gebhart/patrepeval huggingface dataset:
Abstract 750: Nanoliposomal targeting of Ephrin receptor A2 (EphA2): Clinical translation (2016)

Abstract Ephrin receptor A2 (EphA2) is part of the Ephrin family of cell-cell junction proteins highly overexpressed in several solid tumors, and is associated with poor prognosis. We developed a novel EphA2-targeted docetaxel nanoliposome, leveraging organ specificity through enhanced permeability effect and cellular specificity through EphA2 targeting. The goal of the study was to develop the diagnostic framework enabling the clinical implementation of EphA2-based exclusion criteria in future MM-310 trials. We used qFACS and an in vitro assay for liposome (Ls)-cell interaction to identify the minimum number of EphA2 receptors to enable antibody-mediated internalization of Ls. We developed an IHC assay able to differentiate EphA2 - vs + cell lines. We characterized EphA2 staining pattern in tumor samples of various indications and developed a scoring algorithm that allows selection of patients in early clinical trials. While non targeted Ls do not associate with cells in vitro, there is a strong correlation between EphA2 expression and EphA2-Ls cell association independent of the cell line origin. We used the non-targeted Ls to determine the extent of non-specific binding that can be achieved (∼340 Ls/cell) and used partitioning to determine the minimum number of EphA2 receptors necessary to mediate targeting (∼3000 receptors/cell). We have developed and validated a qIHC assay for EphA2 (precision ∼90%, linearity 0.8 and reproducibility ∼5%). We stained a set of ∼200 tumor samples from various indications. EphA2 was found to be expressed in tumor cells, tumor-associated myofibroblasts, and tumor-associated blood vessels. Using an inclusive cutoff of 10%, EphA2 prevalence was found to range from 50% to 100% in the tumor types evaluated. No significant difference in staining was seen between metastasis and primary tumors in matched samples. In summary, we developed a diagnostic framework for prospective selection of EphA2+ patients for MM-310 trials based on a mechanistic single cell cut-off, and a clinical-grade IHC assay. Cancer CellsTumor associated myofibroblastsTumor associated blood vesselsEphA2 Overall ScoreBladder19/20 (95%)0/20 (0%)16/20 (80%)19/20 (95%)Gastric18/20 (90%)3/20 (15%)17/20 (85%)20/20 (100%)Head &amp; Neck16/19 (84%)0/19 (0%)9/19 (47%)19/19 (100%)Lung24/41 (58%)1/41 (2.4%)24/41 (58%)28/41 (68%)Lung-FNA7/9 (78%)––7/9 (78%)Ovarian10/18 (55%)7/18 (39%)17/18 (95%)17/18 (95%)Pancreatic15/19 (79%)0/19 (0%)11/19 (58%)17/19 (89%)Prostate7/23 (27%)7/23 (27%)9/23 (28%)12/23 (52%)TNBC6/77 (7%)0/77 (0%)34/77 (44%)37/77 (48%) Citation Format: Walid S. Kamoun, Shinji Oyama, Tad Kornaga, Theresa Feng, Lia Luus, Minh T. Pham, Dmitri B. Kirpotin, James D. Marks, Melissa Geddie, Lihui Xu, Alexey A. Lugovskoy, Monica Murphy, Carl Morrisson, Daryl C. Drummond. Nanoliposomal targeting of Ephrin receptor A2 (EphA2): Clinical translation. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 750.
Spin-torque switching: Fokker-Planck rate calculation (2005)

We describe a general Fokker-Planck approach to understanding and calculating magnetization switching rates and noise in the recently observed phenomenon of spin-torque switching. In this phenomenon, which has possible applications to information storage, a large current passing from a pinned ferromagnetic (FM) layer to a free FM layer switches the free layer. Beginning with Brown [Phys. Rev. 130, 1677 (1963)], switching rates in magnetic systems have been calculated using the Fokker-Planck equation. In the small-oscillation limit, the equations have been solved analytically, giving a first-principles justification for phenomenological effective temperature theories: the spin-torque effect increases the Arrhenius factor $\mathrm{exp}(\ensuremath{-}E∕kT)$ in the switching rate by raising the effective spin temperature $T$. In the present Rapid Communication we generalize the nonlinear Fokker-Planck equation to the case of a Slonczewski spin torque. As an example, we use a linear approximation to calculate telegraph noise rates, leading to good qualitative agreement with recent experiments. However, our nonlinear formulation is also valid for large precessional oscillations. The method also allows the calculation of current-induced magnetic noise in current perpendicular to plane spin valve read heads.
Magnesium Deficiency-Induced Spasms of Umbilical Vessels: Relation to Preeclampsia, Hypertension, Growth Retardation (1983)

Isolated umbilical arteries and veins, obtained from normal women at the end of pregnancy, were incubated in krebs-Ringer bicarbonate solution and exposed to magnesium at concentrations ranging from 0 to 9.6 millimoles per liter. The basal tension of the vessels increased when magnesium was withdrawn and decreased when the concentration of magnesium was raised. Absence of magnesium in the medium significantly potentiated the contractile response of the vessels to bradykinin, angiotensin II, serotonin, and prostaglandin F2 alpha. It appears that magnesium deficiency may be responsible for spasms of umbilical and placental vasculature. Our findings may provide a rationale for why magnesium sulfate is an effective therapy in preeclamptic syndromes in pregnant women.
The single-incision palatal harvest technique: a strategy for esthetics and patient comfort. (2000)

The use of connective tissue grafts for root coverage and ridge augmentation is a proven, effective treatment modality. Complications associated with the palatal donor site can arise because of incomplete primary closure of the palatal wound or sloughing of the overlying tissue. This article presents a new technique for the atraumatic harvesting of connective tissue grafts from palatal donor sites. The main advantage of this single-incision technique is the primary closure of the palatal flap, resulting in less pain and sensitivity and fewer postoperative complications. A review of the technique and its indications, rationale, and limitations is presented.
Mapping of four discontiguous antigenic determinants on horse cytochrome c (1989)

The epitopes (antigenic determinants) recognized by four different monoclonal antibodies on horse cytochrome c have been partially characterized by differential acetylation of lysine residues of free and antibody-bound cytochrome c. The degree of acetylation in the bound and free antigen molecule was assessed by a double-labeling procedure with [3H]acetic anhydride and [14C]acetic anhydride. Out of the 19 lysine residues of cytochrome c only very few were less reactive in the antigen-antibody complex, i.e. presumably located at the epitope for the antibody under study. The protection varied from 1.5-fold to over 20-fold lower reactivity in antibody-bound cytochrome c. The present results are complemented by previous data obtained by cross-reactivity analysis with cytochromes c from different species, with chemically modified cytochrome c derivatives, and by inhibition of proteolysis of cytochrome c in the presence of the antibodies. From the combined data we conclude that each of the four epitopes depends on the precise spatial folding of the antigen and contains residues which are brought together by the folding of the polypeptide chain. This work exemplifies that mapping of conformation-dependent epitopes can be achieved by applying a combination of mapping procedures of which each by itself provides partial information.
Measurement and modeling of bulk viscosity for polystyrene melts (2021)

Bulk viscosity describes the irreversible resistance to the rate of volume change. Bulk viscosity, which is more than ten thousand times higher than shear viscosity, has been ignored in the field of polymer processing for the past decades. Bulk viscosity may play an important role for compressible polymer melts undergoing strong compression during processing, especially during the packing and holding stage in injection molding. In this study, bulk viscosity of an amorphous Polystyrene melt is investigated through measurements, modeling, and implementation in an injection molding simulation. The results demonstrated that bulk viscosity can be derived from a cooling rate-controlled PVT (pressure-specific volume–temperature) measurement. A new pressure-specific volume–temperature–cooling rate model was developed to obtain smooth and reliable bulk viscosity results. Furthermore, a Cross-William–Landel–Ferry–Arrhenius model was found capable of describing the dependence of temperature, rate of volume change, and mechanical pressure on bulk viscosity of this polymer melt. The proposed modeling was first verified using the non-equilibrium PVT and then was implemented into an injection molding simulation. Simulation results showed that the effects of bulk viscosity not only prevent the material from changing its size but also reduce mechanical pressure variations during the injection molding packing stage.
ChemInform Abstract: NEW SYNTHESIS OF METHYL 2‐(TRIORGANOSILYL)‐3‐BUTENOATES AS A NEW SYNTHON OF 3‐(METHOXYCARBONYL)ALLYL ANION (1983)

Abstract Aus den Allylsilanen entstehen mit hoher Regioselektivität die Carbonsäuren (III), deren Ester in Gegenwart von Lewis‐Säuren mit einer Reihe von Elelftrophilen, z.B. den Carbonylverbindungen (IV), umgesetzt werden.
Acute myeloid leukemia immunopeptidome reveals HLA presentation of mutated nucleophosmin (2019)

Somatic mutations in cancer are a potential source of cancer specific neoantigens. Acute myeloid leukemia (AML) has common recurrent mutations shared between patients in addition to private mutations specific to individuals. We hypothesized that neoantigens derived from recurrent shared mutations would be attractive targets for future immunotherapeutic approaches. Here we sought to study the HLA Class I and II immunopeptidome of thirteen primary AML tumor samples and two AML cell lines (OCI-AML3 and MV4-11) using mass spectrometry to evaluate for endogenous mutation-bearing HLA ligands from common shared AML mutations. We identified two endogenous, mutation-bearing HLA Class I ligands from nucleophosmin (NPM1). The ligands, AVEEVSLRK from two patient samples and C(cys)LAVEEVSL from OCI-AML3, are predicted to bind the common HLA haplotypes, HLA-A*03:01 and HLA-A*02:01 respectively. Since NPM1 is mutated in approximately one-third of patients with AML, the finding of endogenous HLA ligands from mutated NPM1 supports future studies evaluating immunotherapeutic approaches against this shared target, for this subset of patients with AML.
Plug-in HEV charging for maximum impact of wind energy on reduction of CO<inf>2</inf> emissions in propulsion (2012)

This paper studies the reduction in CO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> resulting from synergistic interaction of PHEVs with an electric grid containing significant amount of wind power. A combined optimal charging and optimal power management approach is used to rigorously quantify the optimal CO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> reduction impact. This approach produces results that show that inclusion of any amount of wind power on the grid results in reduced CO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> from transportation. The results also account for the temporal variation in wind power. Furthermore, since it is not practical to implement a different control strategy for days with different amounts of wind, we quantify the loss of optimality resulting from this variability in wind.
The Fifth Notebook of Dylan Thomas (2020)

<JATS1:p>Between May 1930 and August 1935, Dylan Thomas kept numerous notebooks of poems. They contain the drafts of almost all of the work that would form his first two reputation-making collections, 18 Poems (1934) and Twenty-five Poems (1936), and many of those in his third collection, The Map of Love(1939). Thomas sold four of the notebooks, spanning May 1930 to May 1934, to the University of Buffalo in 1941. However, the existence of a fifth notebook, covering the period July 1934 to August 1935, was unknown until 2014, the centenary of his birth. The Fifth Notebook of Dylan Thomas makes this newly-discovered text available to readers and researchers for the first time. It contains the only existing MSS versions of Thomas’s most challenging poems, ‘I, in my intricate image’ and ‘Altarwise by owl-light’, and seventeen other early poems. It contains facsimiles and full transcripts of the originals, is annotated throughout, and has a full scholarly introduction. Exploring the contexts of these brilliant and experimental lyrics – many with substantial reworkings and variant passages – this landmark publication sheds new light on the creative practice of one of the most important and well-known poets of the twentieth century. </JATS1:p>
IC3: Image Captioning by Committee Consensus (2023)

If you ask a human to describe an image, they might do so in a thousand different ways. Traditionally, image captioning models are trained to generate a single "best" (most like a reference) image caption. Unfortunately, doing so encourages captions that are "informationally impoverished," and focus on only a subset of the possible details, while ignoring other potentially useful information in the scene. In this work, we introduce a simple, yet novel, method: "Image Captioning by Committee Consensus" (IC3), designed to generate a single caption that captures high-level details from several annotator viewpoints. Humans rate captions produced by IC3 at least as helpful as baseline SOTA models more than two thirds of the time, and IC3 can improve the performance of SOTA automated recall systems by up to 84%, outperforming single human-generated reference captions, and indicating significant improvements over SOTA approaches for visual description. Code is available at https://davidmchan.github.io/caption-by-committee/
An Implementation of Gaze Recognition System Based on SVM (2010)

시선 인식에 관한 연구는 현재 사용자가 응시하고 있는 위치를 파악하는 것으로 많은 응용 분야를 가지며 지속적으로 발전되어 왔다. 기존의 시선 인식에 관한 대부분의 연구는 적외선 LED 및 카메라, 고가의 헤드마운티드 장비 등을 이용하였기 때문에 범용 사용에 문제점을 가지고 있다. 이에 본 논문에서는 한 대의 PC용 웹 카메라를 사용한 SVM(Support Vector Machine) 기반의 시선 인식 시스템을 제안하고 구현한다. 제안한 시스템은 4방향과 9방향의 시선을 인식하기 위해 모니터를 가로 6, 세로 6, 총 36개의 시선 위치로 나누어 각각 9개, 4개씩 그룹핑 및 학습하여 사용자의 시선을 인식한다. 또한, 시선 인식의 성능을 높이기 위해 차영상 엔트로피를 이용한 영상 필터링 방법을 적용한다. 제안한 시스템의 성능을 평가하기 위하여 기존에 제시되었던 차영상 엔트로피 기반의 시선 인식 시스템, 눈동자 중심점과 눈의 끝점을 이용한 시선 인식 시스템, PCA 기반의 시선 인식 시스템을 구현하고 비교 실험을 수행하였다. 실험 결과 본 논문에서 제안한 SVM 기반의 시선 인식 시스템이 4방향은 94.42%, 9방향은 81.33%의 인식 성능을 보였으며, 차영상 엔트로피를 이용한 영상 필터링 방법을 적용하였을 경우에 4방향은 95.37%, 9방향은 82.25%의 성능을 보여 기존의 시선 인식 시스템보다 높은 성능을 나타내었다. The researches about gaze recognition which current user gazes and finds the location have increasingly developed to have many application. The gaze recognition of existence all about researches have got problems because of using equipment that Infrared(IR) LED, IR camera and head-mounted of high price. This study propose and implement the gaze recognition system based on SVM using a single PC Web camera. The proposed system that divide the gaze location of 36 per 9 and 4 to recognize gaze location of 4 direction and 9 direction recognize user's gaze. Also, the proposed system had apply on image filtering method using difference image entropy to improve performance of gaze recognition. The propose system was implements experiments on the comparison of proposed difference image entropy gaze recognition system, gaze recognition system using eye corner and eye's center and gaze recognition system based on PCA to evaluate performance of proposed system. The experimental results, recognition rate of 4 direction was 94.42% and 9 direction was 81.33% for the gaze recognition system based on proposed SVM. 4 direction was 95.37% and 9 direction was 82.25%, when image filtering method using difference image entropy implemented. The experimental results proved the high performance better than existed gaze recognition system.
Treatment with a Bortezomib-Containing Regimen Is Associated with Better Therapeutic Outcomes in Patients with Waldenstrom's Macroglobulinemia Who Have Familial Disease Predisposition (2011)

Abstract Abstract 1643 We examined the impact of familial predisposition on treatment outcome in 135 Waldenstrom's macroglobulinaemia (WM) patients, 26.7% of whom had first or second degree relative(s) with a B-cell lymphoproliferative disorder. All patients were rituximab-naïve and received a rituximab-containing regimen. There were no significant differences in baseline characteristics between cohorts. Overall (93.9% vs. 75.0%; p=0.029) and CR/VGPR (23.2% vs. 16.7%; p&lt;0.0001) responses, time to progression (45.5 vs. 21 months; p=0.015), and to next therapy (50.0 vs. 33.0 months; p=0.024) favored sporadic patients. By multivariate analysis, familial predisposition was an independent marker for disease progression (Hazard ratio 0.554). We next assessed whether the type of treatment used impacted therapeutic outcome in patients with familial WM. Overall, major and CR/VGPR responses were better among patients with familial but not sporadic WM who received a bortezomib versus non-bortezomib containing regimen (Figure 1). A longer TTP was also observed for familial but not sporadic WM patients who received a bortezomib versus non-bortezomib containing regimen. For patients with familial disease, the median TTP was estimated at &gt;33 versus 20.6 months for bortezomib and non-bortezomib containing therapy, respectively (p=0.08). For sporadic WM patients, the median TTP was estimated at &gt;35 versus 45.5 months for bortezomib and non-bortezomib containing therapy, respectively (p=0.68). The findings of this study convey that familial disease predisposition is an important determinant of response, TTP and TTNT in patients with WM. Treatment with a bortezomib-containing regimen is associated with better therapeutic outcomes in patients with WM who have familial disease predisposition, and may be revealing of signaling pathways that are present in familial patients and amenable to select targeting by proteasome inhibition.Figure 1.Overall, major, and VGPR/CR responses for 135 WM patients with sporadic (A) or familial (B) disease who received either bortezomib or a non-bortezomib containing regimen. *p=0.05; and **p=0.0006 among familial WM patients who received bortezomib versus non-bortezomib containing therapy.Figure 1. Overall, major, and VGPR/CR responses for 135 WM patients with sporadic (A) or familial (B) disease who received either bortezomib or a non-bortezomib containing regimen. *p=0.05; and **p=0.0006 among familial WM patients who received bortezomib versus non-bortezomib containing therapy. Disclosures: No relevant conflicts of interest to declare.
A novel heterotrifunctional peptide-based cross-linking reagent for facile access to bioconjugates. Applications to peptide fluorescent labelling and immobilisation (2008)

A convenient, versatile and straightforward synthesis of a novel heterotrifunctional peptide-based linker molecule is described. This generic bio-labelling reagent contains an amine-reactive N-hydroxysuccinimidyl carbamate moiety, an aldehyde/ketone-reactive aminooxy group and a thiol group with a propensity to form urea, oxime and thioether linkages respectively. The full chemical orthogonality between the free aminooxy and thiol functionalities was demonstrated through the preparation of a fluorescent reagent suitable for the selective staining of a carboxaldehyde-modified surface by means of oxime ligation. The absence of reactivity of these two functions toward the nucleophile-sensitive active carbamate was obtained by using temporary aminooxy- and thiol-protecting groups removable under mild conditions. The utility of the linker molecule to cross-link three different molecular partners has been illustrated by the preparation of fluorescent tripod-functionalised surfaces which may be useful in developing new peptide microarrays and related immunosensors.
Corrigendum to ‘Administration of the Cyclic Peptide COR-1 in Humans (Phase I Study): ex vivo Measurements of anti-b1-Adrenergic Receptor Antibody Neutralization and of Immune Parameters’ [Eur J Heart Fail 2012;14:1230–1239] (2013)

On page 1235, the sentence: A traumatic rupture of the left Achilles tendon occurred 18 days after drug administration in a subject who had received 160 mg COR-1 (>8 600 half lives of the drug) during sledging, and had to be surgically treated. Should have read: A traumatic rupture of the left Achilles tendon occurred 18 days after drug administration in a subject who had received 240 mg COR-1 (>8 600 half lives of the drug) during sledging, and had to be surgically treated.
Susceptibility to antivirals of a human HBV strain with mutations conferring resistance to both lamivudine and adefovir† (2005)

Mutations within the hepatitis B virus (HBV) polymerase gene conferring drug-resistance are selected during prolonged lamivudine (3TC) or adefovir dipivoxil (ADV) treatment. Because there is no other approved drug against HBV, treatments with 3TC or ADV are used either sequentially or in addition, depending on treatment response or failure. Considering the use of de novo or add-on 3TC+ADV bitherapy, we investigated the possibility of the emergence of an HBV strain harboring polymerase mutations conferring resistance to both 3TC (rtL180M+M204V) and ADV (rtN236T). We constructed the L180M+M204V+N236T mutant and determined its replication capacity and its susceptibility to different nucleos(t)ide analogs in transiently transfected hepatoma cell lines. The triple mutant replicates its genome in vitro, but less efficiently than either the wild-type (wt) HBV or L180M+M204V and N236T mutants. Phenotypic assays indicated that the L180M+M204V+N236T mutant is resistant to pyrimidine analogs (3TC, -FTC, beta-L-FD4C, L-FMAU). Compared with wt HBV, this mutant displays a 6-fold decreased susceptibility to ADV and entecavir and a 4-fold decreased susceptibility to tenofovir. Interferon alfa inhibited equally the replication of wt and L180M+M204V+N236T HBV. In conclusion, the combination of rtL180M+M204V and rtN236T mutations impairs HBV replication and confers resistance to both 3TC and ADV in vitro. These results suggest that the emergence of the triple mutant may be delayed and associated with viral resistance in patients treated with 3TC+ADV. However, other nucleos(t)ide analogs in development showed an antiviral activity against this multiresistant strain in vitro. This provides a rationale for the clinical evaluation of de novo combination therapies.