gebhart/patrepeval huggingface dataset:
Non-random Escape Pathways from a Broadly Neutralizing Human Monoclonal Antibody Map to a Highly Conserved Region on the Hepatitis C Virus E2 Glycoprotein Encompassing Amino Acids 412–423 (2014)

A challenge for hepatitis C virus (HCV) vaccine development is to define epitopes that are able to elicit protective antibodies against this highly diverse virus. The E2 glycoprotein region located at residues 412-423 is conserved and antibodies to 412-423 have broadly neutralizing activities. However, an adaptive mutation, N417S, is associated with a glycan shift in a variant that cannot be neutralized by a murine but by human monoclonal antibodies (HMAbs) against 412-423. To determine whether HCV escapes from these antibodies, we analyzed variants that emerged when cell culture infectious HCV virions (HCVcc) were passaged under increasing concentrations of a specific HMAb, HC33.1. Multiple nonrandom escape pathways were identified. Two pathways occurred in the context of an N-glycan shift mutation at N417T. At low antibody concentrations, substitutions of two residues outside of the epitope, N434D and K610R, led to variants having improved in vitro viral fitness and reduced sensitivity to HC33.1 binding and neutralization. At moderate concentrations, a S419N mutation occurred within 412-423 in escape variants that have greatly reduced sensitivity to HC33.1 but compromised viral fitness. Importantly, the variants generated from these pathways differed in their stability. N434D and K610R-associated variants were stable and became dominant as the virions were passaged. The S419N mutation reverted back to N419S when immune pressure was reduced by removing HC33.1. At high antibody concentrations, a mutation at L413I was observed in variants that were resistant to HC33.1 neutralization. Collectively, the combination of multiple escape pathways enabled the virus to persist under a wide range of antibody concentrations. Moreover, these findings pose a different challenge to vaccine development beyond the identification of highly conserved epitopes. It will be necessary for a vaccine to induce high potency antibodies that prevent the formation of escape variants, which can co-exist with lower potency or levels of neutralizing activities.
Chemically Modified Messenger RNA: Modified RNA Application for Treatment of Achilles Tendon Defects (2018)

Different regenerative medicine approaches for tendon healing exist. Recently, especially gene therapy gained popularity. However, potential mutagenic and immunologic effects might prevent its translation to clinical research. Chemically modified mRNA (cmRNA) might bypass these limitations of gene therapy. Therefore, the purpose of this study was to evaluate the early healing properties of Achilles tendon defects in rats treated with basic fibroblast growth factor (bFGF) cmRNA. Forty male Lewis rats were used for the study and randomly assigned to two study groups: (1) treatment with cmRNA coding for bFGF and (2) noncoding cmRNA control. Protein expression was measured using in vivo bioluminescence imaging at 24, 48, and 72 h, as well as 14 days. Animals were euthanized 2 weeks following surgery. Biomechanical, histological, and immunohistological analyses were performed with the significance level set at p < 0.05. Protein expression was evident for 3 days. At 14 days, bioluminescence imaging revealed only little protein expression. Biomechanically, tendons treated with bFGF cmRNA showed a construct stiffness closer to the healthy contralateral side when compared with the control group (p = 0.034), without any significant differences in terms of load to failure. Hematoxylin and eosin staining detected no side effects of the treatment, as signs of inflammation, or necrosis. Furthermore, it revealed the shape of the nuclei to be more oval in the bFGF group in the tendon midsubstance (p = 0.043) with a reduced cell count (p = 0.035). Immunohistological staining for type I, II, III, and IV collagen did not differ significantly between the two groups. In conclusion, this pilot study demonstrates the feasibility of a novel messenger RNA (mRNA)-based therapy for Achilles tendon defects using chemically modified mRNA coding for bFGF.
A Nonpolara-Plane GaN Grown on a Hemispherical Patternedr-Plane Sapphire Substrate (2011)

A high-quality a-plane GaN layer with a pit-free, mirror-like surface was grown on a hemispherical patterned r-plane sapphire substrate (PSS) by metal–organic chemical vapor deposition. The use of the r-plane PSS reduced the density of defects such as basal plane staking faults and threading dislocations of the a-plane GaN. The low-temperature-photoluminescence intensity of the emissions at 3.25 and 3.39 eV related with the defects increased along with the near-band-edge emission at 3.46 eV. The intensity of yellow emission at 2.2 eV on the PSS was remarkably decreased, which indicates the improvement of the crystal quality because of the defect reduction. The InGaN light emitting diode grown on the PSS showed an output power of 7.4 mW at 100 mA, which was about 7 times higher than that on the planar substrate.
An electrochemical transistor using a solid electrolyte (1980)

Transistor action has been observed at elevated temperatures (800 °C) with a structure composed of two ceramic ZrO2 electrochemical cells separated by an enclosed volume. One cell emits O2 from an ambient atmosphere into the volume (base region) where it is collected and returned to the ambient by the opposing cell. Electrical operation can be understood in terms of the current limitation presented by the Pt cathode of the collector cell. Small signal voltage, current, and power amplification are observed with a frequency response limited by the double-layer capacity of the collector. This approach to transistor action should be applicable to other solid-electrolyte systems.
Influence of nonexcitable cells on spiral breakup in two-dimensional and three-dimensional excitable media (2003)

We study spiral wave dynamics in the presence of nonexcitable cells in two-dimensional (2D) and three-dimensional (3D) excitable media, described by the Aliev-Panfilov model. We find that increasing the percentage of randomly distributed nonexcitable cells can prevent the breaking up of a spiral wave into a complex spatiotemporal pattern. We show that this effect is more pronounced in 2D than 3D excitable media. We explain the observed 2D vs 3D differences by a different dependence of the period and diastolic interval of the spiral wave on the percentage of nonexcitable cells in 2D and 3D excitable media.
Anti‐tumor and Anti‐ovarian Autoantibodies in Women with Ovarian Cancer (2007)

Serum autoantibodies are significantly associated with OVCA. Anti-tumor antibodies may provide a useful marker for the detection of ovarian cancer.
Martensitic transformation and texturein novel bcc Fe-Mn-Al-Ni-CralloysE (2011)

Evolutionsof martensitic transformation and textureduring cold rolling innovel bcc Fe-Mn-Al-Ni-Cr alloyswere studied.X-ray diffraction (XRD)and electron backscattering diffraction (EBSD)analysesrevealed that this alloy undergoes α→ɛ→γ’ martensitic transformation during deformation. At a20% cold rolling strain, most of the α phase transformed into γ’, and the transformed γ’ phase had aKurdjumov-Sachs (K-S)relationship with the parent α phase.Strong {hkl} < 111 > and weak {110} < 001 > transformation textures were formedafter deformation. This texture evolutionappeared to be related tothe variant selectionthat occurredduringthe martensitic transformation.
TH-E-217BCD-04: MA Modulation and Iterative Reconstruction: Evaluation Using a New CT Phantom (2012)

Purpose: The routine clinical CT use of tube current modulation (TCM) and iterative reconstruction algorithms, which can be used to reduce radiation dose, necessitates evaluating their effects on image quality. This study's purpose was to use a new phantom (Mercury Phantom) to evaluate the quality of images acquired with TCM and iterative reconstruction algorithms as implemented by two different CT manufacturers. Methods: The phantom consists of four cylindrical and three tapered regions. The phantom was designed to measure noise-power spectrum (NPS) and modulation transfer function (MTF) across a range of diameters'” 16, 23, 30, and 37 cm'”and at multiple, clinically relevant insert materials from air to iodinated tissue. Images were acquired on a Siemens Flash and GE 750HD using a range of TCM and proprietary reconstruction algorithms: ASIR, IRIS, and SAFIRE. Custom software measured the non-stationarity of NPS as a function of reconstruction and TCM. Contrast and MTF were measured for each insert for each reconstruction algorithm. Results: Measured HU of different materials varied minimally as a function of reconstruction algorithm and dose reduction technique. However, as a function of phantom size from the 16-cm to 37-cm diameter, the [air,Polystyrene,Acrylic,Teflon] HU of 120-kVp images changed by approximately [50,−20,−8,−130] for the 750HD and [35,0,6,−75] for the Flash. MTFs of the linear reconstruction algorithms were independent of size, TCM, and contrast, but for iterative algorithms, the MTFs depended on the object contrast and improved by as much as 25%. Peak NPS decreased from 37-cm to 16-cm (∼86%), decreased for iterative reconstruction relative to linear algorithms (∼21%), and decreased radially from the phantom's center (∼25%). mA modulation performance differed considerably between the two systems. Conclusion: The Mercury Phantom can be used to assess trade-offs in CT image quality and dose reduction techniques for a range of sizes incorporating TCM and iterative reconstruction. Joshua M. Wilson Funded, in part, by Research Agreement with GE Healthcare. Ehsan Samei Research grant: NIH R01 EB001838; Research grant: General Electric; Research grant: Siemens Medical; Research grant: Carestream Health; Share-holder: Zumatek Inc; Advisory Board: IBA
In vivo identification of potential uranium protein targets in zebrafish ovaries after chronic waterborne exposure (2017)

Ecotoxicological studies have indicated the reprotoxicity of uranium (U) in zebrafish, but its molecular mechanisms remain unclear. Due to the non-covalent nature of U-protein complexes, canonical proteomics approaches are often not relevant as they usually use denaturating reagents or solvents. In this study, non-denaturating (ND) methods were used to obtain insight into the nature of U potential targets in ovaries of reproduced and non-reproduced zebrafish after 20 days of exposure to an environmentally relevant U concentration (20 μg L<sup>-1</sup>). After the ND sample preparation, 1-dimensional (SEC) and 2-dimensional (OGE × SEC) separations followed by ICP-sector-field MS measurements (U, P, Fe, Cu, and Zn) enabled the determination of chemical characteristics (MW, pI) of the metal-protein complexes. Phosphorus and U coelution confirmed the affinity of U for P-containing proteins. In addition, 2D separation allowed the discrimination of Fe-metalloproteins as potential U targets. Finally, 20 protein candidates for U complexation were identified after tryptic digestion conditions by LC-ESI FT MS and a database search. Potential U targets were mainly involved in three biological processes: oxidative stress regulation (SOD, GST), cytoskeleton structure (actin) and embryo early development (vtg, initiation factor).
Nanomapping of CD1d–glycolipid complexes on THP1 cells by using simultaneous topography and recognition imaging (2013)

CD1d molecule, a monomorphic major histocompatibility complex class I-like molecule, presents different types of glycolipids to invariant natural killer T (iNKT) cells that play an important role in immunity to infection and tumors, as well as in regulating autoimmunity. Here, we present simultaneous topography and recognition imaging (TREC) analysis to detect density, distribution and localization of single CD1d molecules on THP1 cells that were loaded with different glycolipids. TREC was conducted using magnetically coated atomic force microscopy tips functionalized with a biotinylated iNKT cell receptor (TCR). The recognition map revealed binding sites visible as dark spots, resulting from oscillation amplitude reduction during specific binding between iNKT TCR and the CD1d-glycolipid complex. THP1 cells were pulsed with three different glycolipids (α-GalCer, C20 and OCH12) for 4 and 16 hr. Whereas CD1d-α-GalCer and CD1d-C20:2 complexes on cellular membrane formed smaller microdomains up to ~10 000 nm(2) (dimension area), OCH12 loaded CD1d complexes presented larger clusters with a dimension up to ~30 000 nm(2). Moreover, the smallest size of recognition spots was about 25 nm, corresponding to a single CD1d binding site. TREC successfully revealed the distribution and localization of CD1d-glycolipid complexes on THP1 cell with single molecule resolution under physiological conditions.
Flexible Endoscopy in Primary Dye Testing of the Lacrimal System (1990)

The Olympus PF-22 angioscope was used to examine the inferior meatus during primary dye testing in 80 lacrimal systems in 48 patients. Dye testing was done bilaterally in 32 subjects with no known abnormalities of lacrimal excretory function; it also was performed on the apparently normal contralateral side of 16 patients with unilateral epiphora. Dye was observed in the nose in 79 of 80 lacrimal systems (99%). Dye was not observed in one patient, who appeared to have a dysfunctional lacrimal excretory system. Primary dye testing of the lacrimal system is reliable when the Olympus PF-22 angioscope is used to examine the inferior meatus.
On Face Segmentation, Face Swapping, and Face Perception (2017)

We show that even when face images are unconstrained and arbitrarily paired, face swapping between them is actually quite simple. To this end, we make the following contributions. (a) Instead of tailoring systems for face segmentation, as others previously proposed, we show that a standard fully convolutional network (FCN) can achieve remarkably fast and accurate segmentations, provided that it is trained on a rich enough example set. For this purpose, we describe novel data collection and generation routines which provide challenging segmented face examples. (b) We use our segmentations to enable robust face swapping under unprecedented conditions. (c) Unlike previous work, our swapping is robust enough to allow for extensive quantitative tests. To this end, we use the Labeled Faces in the Wild (LFW) benchmark and measure the effect of intra- and inter-subject face swapping on recognition. We show that our intra-subject swapped faces remain as recognizable as their sources, testifying to the effectiveness of our method. In line with well known perceptual studies, we show that better face swapping produces less recognizable inter-subject results. This is the first time this effect was quantitatively demonstrated for machine vision systems.
Heralded State Preparation in a Superconducting Qubit (2012)

We demonstrate high-fidelity, quantum nondemolition, single-shot readout of a superconducting flux qubit in which the pointer state distributions can be resolved to below one part in 1000. In the weak excitation regime, continuous measurement permits the use of heralding to ensure initialization to a fiducial state, such as the ground state. This procedure boosts readout fidelity to 93.9% by suppressing errors due to spurious thermal population. Furthermore, heralding potentially enables a simple, fast qubit reset protocol without changing the system parameters to induce Purcell relaxation.
Mumps III. Comparison of Methods for Detection of Viruria (1962)

Of 110 urine specimens collected from 21 patients with culturally confirmed mumps, 58 were positive for mumps virus. In 56 virus was recovered by cell culture only, in one by hen's egg method only, and one urine by both methods. In the primary cell cultures cytopathic effect was the most sensitive indicator of virus. Hemadsorption was demonstrated on passage, however, in 90% of specimens exhibiting a cytopathic effect. Hemagglutinin was present in 88% of fluids from cultures with cells positive for hemadsorption. Mumps virus was detected as late as the 15th day of illness and in 80% of urines collected from these patients during the first 5 days of illness.
Design and Formulative Analysis of VLSI Syndrome Generator for RS(128,Kx) and RS(64,Ky) (2014)

A VLSI architecture of Syndrome generator is part of well known Reed Solomon codes which is capable of generating syndromes while receiving RS (N, K) Codes from the transmitter. RS codes are customized to achieve a suitable VLSI realization of syndromes which can be further used in error detecting algorithms such as Euclidean, Erasures, Berlekamp"s iterative algorithm and Massey Linear feedback shift register synthesis algorithm. It is assumed to be one of the pipelining stages in the Reed Solomon decoding technique. A MATLAB implementation of syndrome generator with various RS codes having different ranges of bit symbols and codeword was reveal for the purpose of determining syndromes. Hardware intricacy depends only on 2p parity check bytes. Message is encoded in Galois field having 2^m elements. Each Codeword enclose "N" symbol generates syndromes for those "N" symbols. It represented implementation of RS (128, Kx) and RS (64, Ky) with the different values of bits/symbol "m" and different range of K x & K y and look into how limit of Zeros and Syndrome varies.
Facile synthesis of C–Fe3O4–C core–shell nanotubes by a self-templating route and the application as a high-performance anode for Li-ion batteries (2013)

In this study, we synthesized C–Fe3O4–C core–shell nanotubes through a facile chemical vapor deposition (CVD) method using Fe2O3 nanotubes as the self-templates. The hydrothermal product α-Fe2O3 hematite exhibits a tubular structure with an inner diameter of 70–100 nm, a wall thickness of 10–20 nm, and a length of 300–800 nm. After the CVD reaction in C2H2, α-Fe2O3 could be transformed into C–Fe3O4–C with the tubular structure reserved. The tubular C–Fe3O4–C is constructed by an Fe3O4 nanotube core and 5 nm thick carbon shells on both inner and outer surfaces of the Fe3O4 nanotube. The C–Fe3O4–C nanotube anode exhibits a stable cycling with a capacity over 700 mA h g−1 retained after 120 cycles at 100 mA g−1. The improved electrochemical properties of C–Fe3O4–C nanotubes compared with bare α-Fe2O3 could be attributed to the introduction of the carbon shells, which not only supplya high conductive channel and buffer matrix, but also keep the structural stability of the Fe3O4 nanotube upon cycling.
Supplementary Data from Low-Molecular-Weight Cyclin E Can Bypass Letrozole-Induced G<sub>1</sub> Arrest in Human Breast Cancer Cells and Tumors (2023)

Supplementary Data from Low-Molecular-Weight Cyclin E Can Bypass Letrozole-Induced G&lt;sub&gt;1&lt;/sub&gt; Arrest in Human Breast Cancer Cells and Tumors
Epigenetic mechanisms controlling human leukemia stem cells and therapy resistance (2022)

Abstract Many human cancers, including acute myeloid leukemia (AML), arise from mutations of stem and progenitor cells. Immunophenotypic profiling has shown that leukemias develop hierarchically, with mutations in leukemia stem cells associated with disease propagation and relapse 1,2 . Although leukemia initiating cells can be enriched using cell surface markers, their frequency tends to be variable and low, obscuring mechanisms and hindering effective therapies 3,4 . To define AML stem cells in human patients, we performed functional genomic profiling of diverse leukemias using label tracing techniques designed to preserve hematopoietic stem cell (HSC) function in vivo. We found that propagation of human AML is mediated by a rare but distinct quiescent label-retaining cell (LRC) population that evades detection by currently known immunophenotypic markers. We show that human AML LRC quiescence is reversible, sparing genetic clonal competition that maintains its epigenetic inheritance. LRC quiescence is defined by distinct promoter-centered chromatin and gene expression dynamics and controlled by a distinct AP-1/ETS transcription factor network, including JUN in particular, which is associated with disease persistence and chemotherapy resistance in diverse patients. These results enable prospective isolation and functional genetic manipulation of immunophenotypically-varied leukemia stem cells in human patient specimens, as well as establish key functions of epigenetic plasticity in leukemia development and therapy resistance. We anticipate that these findings will lead to the elucidation of essential properties of leukemia stem cell quiescence and the design of therapeutic strategies for their clinical identification and control.
Effect of Osmotic Agents on the Vitreous Body (1969)

The weight of the rabbit vitreous body is reduced by average clinical doses of hyperosmolar agents. The weight change is 2.7% with orally administered glycerol, and 3.7% and 3.9% with intravenously administered urea and mannitol respectively. This study substantiates the clinical observation that vitreous volume can be reduced by osmotic therapy.
Process intensification: laminar flow heat transfer (1986)

L'evaluation de la performance du transfert de chaleur en ecoulement laminaire dans de fines matrices est effectuee d'un point de vue theorique, et grossierement confirmee par des experiences utilisant de l'eau dans deux types de construction de plaques. Les coefficients de transfert de chaleur volumetrique observes ont ete de 7 MW m −3 K −1 , alors qu'il sont de 0,2 MW m −3 K −1 dans les echangeurs tubulaires et 1,25 MW m −3 K −1 dans les echangeurs a plaques. On a essaye sous diverses conditions d'ecoulement la resistance d'une matrice a l'encrassement par une suspension a 0,026% provenant d'une tour de refroidissement
Transcriptional regulation of the 5-HT1Areceptor: implications for mental illness (2012)

The serotonin-1A (5-HT(1A)) receptor is an abundant post-synaptic 5-HT receptor (heteroreceptor) implicated in regulation of mood, emotion and stress responses and is the major somatodendritic autoreceptor that negatively regulates 5-HT neuronal activity. Based on animal models, an integrated model for opposing roles of pre- and post-synaptic 5-HT(1A) receptors in anxiety and depression phenotypes and response to antidepressants is proposed. Understanding differential transcriptional regulation of pre- versus post-synaptic 5-HT(1A) receptors could provide better tools for their selective regulation. This review examines the transcription factors that regulate brain region-specific basal and stress-induced expression of the 5-HT(1A) receptor gene (Htr1a). A functional polymorphism, rs6295 in the Htr1a promoter region, blocks the function of specific repressors Hes1, Hes5 and Deaf1, resulting in increased 5-HT(1A) autoreceptor expression in animal models and humans. Its association with altered 5-HT(1A) expression, depression, anxiety and antidepressant response are related to genotype frequency in different populations, sample homogeneity, disease outcome measures and severity. Preliminary evidence from gene × environment studies suggests the potential for synergistic interaction of stress-mediated repression of 5-HT(1A) heteroreceptors, and rs6295-induced upregulation of 5-HT(1A) autoreceptors. Targeted therapeutics to inhibit 5-HT(1A) autoreceptor expression and induce 5-HT(1A) heteroreceptor expression may ameliorate treatment of anxiety and major depression.
Partial Embedding Approach for Knowledge Completion (2018)

지식 그래프는 실세계의 개체들과 개체 사이의 관계로 구성된 네트워크를 의미하며, 최근에는 대용량 데이터를 기반으로 구축되고 있다. 대부분의 지식 그래프들은 누락된 엔티티 또는 관계들로 인해 불완전성에 대한 문제점이 존재한다. 이를 해결하기 위해 지난 연구들은 지식 그래프를 다차원 공간상에 임베딩하는 방법을 적용했다. 그러나 이러한 연구들은 지식 그래프가 변화하지 않는다는 가정을 하고 있다. 이로 인해 새로운 트리플이 추가되어 빠르게 진화하는 실세계의 지식 그래프에 적용하기 위해 반복적인 임베딩 모델의 재학습은 고비용의 연산이 요구되며, 실용적이지 못하다. 따라서 본 논문에서는 변화하는 지식 그래프를 대상으로 하는 부분 임베딩 기반의 지식 완성 방법을 제안한다. 지식 완성의 대상이 되는 관심 관계들을 추출하기 위해 온톨로지의 공리와 문맥 정보를 활용했으며, 이를 기반으로 엔티티와 관계들을 임베딩하고 학습하여 지식 완성을 수행했다. 제안하는 방법의 성능을 측정하기 위해 Freebase와 WiseKB 데이터셋을 대상으로 최신 지식 완성 연구들과의 비교 실험을 진행하였고, 평균적으로 학습시간이 약 49%∼90% 감소했으며, 전체적인 성능이 약 6.7% 증가하는 것을 확인했다.