cell extracts. The behavior of the evaluated ruthenium-phthalocyanine complexes point to the potential use of <b>(I)</b> as a metal-based drug in clinical therapy. Changes in axial ligands can modulate the photosensitizer activity of the ruthenium phthalocyanine complexes.
The T-Cell Response to SARS-CoV-2 Vaccination in Inflammatory Bowel Disease is Augmented with Anti-TNF Therapy (2022)

Lay Summary T-cell and antibody responses to severe acute respiratory syndrome coronavirus 2 vaccination in inflammatory bowel disease patients are poorly correlated. T-cell responses are preserved by most biologic therapies, but augmented by anti-tumor necrosis factor (anti-TNF) treatment. While anti-TNF therapy blunts the antibody response, cellular immunity after vaccination is robust.
Is the whole greater than the sum of its parts? De novo assembly strategies for bacterial genomes based on paired-end sequencing (2015)

In summary, this study provides systematic evaluations of de novo assembly from paired end sequencing data. Among the assembly strategies, we find that overlapping paired-end reads is not always beneficial for bacteria genome assembly and should be avoided or used with caution especially for genomes containing high fraction of repetitive sequences. Because increasing numbers of projects aim at bacteria genome sequencing, our study provides valuable suggestions for the field of genomic sequence construction.
Wilms' tumor protein WT1 as an ovarian transcription factor: decreases in expression during follicle development and repression of inhibin-alpha gene promoter. (1995)

WT1, a gene deleted in some Wilms' tumors, encodes a transcription factor with zinc fingers and shares homology with proteins in the early growth response gene family. Although defects in the WT1 gene are associated with nephroblastoma and genitourinary malformation, the specific function of WT1 in the gonads remains unclear. We investigated the expression of WT1 transcripts in rat ovary during follicle development by Northern blotting, RNase protection assay, and in situ hybridization. Abundant WT1 transcripts were found in the ovary, testis, uterus, and kidney, with lower levels in the heart and pancreas. Treatment with estrogen or gonadotropins did not affect the concentration of ovarian WT1 mRNA. In situ hybridization analysis indicated that ovarian WT1 mRNA is expressed exclusively in the surface epithelium and granulosa cells of primordial, primary, and secondary follicles, and its levels decrease during follicle growth. Although RNase protection assay suggested the presence of four alternatively spliced forms of WT1 mRNA, the ratio of these transcripts remains constant during ovarian growth. Developmental changes in the expression of two granulosa cell differentiation marker genes, inhibin-alpha and FSH receptor, were found to be inversely correlated with WT1 levels. Because potential WT1-binding sites were found in the promoter of inhibin-alpha gene, we further tested whether WT1 might regulate the expression of this gene. Cotransfection of a WT1 expression vector with a promoter reporter plasmid of inhibin-alpha resulted in the repression of promoter activities in CHO cells in a dose-dependent manner. These results suggest that WT1 is expressed in high levels in granulosa cells of primordial, primary, and secondary follicles but decreases with follicle development. This transcription factor might be a repressor of ovarian differentiation genes in the granulosa cells and play a role in arresting the differentiation of immature follicles.
HIV Revealed (1989)

IN the relatively brief period since the discovery of the human immunodeficiency virus (HIV) and its identification as the cause of the acquired immunodeficiency syndrome (AIDS), an extraordinary amount of information has emerged about the genetic structure of the virus and the intricacies of the in vitro biologic process of viral infection. However, because the circumstances of infection can be readily manipulated in the laboratory, whereas reliable data on the progress of infection in humans are difficult to obtain, much less is known about how HIV initiates and maintains a natural infection. Humans are genetically heterogeneous, lead idiosyncratic lives, and . . .
A frequency comb calibrated solar atlas (2013)

Context. The solar spectrum is a primary reference for the study of physical processes in stars and their variation during activity cycles. High resolution spectra of the Sun are easily obtained from spatially selected regions of the solar disk, while those taken over the integrated disk are more problematic. However, a proxy can be obtained by using solar light reflected by small bodies of the solar system.
π-Conjugated Carbazole Cations Enable Wet-Stable Quasi-2D Perovskite Photovoltaics (2022)

Quasi-two-dimensional halide perovskites are commonly used in solar cells, as they are more stable than their three-dimensional analogues. Nevertheless, it is still challenging to meet the stability requirements under high-humidity conditions. Here, we design π-conjugated carbazole (CA) cations to increase the water resistance of perovskite. We control the crystallization kinetics by the anti-solvent strategy to locate the hydrophobic low-⟨n⟩-value phase on the surface of the perovskite film. The resulting CA2MA4Pb5I16 film does not decompose after being immersed in water for several minutes. We further regulate the vertical orientation of perovskite crystals by introducing NH4SCN additive, resulting in improved carrier transport dynamics. As a result, the optimized CA2MA4Pb5I16 device achieves a notable power conversion efficiency (PCE) of 18.23% and retains more than 85% of the original PCE after 2000 h under a relative humidity of 65% at 25 °C. This is one of the most stable reported unencapsulated perovskite solar cells in high-humidity environments.
Low-complexity scalable image compression (2002)

We have developed a scalable image compression scheme with a good performance-complexity trade-off. Like JPEG, it is based on the 8/spl times/8 block discrete cosine transform (DCT), but it uses no additional quantization or entropy coding (such as Huffman or arithmetic coding). Bit-rate or quality scalability is enabled by encoding the DCT coefficients bit plane by bit plane, starting at the most significant plane. The individual bit planes are efficiently encoded using simple rectangular zones. Our method offers about the same compression performance as JPEG, but at a significant lower complexity and with the additional feature of scaling the bit rate by simply truncating the generated bit string.
Modeling of wind farm controllers (2006)

This paper describes modeling of wind farm controllers. The paper contributes to the IEA Annex XXI "Dynamic models of wind farms for power system studies" and was presented at the Annex XXI workshop in EWEC 2006. The wind farm controllers are developed with features, which make the wind farms able to participate in the control of the power system. The modeled wind farms provide active and reactive power control in the point of common coupling of the wind farm, which can be combined with automatic frequency and voltage control with droop and dead band. Two types of wind farms are presented. The first using variable speed wind turbines with doubly fed induction generators and fixed speed wind turbines with active stall control.
Synthesis, breathing, and gas sorption study of the first isoreticular mixed-linker phosphonate based metal–organic frameworks (2012)

The synthesis of the first water stable isoreticular phosphonate based mixed-linker metal-organic frameworks (MOFs) is achieved via the use of the N-donor heterocyclic co-ligands. Furthermore, these isoreticular phosphonate frameworks show selective CO(2)/N(2) uptake at low pressures.