gebhart/patrepeval huggingface dataset:
Evaluation of the Pulmonary Toxicity of a Fume Generated from a Nickel-, Copper-Based Electrode to be Used as a Substitute in Stainless Steel Welding (2014)

Epidemiology has indicated a possible increase in lung cancer among stainless steel welders. Chromium (Cr) is a primary component of stainless steel welding fume. There is an initiative to develop alternative welding consumables [nickel (Ni)- and copper (Cu)-based alloys] that do not contain Cr. No study has been performed to evaluate the toxicity of fumes generated from Ni- and Cu-based consumables. Dose-response and time-course effects on lung toxicity of a Ni- and Cu-based welding fume (Ni-Cu WF) were examined using an in vivo and in vitro bioassay, and compared with two other well-characterized welding fumes. Even though only trace amounts of Cr were present, a persistent increase in lung injury and inflammation was observed for the Ni-Cu WF compared to the other fumes. The difference in response appears to be due to a direct cytotoxic effect by the Ni-Cu WF sample on lung macrophages as opposed to an elevated production of reactive oxygen species (ROS).
Efficacy of pulsed-xenon ultraviolet light on reduction of <i>Mycobacterium fortuitum</i> (2020)

Our results demonstrate that using pulsed-xenon devices is a highly effective modality to reduce microbial counts with this relatively ultraviolet germicidal irradiation-resistant mycobacterium in a time-dependent manner.
Small but Mighty: Functional Peptides Encoded by Small ORFs in Plants (2017)

Peptides encoded by small open reading frames (sORFs, usually <100 codons) play critical regulatory roles in plant development and environmental responses. Despite their importance, only a small number of these peptides have been identified and characterized. Genomic studies have revealed that many plant genomes contain thousands of possible sORFs, which could potentially encode small peptides. The challenge is to distinguish translated sORFs from nontranslated ones. Here, we highlight advances in methodologies for identifying these hidden sORFs in plant genomes, including ribosome profiling and proteomics. We also examine the evidence for new peptides arising from sORFs and discuss their functions in plant development, environmental responses, and translational control.
Culture of Cells from Juvenile Worms of Schistosoma mansoni (1993)

Tissue disruption methods were developed and serum-free cell culture media formulated for the maintenance in vitro of cells from juvenile worms (day 18 after infection) of Schistosoma mansoni. Cultures maintained viability for up to 6 mo when plated on a feeder layer of irradiated rat liver cells and survived primarily as clusters of small (2.5-4 microns diameter) cells with a high nuclear-to-cytoplasmic ratio and relatively few organelles identified by electron microscopy. Cultures synthesized a protein profile similar to that of intact worms, and the cell clusters maintained a time- and concentration-dependent contractile response to serotonin. Cells synthesizing DNA were detected by precursor incorporation and flow cytometry in cultures initially and also after several weeks in vitro, although the percentage of cells synthesizing DNA decreased with time. Efforts to identify peptide growth factor-responsive tyrosine phosphorylation were negative, and the overall amount of S. mansoni phosphotyrosine-containing proteins identified by western blot with anti-phosphotyrosine monoclonal antibody was much less than that found in a peptide growth factor-responsive mouse cell line.
Cell proliferation and promotion of rat liver carcinogenesis: different effect of hepatic regeneration and mitogen induced hyperplasia on the development of enzyme-altered foci (1990)

A series of experiments was performed to investigate the effect of different types of cell proliferation on the development of enzyme-altered preneoplastic hepatic foci in male Wistar rats. Animals were given a single dose of diethylnitrosamine (100 mg/kg body weight). After a 2-week recovery period liver cell proliferation was repeatedly induced by four or eight necrogenic doses of carbon tetrachloride (compensatory cell proliferation), or by four or eight treatments with three different liver mitogens, namely lead nitrate, ethylene dibromide and nafenopin (direct hyperplasia). The carcinogen altered hepatocytes were monitored as gamma-glutamyltransferase positive or adenosine triphosphatase negative foci. The results indicate that compensatory cell proliferation induced by both four and eight carbon tetrachloride treatments enhanced the growth of diethylnitrosamine-initiated hepatocytes to enzyme-altered foci. On the contrary, repeated waves of cell proliferation induced by liver mitogens did not result in any significant number of enzyme-altered foci.
Sedimentation and Flocculating Properties of Solid Particles in Enzymatic Treated Rice Washing Drainage and its Electrostatic Properties (2009)

本研究では，洗米排水成分添加による精製米デンプン粒子への凝集・沈降性付加について検討を行った．その結果，洗米排水への酵素添加は，サンプル中のリン酸イオン濃度を特異的に増加させ，その後，精製米デンプン添加により，リン酸濃度の速やかな減少が確認された．さらに，解離型リン酸が存在するpH領域内（pH 3～6）において，特異的に精製米デンプンの凝集・沈降性付加効果を確認するとともに，FT-IR解析の結果，P-O吸収帯の透過率の減少が確認された．以上の検討結果より，酵素処理により洗米排水中固形成分から溶出（放出）したリン酸イオンは，精製米デンプンと結合後，リン酸基由来の負電荷をデンプン表層に形成．さらに，多価陽イオンによる静電的な架橋形成により，精製デンプンのマクロ分子を形成，至っては凝集・沈降性付加ならびに促進が可能となったと推察された．
Imaging of Small Defects in Nonmagnetic Tubing Using a SQUID Magnetometer (1993)

Abstract Using a recently developed superconducting quantum interference device (SQUID) magnetometer system which offers higher resolution and greater sensitivity than previous designs, we have created high-resolution spatial maps of the magnetic anomalies created by small defects in thin-walled, nonmagnetic tubes. Images obtained using three different sensing methods (injected current, induced current, and ferromagnetic decoration) are presented, and compared in terms of sensitivity and signal-to-noise ratio (SNR). All three methods possess the sensitivity to detect holes on a tube's outer diameter as small as 0.37 mm diameter × 0.54 mm deep, with varying SNR, as well as holes on the tube's inner diameter as small as 1.0 mm diameter × 0.3 mm deep. The ferromagnetic decoration method produces the strongest signals and excellent SNRs. Using this approach, we have detected inner- and outer-diameter slots with dimensions 0.76 × 0.15 × 0.08 mm3. In addition, we examine results of numerical inversion calculations applied to the experimental images. With inversion techniques it is possible to determine the original current density distribution given the measured magnetic field, hence revealing the approximate shape and location of defects.
Tripling the Nation's Clean Energy Technologies: A Case Study in Evaluating the Performance of Energy Policy Models (2005)

The economic discussions of national energy policies have usually been driven by scenarios from the Energy Information Administration (EIA) and the Stanford University’s Energy Modeling Forum (EMF). The modeling results from these groups very often suggest negative economic impacts as a result of any deviation from the standard reference case projections of the U.S. economy. Yet, there is a strong literature that offers a significantly different set of modeling results. In the case of clean energy technologies that pay for themselves over (say) a 5-10 year period, one might reasonably conclude that an accelerated investment in such technologies would generate a small but net positive benefit for the overall U.S. economy. After an overview of the relevant literature, we explore this idea in a thought experiment that assumes a tripling of combined heat and power technologies with overall system efficiencies that exceed 70 percent (compared to the current U.S. electric system grid efficiency of 31 percent). We first map all spending changes into an input-output spreadsheet model (based on the IMPLAN database for the US) to determine the likely impact on the nation’s total valueadded production. We then map similar assumptions into Argonne National Laboratory’s AMIGA Modeling System, a 200-sector equilibrium model of the U.S. energy system and economy. In comparing these results, we find a small but net positive impact on GDP in both instances. The comparison suggests that standard input-output analysis might provide a useful diagnostic tool to evaluate the performance of other well-known energy policy models.
Voltage-gated potassium channel proteins and stereoselective S-nitroso-l-cysteine signaling (2020)

S-nitroso-l-cysteine (L-CSNO) behaves as a ligand. Its soluble guanylate cyclase-independent (sGC-independent) effects are stereoselective - that is, not recapitulated by S-nitroso-d-cysteine (D-CSNO) - and are inhibited by chemical congeners. However, candidate L-CSNO receptors have not been identified. Here, we have used 2 complementary affinity chromatography assays - followed by unbiased proteomic analysis - to identify voltage-gated K+ channel (Kv) proteins as binding partners for L-CSNO. Stereoselective L-CSNO-Kv interaction was confirmed structurally and functionally using surface plasmon resonance spectroscopy; hydrogen deuterium exchange; and, in Kv1.1/Kv1.2/Kvβ2-overexpressing cells, patch clamp assays. Remarkably, these sGC-independent L-CSNO effects did not involve S-nitrosylation of Kv proteins. In isolated rat and mouse respiratory control (petrosyl) ganglia, L-CSNO stereoselectively inhibited Kv channel function. Genetic ablation of Kv1.1 prevented this effect. In intact animals, L-CSNO injection at the level of the carotid body dramatically and stereoselectively increased minute ventilation while having no effect on blood pressure; this effect was inhibited by the L-CSNO congener S-methyl-l-cysteine. Kv proteins are physiologically relevant targets of endogenous L-CSNO. This may be a signaling pathway of broad relevance.
Anticancer effects of selenium: Linkage from metabolome to signal transduction (2004)

1380 Selenium (Se) has been shown in clinical trials to be effective in reducing the risk of different cancers including lung cancer. Consequently, the mechanism of this anticancer effect has been under active investigation. Although it is clear that Se induces apoptosis of cancer cells, the regulatory mechanism(s) of this effect is yet to be understood. In addition, different forms of Se appear to have different mechanism(s) of cytotoxicity. To obtain a broad understanding of the toxic effect of Se on lung cancer cells, we employed our metabolomic approach of using NMR and mass spectrometry to define biochemical changes induced by selenite in A549 cells. Figure 1 illustrates the metabolic differences between control and selenite-treated cells, as determined from 1H NMR analysis of crude cell extracts. The accumulation of phosphoryl choline (PC) induced by selenite could be related to an activation of phosphatidylcholine-specific phospholipase C by protein kinase C (PKC). The PC release could also signify increased diacylglycerol production, which in turn modulates PKC activity. Depending on the specific isoforms, activated PKC could inhibit or activate proteins via phosphorylation. The selenite-induced accumulation of metabolites related to the urea cycle ( e.g. Arg, Gln, and ornithine) is consistent with phosphorylation or altered regulation of enzymes such as ornithine decarboxylase and nitric oxide synthase by PKC. Thus, profiling of metabolic changes in response to anticancer agents such as selenite can provide insights into upstream regulatory mechanism(s).
Defect visualization in large area YBCO thin films by magneto-optical scanning technique (1999)

Flux penetration in large area YBCO thin films has been studied by a magneto-optical scanning technique. With a new apparatus HTS films as large as 20 cm/spl times/20 cm can be investigated by scanning the films through an inhomogeneous magnetic field. The apparatus has been built to realize an effective homogeneity control of the electrical properties of large area HTS thin films used for device fabrication. Magnetic flux penetration into YBCO thin films of different sizes and with intrinsic defects as well as artificial ones have been studied at 50 K. Magneto-optical measurements are compared with optical microscopy (OM) and inductive j/sub c/-characterizations. A correlation between the kind of defect and its influence on the electrical properties has been studied with regard to device applications, YBCO films structured especially for high current applications were investigated magneto-optically. These results will be compared to optical photographs of the quenching process caused by currents I>I/sub c/.
CMOS image sensor wafer-level packaging (2011)

This article presents the advances in wafer-level processing and integration techniques for CMOS image sensor module manufacturing. CMOS image sensors gave birth to the low-cost, high-volume camera phone market and are being adopted for various high-end applications. The backside illumination technique has significant advantages over the front-side illumination due to separation of the optical path from the metal interconnects. Wafer bonding plays a key role in manufacturing backside illuminated sensors. The cost-effective integration of miniaturized cameras in various handheld devices becomes realized through the introduction of CMOS image sensor modules or camera modules manufactured with wafer-level processing and integration techniques. We developed various technologies enabling wafer-level processing and integration, such as (a) wafer-to-wafer permanent bonding with oxide or polymer layers for manufacturing backside illuminated sensor wafers, (b) wafer-level lens molding and stacking based on UV imprint lithography for making wafer-level optics, (c) conformal coating of various photoresists within high aspect ratio through-silicon vias, and (d) advanced backside lithography for various metallization processes in wafer-level packaging. Those techniques pave the way to the future growth of the digital imaging industry by improving the electrical and optical aspects of devices as well as the module manufacturability.
Preliminary development of a new individualised questionnaire measuring quality of life in older men with age-related hormonal decline: the A-RHDQoL. (2003)

The new 21-item A-RHDQoL is an individualised questionnaire measuring perceived impact of age-related hormonal decline on the QoL of older men. The internal consistency reliability and content validity of the A-RHDQoL are established, but the measure is at an early stage of its development and its sensitivity to change and other psychometric properties need now to be evaluated in clinical trials of hormone replacement in older men.
The Ideal Quenching Medium? – Characterisation of Ionic Liquids for Heat Treatment of Metallic Components (2013)

Abstract Quenching as a part of heat treatment is an important process in the manufacturing chain of metallic components. One of the most common processes is immersion quenching in vaporising liquids. Unfortunately, this process is affected by the Leidenfrost-phenomenon. This effect can generate inhomogeneous quenching and thus asymmetrical residual stresses and avoidable distortion. In this work, ionic liquids have been investigated as new quenching media, which can be used as baths near room temperature. Aluminium cylinders have been quenched in baths of different ionic liquids with varying water contents and bath temperatures. The time-temperature curves have been recorded and the heat transfer coefficients were determined and compared to quenching in water. Addition of a few percents water to the ionic liquids increases the cooling rate significantly. Even at higher water contents, bubble boiling and convection are predominant and almost no Leidenfrost-effect occurs. This offers a huge potential to accelerate and homogenise immersion quenching.
Highly birefringent microstructured optical fiber for distributed hydrostatic pressure sensing with sub-bar resolution (2022)

We demonstrate distributed optical fiber-based pressure measurements with sub-bar pressure resolution and 1 m spatial resolution over a ∼100 m distance using a phase-sensitive optical time-domain reflectometry technique. To do so, we have designed a novel highly birefringent microstructured optical fiber that features a high pressure to temperature sensitivity ratio, a high birefringence and a mode field diameter that is comparable to that of conventional step-index single mode fibers. Our experiments with two fibers fabricated according to the design confirm the high polarimetric pressure sensitivities (-62.4 rad×MPa<sup>-1</sup>×m<sup>-1</sup> and -40.1 rad×MPa<sup>-1</sup>×m<sup>-1</sup>) and simultaneously low polarimetric temperature sensitivities (0.09 rad×K<sup>-1</sup>×m<sup>-1</sup> and 0.2 rad×K<sup>-1</sup>×m<sup>-1</sup>), at a wavelength of 1550 nm. The fiber features a sufficiently uniform birefringence over its entire length (2.17×10<sup>-4</sup> ± 7.65×10<sup>-6</sup>) and low propagation loss (∼3 dB/km), which allows envisaging pressure measurements along distances up to several kilometers.
Table S1 from Prediction of the Optimal Dosing Regimen Using a Mathematical Model of Tumor Uptake for Immunocytokine-Based Cancer Immunotherapy (2023)

&lt;p&gt;Supplementary Table S1: Characteristics in terms of CEA status, dose received and cancer indication of the 14 patients from the functional imaging study.&lt;/p&gt;
SIX1 reprograms myogenic transcription factors to maintain the rhabdomyosarcoma undifferentiated state (2022)

Rhabdomyosarcoma (RMS) is a pediatric muscle sarcoma characterized by expression of the myogenic lineage transcription factors (TFs) MYOD1 and MYOG. Despite high expression of these TFs, RMS cells fail to terminally differentiate, suggesting the presence of factors that alter their functions. Here, we demonstrate that the developmental TF SIX1 is highly expressed in RMS and critical for maintaining a muscle progenitor-like state. SIX1 loss induces differentiation of RMS cells into myotube-like cells and impedes tumor growth in vivo. We show that SIX1 maintains the RMS undifferentiated state by controlling enhancer activity and MYOD1 occupancy at loci more permissive to tumor growth over muscle differentiation. Finally, we demonstrate that a gene signature derived from SIX1 loss correlates with differentiation status and predicts RMS progression in human disease. Our findings demonstrate a master regulatory role of SIX1 in repression of RMS differentiation via genome-wide alterations in MYOD1 and MYOG-mediated transcription.
Unexpected role of anticoagulant protein C in controlling epithelial barrier integrity and intestinal inflammation (2011)

The protein C (PC) pathway is a well-characterized coagulation system. Endothelial PC receptors and thrombomodulin mediate the conversion of PC to its activated form, a potent anticoagulant and anti-inflammatory molecule. Here we show that the PC pathway is expressed on intestinal epithelial cells. The epithelial expression of PC and endothelial PC receptor is down-regulated In patients with inflammatory bowel disease. PC(-/-)/PC(Tg) mice, expressing only 3% of WT PC, developed spontaneous intestinal inflammation and were prone to severe experimental colitis. These mice also demonstrated spontaneous elevated production of inflammatory cytokines and increased intestinal permeability. Structural analysis of epithelial tight junction molecules revealed that lack of PC leads to decreased JAM-A and claudin-3 expression and an altered pattern of ZO-1 expression. In vitro, treatment of epithelial cells with activated PC led to protection of tight junction disruption induced by TNF-α, and in vivo, topical treatment with activated PC led to mucosal healing and amelioration of colitis. Taken together, these findings demonstrate that the PC pathway is a unique system involved in controlling intestinal homeostasis and inflammation by regulating epithelial barrier function.
Ultrafast photophysics of metal halide perovskite multiple quantum wells: device implications and reconciling band alignment (2019)

Metal halide perovskite quantum wells (QWs) have been used to fabricate efficient optoelectronic devices, and exhibit stability superior to that of their bulk 3D counterparts. The perovskite QWs are tuned in synthesis so that they possess different bandgaps and exciton binding energies owing to variable quantum confinement as a function of QW thickness. Accordingly, the device performance of these materials depends on the efficiency of various interwell carrier dynamical processes, principally exciton and charge transfer. I will discuss the use of transient absorption and ultrafast two-dimensional electronic spectroscopy to probe interwell exciton transfer on timescales of 100s of femtoseconds, and show that interwell charge transfer occurs on timescales of 10s to 100s of picoseconds. These results, in addition to photoelectron spectroscopy experiments, are used to reconcile conflicting observations of type-I and type-II band alignment amongst perovskite QWs.
Binding and ordering of C60 on Pd(110): Investigations at the local and mesoscopic scale (2001)

We present a comprehensive study on the binding and ordering of C60 on a Pd(110) surface employing scanning tunneling microscopy (STM), low-energy electron diffraction (LEED), x-ray photoelectron spectroscopy (XPS) and x-ray photoelectron diffraction (XPD). Three well-ordered structures evolving at elevated temperatures were identified, with (∓2 ±5 7 −1), (4×5), (4×8) unit cells and a coverage of 1, 0.82 and 0.77 physical monolayers, respectively. The rearrangement of Pd substrate atoms turns out to play a crucial role in the evolution of thin C60 films. In STM images alternating bright and dark molecular rows are found for the regular structures. This height difference is attributed to a restructuring of the Pd substrate. Whereas the C60 molecules of the bright molecular rows are embedded in one layer deep microscopic pits, C60 accommodated in two layer deep pits account for the dark molecular rows. XPD results complete the understanding of the film structure. They reveal that the orientation of the C60 cages is unique in the regular structures; the molecules are facing with a 5–6 bond towards the substrate.
The role of hepatic type 1 plasminogen activator inhibitor (PAI‐1) during murine hemorrhagic shock† (2005)

Hemorrhagic shock (HS) followed by resuscitation (HS-R) is characterized by profound physiological changes. Even if the patient survives the initial blood loss, these poorly understood changes can lead to morbidity. One of the tissues most often affected is liver. We sought to recognize specific hepatic changes induced by this stressor to identify targets for therapeutic intervention. Gene array analyses using mouse liver mRNAs were used to identify candidate genes that contribute to hepatic damage. To verify the role of one of the genes identified using the arrays, mice were subjected to HS-R, and multiple parameters were analyzed. A profound increase in plasminogen activator inhibitor type 1 (PAI-1) mRNA was observed using hepatic mRNAs from C57Bl/6 mice after HS, both with and without resuscitation. Constitutive loss of PAI-1 resulted in notable tissue preservation and lower (P < .05) alanine aminotransferase (ALT) levels. Fibrin degradation products (FDPs) and interleukins 6 and 10 (IL-6 and IL-10) were unaffected by loss of PAI-1; however, enhanced urokinase activity, an elevation of active hepatocyte growth factor (HGF), an increase in unprocessed transforming growth factor-beta1 (TGF-beta1), and retention of ERK phosphorylation after HS-R were associated with improved hepatic function. In conclusion, PAI-1 protein is a negative effector of hepatic damage after HS-R through its influence on classic regulators of hepatic growth, as opposed to its role in fibrinolysis.