gebhart/patrepeval huggingface dataset:
Multiplexed endoscopic imaging of Barrett’s neoplasia using targeted fluorescent heptapeptides in a phase 1 proof-of-concept study (2020)

Improved methods for early cancer detection arising from Barrett’s oesophagus (BE) are still needed. Imaging molecular expression patterns in BE patients can target neoplasia. We demonstrate a multiplexed fluorescence imaging approach to detect premalignant lesions with two fluorescently labeled heptapeptides specific for EGFR and ErbB2. Twenty-two BE patients underwent endoscopic imaging with a multimodal scanning fiber endoscope (mmSFE). In this pilot study, 92% of neoplastic lesions could be imaged by comparison with pathology, with only 11% false positives. This first-in-human study demonstrates feasibility to concurrently detect multiple targets in vivo and potential for early detection of cancers that are molecularly heterogeneous.

### Background

Oesophageal adenocarcinoma (EAC) is a deadly disease that has increased dramatically in incidence over the past several decades.1 2 Endoscopic screening with white light illumination and random biopsy is limited by sampling error.3 Dysplasia often presents with flat architecture and patchy distribution.4 EGFR and ErbB2 are transmembrane tyrosine kinase receptors that stimulate epithelial cell growth, proliferation and differentiation.5 Overexpression of these targets reflects a higher risk for cancer progression.6–8 Multiplexed imaging methods take advantage of the broad spectrum of light over the visible and near-infrared (NIR) regimen. We aim to demonstrate clinical feasibility to visualise EGFR and ErbB2 expression simultaneously in vivo to detect Barrett’s neoplasia.

### Methods

Consecutive patients referred for either evaluation or therapy of Barrett’s neoplasia were recruited for the study (NCT03589443). An mmSFE was designed to collect multiplexed fluorescence images concurrently. Target/background (T/B) ratios were calculated for each fluorescence image. More details on the methods and the multiplexed imaging technology can be found in the online supplemental file.

### Supplementary data

[gutjnl-2020-322945supp001.pdf]

### Results

The peptide QRHKPRE specific for EGFR was labelled with Cy5 via a GGGSK linker, (figure 1A).9 KSPNPRF, specific for ErbB2, was labelled with IRDye800 via a GGGSC linker (figure 1B). …
Mass-Transport-Limited Oxygen Reduction Reaction on AA2024-T3 and Selected Intermetallic Compounds in Chromate-Containing Solutions (2001)

Oxygen reduction reaction (ORR) kinetics were investigated on synthesized Al-Cu, Al-Cu-Mg, and Al-Cu-Fe-Mn intermetallic phases and compared to AA2024-T3 (UNS A92024), as well as high-purity Al, Cu, and Au. These tests were conducted in 0.1 M sodium sulfate (Na2SO4) with and without either 0.005 M sodium chloride (NaCl, pH 6), 0.01 M sodium chromate (Na2CrO4, pH 8), or 0.0062 M Na2CrO4 + 0.0038 M chromic acid (H2CrO4, pH 6) additions using stationary and rotating disk electrodes. Mass-transport-rate-controlled ORR were near theoretical values on all Cu-bearing materials and Au in 0.1 M Na2SO4 with and without 0.005 M NaCl. Theoretical limiting current densities (CD) were not achieved in the mass-transport-controlled regime on Al because of the rate limitation of electron transfer through its oxide film. Four effects of chromate additions on such cathodic reaction rates were identified as follows: —Little intrinsic effect of chromate pretreatment on mass-transport-controlled ORR on high-purity Cu, Cu-containing Al-based intermetallics, and Au electrodes in the absence of open-circuit corrosion. Charge transfer-controlled and mixed-controlled ORR are lowered possibly by the blocking of O2 adsorption sites by chromate anions.—Decreased net cathodic kinetics on AA2024-T3 as a function of the degree to which chromate suppressed open-circuit pitting corrosion prior to cathodic polarization.—Increased net cathodic kinetics on high-purity Al.—Decreased ORR kinetics on S-Al2CuMg as a result of minimization of Al(Mg) dissolution and, subsequently, minimization of the formation of a high, Cu-rich surface. Comments are made regarding the influence of each of these phenomena on open-circuit pitting of AA2024-T3.
162 Multi-modality imaging in survivors of COVID-19 (2021)

<h3>Background</h3> Widespread abnormalities of the myocardium have been reported in patients with COVID-19. However, these patients often have substantial co-morbidities and it is essential to understand whether cardiac abnormalities represent pre-existing disease or are the consequence of COVID-19. <h3>Objective</h3> To determine the contribution and cardiac impact of co-morbidities in patients who have recovered from COVID-19. <h3>Methods</h3> In a prospective observational study, adult patients hospitalized with confirmed COVID-19 were recruited from the Edinburgh Heart Centre between May and November 2020 and compared to healthy and co-morbidity-matched volunteers. Patients underwent gadolinium and manganese-enhanced magnetic resonance imaging and coronary computed tomography angiography. <h3>Results</h3> Twenty-three patients (54±11 years, 20 male) who recovered from COVID-19 were recruited. Half (n=11, 48%) required admission to the intensive care unit and a third (n=7, 31%) received non-invasive or invasive ventilation. Patients had a high prevalence of known cardiovascular disease (n=18, 78%), associated risk factors (n=11, 45%) and coronary artery disease (n=8, 35%). Compared with younger healthy volunteers (n=10), myocardial native T1 values (1202±25 versus 1162±27 ms, P=0.008, <b>figure 1</b>) and extracellular volume fraction (31.9±1.7 versus 29.8±0.5 %, P=0.001, <b>figure 1</b>) were higher with no differences in manganese uptake. Compared to co-morbidity-matched volunteers (n=20), there were no differences in native T1 values (1202±25 versus 1196±39 ms, P=0.61, <b>figure 1</b>), extracellular volume fraction (31.9±1.7 versus 31.0±0.5 %, P=0.11), presence of late gadolinium enhancement or manganese uptake. These findings remained irrespective of COVID-19 disease severity, presence of concomitant myocardial injury or coronary artery disease. <h3>Conclusions</h3> Patients who have recovered following hospitalization with COVID-19 have no evidence of a major excess in myocardial injury or dysfunction compared to co-morbidity-matched volunteers. The presence of co-morbidities likely explains many of the previously reported myocardial abnormalities. <h3>Conflict of Interest</h3> None
Mitochondrial DNA sequence variation and phylogeography among Salmo trutta L. (Greek brown trout) populations (1997)

To investigate the phylogenetic relationships and geographical structure among brown trout S. trutta L. Populations from the South Adriatic-Ionian and Aegean sea basins, mitochondrial DNA sequence comparisons were used. A 310-base-pair (bp) segment of the control region (D-loop), and an additional 280-bp segment of the cytochrome beta gene were sequenced from representatives of 13 brown trout populations. Phylogenetic analyses, conducted after combining the data presented with published data from other Eurasian brown trout, revealed four major phylogenetic groups, three of which were found widely distributed within the southern Balkan region. The phylogeographical patterns revealed by mtDNA represent one of the few cases where phylogenetic discontinuity in a gene tree exists without obvious geographical localization within a species' range and has most likely resulted from the differentiation of the major mtDNA clades during Messinian or early Pleistocene times. Finally, the genetic relationships among the populations suggested by mtDNA were generally not in accordance with either allozyme or morphological data.
Dynamic neural network-based robust observers for second-order uncertain nonlinear systems (2011)

A dynamic neural network (DNN) based robust observer for second-order uncertain nonlinear systems is developed. The observer structure consists of a DNN to estimate the system dynamics on-line, a dynamic filter to estimate the unmeasurable state and a sliding mode feedback term to account for modeling errors and exogenous disturbances. The observed states are proven to asymptotically converge to the system states though Lyapunov-based stability analysis.
EXPERIMENTAL STUDY ON MINERAL PROCESSING OF LEAD-ZINC ORE IN YUNNAN (2010)

Base on studying of mineralogical research technology,Lead-zinc selective flotation is determined fromthe lead-zinc sulphide ore of Yunnan and the test indexes are achieved as following:Pb concentrate: Pbgrade 65.44%,recovery 81.74%;Zn concentrate: Zn grade 55.42%,recovery 94.57%.The test results show that this process flow is suitable for this ore.
Synthesis, Structure and Properties of Several New Oxychalcogenide Materials with the General Formula A2O2M2OSe2 (A = La−Sm, M = Fe, Mn) (2011)

We report the synthesis of a series of manganese-containing oxychalcogenides with general formula A2O2Mn2OSe2 (A = La, Ce, Pr) as well several new A2O2Fe2OSe2 materials (A = La−Sm). We report the structural, magnetic, and conduction properties of the manganese-containing materials: La2O2Mn2OSe2, Ce2O2Mn2OSe2, and Pr2O2Mn2OSe2. These materials are isostructural with La2O2Fe2OSe2, and are shown to undergo a phase transition on cooling, apparently related to displacement of oxide ions from the [Mn2O]2+ plane. Peak splitting has been observed in the Pr3+ containing material at low temperatures, consistent with a reduction to orthorhombic symmetry. All of the manganese containing materials order antiferromagnetically on cooling with k = (0, 0, 0), TN = 164−184 K, and have a 12 K Mn2+ moment of around 4 μB. The magnetic structure of La2O2Co2OSe2 is also reported. Conductivity studies have shown that La2O2Mn2OSe2 and La2O2Co2OSe2 are both semiconducting, with activation energies of ∼0.24 and 0.35 eV.
Analysis of T cell antigen receptor expression by porcine natural killer T cells (2018)

Abstract Invariant natural killer T (iNKT) cells are an innate-like T cell subset expressed by some, but not all mammals. Unlike conventional T cells, iNKT cells express a semi-invariant T cell receptor (TCR) (Vα24-Jα18/Vβ11 in human and Vα14-Jα18/Vβ8.2, Vβ2, or Vβ7 chains in mice) that recognizes glycolipid antigens presented by the non-polymorphic molecule CD1d. Once activated, iNKT cells generate an extensive array of immune responses that may be useful for treating cancer, autoimmunity and infectious disease in humans. In addition, there may be potential to target iNKT cells for veterinary applications. Pigs express iNKT cells that can be detected using mouse or human CD1d-tetramer reagents loaded with the prototypic iNKT cell ligand, α-galactosylceramide (α-GalCer). We exploited this phenomenon to define the TCR repertoire of iNKT cells (CD3α+CD1d tetramer+) compared to conventional T cells (CD3α+CD1d tetramer−) sorted from the peripheral blood of commercial mixed-breed pigs. We found that iNKT cells are highly enriched for the α-chain and CDR3α loop from Vα87*-Jα60* that possess a high level of amino acid sequence homology with human Vα24 (85%) and Jα18 (86%) as well as mouse Vα14 (74%) and Jα18 (79%). Particularly striking was that the most abundant CDR3α sequence was a near perfect match for the human invariant CDR3α. Porcine iNKT cells were also biased for Vβ84* which is homologous to Vβ11 (74%) in humans, as well as Vβ8.2 (71%) and Vβ2 (80%) in mice. Our findings indicate that the porcine iNKT cell TCR is highly homologous to mouse and particularly human iNKT cell TCR, which suggests that iNKT cells among these species play a similar role in immunity and disease.
Monometallic Carbonyl‐Derived CeO2‐Supported Rh and Co Bicomponent Catalysts for CO‐Free, High‐Yield H2 Generation from Low‐Temperature Ethanol Steam Reforming (2012)

Abstract CeO 2 ‐supported Rh and Co bicomponent catalysts derived from monometallic carbonyls and prepared from metal nitrates for low‐temperature ethanol steam reforming (ESR) have been studied by catalytic testing using a multi‐channel reactor, temperature‐programmed reduction (TPR), X‐ray photoelectron spectroscopy (XPS), thermogravimetric analysis (TGA), H 2 chemisorption, transmission electron microscopy‐energy dispersive X‐ray analysis (TEM‐EDX), powder X‐ray diffraction (PXRD) and IR spectroscopy. Reaction product analysis shows that low‐temperature ESR proceeds mainly through 1) adsorbed oxametallacycle decarbonylation (OD) and acetaldehyde steam reforming (ASR) on Rh/CeO 2 , 2) ethanol dehydrogenation to acetaldehyde, ASR, and water–gas shift (WGS) on Co/CeO 2 , and 3) OD, ASR, and WGS on (Rh+Co)/CeO 2 . The addition of Co to Rh/CeO 2 results in decreased catalytic selectivity towards CO and CH 4 . The carbonyl‐derived (Rh+Co)/CeO 2 displays marked advantage over the nitrate‐prepared catalyst, leading to CO‐free H 2 generation with H 2 yields as high as 4.3 mol mol −1 at temperatures as low as 300 °C. Combined studies by TPR, XPS, H 2 chemisorption, and TEM‐EDX suggest significant interaction between the Rh and Co atoms in carbonyl‐derived (Rh+Co)/CeO 2 , in contrast to nitrate‐prepared catalysts, which is assumed to promote efficient WGS during the ESR process. Catalyst deactivation, possibly as a result of catalyst sintering, metal oxidation, and coke deposition during ESR, is discussed in terms of TPR, XPS, TGA, TEM, and PXRD. A WGS‐ESR bilayered catalyst system of Rh/CeO 2 ‐(Rh+Co)/CeO 2 is successfully applied to the CO‐free and high‐yield production of H 2 from low‐temperature ESR.
Advantage and feasibility of immersion lithography (2004)

Immersion lithography has an advantage in the numerical aperture of optics by a factor of refractive index n of the liquid filled into the space between the bottom lens and wafer. In case of 193-nm exposure tools, water (n = 1.44) has been found as the best liquid. It is shown, by using imaging simulations, that ArF (193-nm) immersion lithography (NA = 1.05 to 1.23) has almost equivalent performance to F2 (157-nm) dry (NA = 0.85 to 0.93) lithography. Issues in the ArF immersion exposure tools are discussed with fluid-dynamic and thermal simulations results. In the fundamental issues, there seems to be no showstoppers so far, however, there exist several challenges to realize viable exposure tools.
Effectively infinite thermal conductivity and zero-index thermal cloak (2020)

Thermal conductivities are the key to heat transfer, and high thermal conductivities are generally beneficial and sometimes indispensable to design thermal metadevices. Therefore, the exploration of high thermal conductivities never stops. However, infinite thermal conductivities have not yet been discovered. To solve the problem, we propose an exact approach to effectively infinite thermal conductivities with a constant-temperature boundary condition, which can be easily realized by an external thermostatic sink. Since (effectively) infinite thermal conductivities just correspond to zero refractive indexes in photonics, they have direct applications in designing zero-index thermal metadevices. For example, we experimentally demonstrate zero-index thermal cloaks which can work in highly conductive backgrounds with simple structures. These results provide insights into thermal metadevices and thermal management with effectively infinite thermal conductivities.
Anodic oxide film influence on formation of anode spots and glow discharge stability (1993)

The three stages of anode surface area evolution in an industrial CO2 laser owing to the formation of oxide films have been recognized. The increase of the current at which the glow-to-arc transition occurs by transition to the final (homogeneous) stage has been established. The disappearance of the anode current spot under presence of the homogeneous low-conducting coating on the anode surface has been shown using 2D simulation. The performed studies enable one to highlight the dominant role of the surface state in anode spot formation in an elevated pressure glow discharge.
Prediction of late relapse in patients with estrogen-receptor–positive breast cancer. (2014)

11065 Background: Proliferation plays an important role in the prediction of early relapse of ER+ breast cancer. This constitutes the basis of almost all of the currently available prognostic tools including gene expression based signatures (e.g. OncotypeDX, Mammaprint, and ProSigna). However, these tools are poor predictors of late relapses (greater than 8 years from initial diagnosis) and there is a dire need for a classifier that can accurately identify patients who remain at high risk of long-term relapse in spite of standard therapy. A better understanding of the mechanisms leading to late relapse could lead to improved strategies for management of these patients. Methods: Gene expression of 1,518 primary tumors from the METABRIC dataset, which contains long-term follow up for breast cancer specific survival (BCSS), was divided into training and validation sets balanced for late relapse cases. An innovative multistate gene methodology was used to identify predictors of late relapse in the training set and confirmed in validation set. Results: Analysis of the training set (n=382; 48 late relapse cases) identified 20 genes that were most predictive of late relapse. Late Relapse Score (LateR) was developed using these genes to optimally separate patients into low and high risk groups (P=0.002). In the validation set (n= 367; 47 late relapse cases), the LateR risk stratification (61% low risk) predicted late relapse (low LateR 0.87 (95%CI 0.80-0.95); high LateR 0.70 (95%CI 0.60-0.81); p=0.03). Furthermore, the combination of INDUCT score and LateR lead to more accurate prediction (p=0.002). In the LateR high risk group, pro-inflammatory cytokines are significantly up-regulated and genes involved in immune response are significantly down-regulated. Conclusions: Immune system plays a major role in the development of late relapse. LateR accurately predicts the likelihood of late relapse for patients with ER+ breast cancer. Together with the INDUCT test for early relapse, LateR provides a valuable tool for assessing the likelihood of relapse and might help the patient and their physicians make appropriate long-term treatment decisions.
A novel sorbent for transport reactors and fluidized bed reactors (1998)

Coal Fired Gasifier Combined Cycles (GCC) have both high efficiency and very low emissions. GCCs critically need a method of removing the H{sub 2}S produced from the sulfur in the coal from the hot gases. There has been extensive research on hot gas cleanup systems, focused on the use of a zinc oxide based sorbent (e.g., zinc titanate). TDA Research, Inc. (TDA) is developing a novel sorbent with improved attrition resistance for transport reactors and fluidized bed reactors. The authors are testing sorbents at conditions simulating the operating conditions of the Pinon Pine clean coal technology plant. TDA sulfided several different formulations at 538 C and found several that have high sulfur capacity when tested in a fluidized bed reactor. TDA initiated sorbent regeneration at 538 C. The sorbents retained chemical activity with multiple cycles. Additional tests will be conducted to evaluate the best sorbent formulation.
Pathogenesis of Salmonella-induced enteritis (2003)

Infections with Salmonella serotypes are a major cause of food-borne diseases worldwide. Animal models other than the mouse have been employed for the study of nontyphoidal Salmonella infections because the murine model is not suitable for the study of Salmonella-induced diarrhea. The microbe has developed mechanisms to exploit the host cell machinery to its own purpose. Bacterial proteins delivered directly into the host cell cytosol cause cytoskeletal changes and interfere with host cell signaling pathways, which ultimately enhance disease manifestation. Recently, marked advances have been made in our understanding of the molecular interactions between Salmonella serotypes and their hosts. Here, we discuss the molecular basis of the pathogenesis of Salmonella-induced enteritis.
IGF-1R/MDM2 Relationship Confers Enhanced Sensitivity to RITA in Ewing Sarcoma Cells (2012)

Ewing sarcoma is one of the most frequent bone cancers in adolescence. Although multidisciplinary therapy has improved the survival rate for localized tumors, a critical step is the development of new drugs to improve the long-term outcome of recurrent and metastatic disease and to reduce side effects of conventional therapy. Here, we show that the small molecule reactivation of p53 and induction of tumor cell apoptosis (RITA, NSC652287) is highly effective in reducing growth and tumorigenic potential of Ewing sarcoma cell lines. These effects occur both in the presence of wt-p53 as well as of mutant or truncated forms of p53, or in its absence, suggesting the presence of additional targets in this tumor histotype. Further experiments provided evidence that RITA modulates an important oncogenic mark of these cell lines, insulin-like growth factor receptor 1 (IGF-1R). Particularly, RITA causes downregulation of IGF-1R protein levels. MDM2 degradative activity is involved in this phenomenon. Indeed, inhibition of MDM2 function by genetic or pharmacologic approaches reduces RITA sensitivity of Ewing sarcoma cell lines. Overall, these data suggest that in the cell context of Ewing sarcoma, RITA may adopt additional mechanism of action besides targeting p53, expanding its field of application. Noteworthy, these results envisage the promising utilization of RITA or its derivative as a potential treatment for Ewing sarcomas.
Ruthenium-Catalyzed Isomerizations of Allylic and Propargylic Alcohols in Aqueous and Organic Media: Applications in Synthesis (2008)

Recent research work on ruthenium-catalyzed isomerizations of allylic and propargylic alcohols into carbonyl compounds is reviewed. Tandem processes based on these isomerization reactions are also included.
Matching algorithms for three-stage bufferless clos network switches (2003)

Three-stage Clos network switches are an attractive solution for future broadband packet routers due to their modularity and scalability. Most three-stage Clos network switches assume either all modules are space switches without memory (bufferless), or employ shared memory modules in the first and third stages (buffered). The former is also referred to as the space-space-space (S <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> ) Clos network switch, while the latter is referred to as the memory-space-memory (MSM) Clos network switch. We provide a survey of recent literature concerning switching schemes in the S <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> Clos network switch. The switching problem in the S <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> Clos network switch can be divided into two major parts, namely port-to-port matching (scheduling) and route assignment between the first and third stages. Traditionally, researchers have proposed algorithms to solve these issues separately. Recently, a new class of switching algorithms, called matching algorithms for Clos (MAC), has been proposed to solve scheduling and route assignment simultaneously. We focus on the MAC schemes and show that the new class of algorithms can achieve high performance and maintain good scalability.