gebhart/patrepeval huggingface dataset:
EUV pellicle development for mask defect control (2006)

The absence of a reliable non-removable pellicle is a significant obstacle in the development of EUV lithography. In this paper we present analytical and experimental results of a pellicle concept. The concept is based on the development of an EUV transmissive film supported with a wire-mesh. The form factor of the proposed solution is not different from a standard pellicle application, thus this would not require dramatic tool design changes. Results from developmental studies of two materials, silicon (Si) and ruthenium (Ru), are presented. As expected, Si shows oxidation on both surfaces of the thin film, while the less transmissive Ru has excellent resistance to oxidation. Spectral analysis at EUV wavelengths of pellicle coupons agrees very well with the theoretical analysis.
Laboratory grazing-emission x-ray fluorescence spectrometer (1995)

We have developed a laboratory grazing-emission x-ray fluorescence (GEXRF) spectrometer. The instrument utilizes in vacuo wavelength-dispersive detection. Due to the high resolution of a crystal monochromator at long wavelengths, the range of applicability of grazing x-ray techniques is substantially extended to the longer wavelengths as compared to techniques used presently. It is demonstrated that interference fringes in the take-off angle dependence of the fluorescent x-ray intensity of a layered sample can be resolved using a conventional x-ray tube.
Mask technologies for soft-x-ray projection lithography at 13 nm (1993)

We describe a variety of technologies for patterning transmissive and reflective soft x-ray projectionlithography masks containing features as small as 0.1 µm. The transmission masks fabricated for use at 13 nm are of one type, a Ge-absorbing layer patterned on a boron-doped Si membrane. Reflective masks were patterned by various methods that included absorbing layers formed on top of multilayer reflectors, multilayer-reflector-coating removal by reactive ion etching, and ion damage of multilayer regions by ion implantation. For the first time, we believe, a process for absorber repair that does not significantly damage the reflectance of the multilayer coating on the reflection mask is demonstrated.
Design and Construction Integration Using Object Oriented Project Model with Multiple-Views (1991)

Generating, sharing and maintaining project data among multiple disciplines and throughout a project life cycle is difficult task in the highly fragmented A/E/C industry. Presently, the A/E/C/ industry dose not have a common standards for exchanging project data to allow applications to share graphical and non-graphical information produced and consumed at the various stages of a project cycle. The scope of this research is to establish an object-oriented project model (PMAPM) supporting multiple views that are required by the various participants of an A/E/C project. The objective is the eventual development of an integrated system which includes activities from project planning to the facility management. The object-oriented project model is intended to link CAD systems, relational database, knowledge-based systems and other conventional application software; these applications can easily be treated as a view-function embedded in a view-object of PMAPM.
Proteolytic Activation of Pro-Macrophage-Stimulating Protein by Hepsin (2011)

Macrophage-stimulating protein (MSP) is a plasminogen-related growth factor and ligand for the receptor tyrosine kinase RON. The MSP/RON system promotes wound healing and invasive tumor growth and suppresses proinflammatory immune response. MSP binding to RON requires proteolytic conversion of the inactive single-chain form (pro-MSP) into the disulfide-linked α/β heterodimer. The pro-MSP cleavage sequence (Ser-Lys-Leu-Arg(483)↓Val(484)) closely matches the substrate recognition sequences of hepsin, a type II transmembrane serine protease, that is overexpressed in several cancers. Here, we show that recombinant hepsin cleaves pro-MSP at the consensus site Arg(483)-Val(484) with superior efficiency compared with the known activators MT-SP1 and hepatocyte growth factor activator (HGFA). At least 50% of pro-MSP was processed within 1 hour at a hepsin concentration of 2.4 nmol/L and at a molar enzyme to substrate ratio of 1:500. An uncleavable single-chain variant of MSP weakly bound to a RON-Fc fusion protein, whereas hepsin-cleaved MSP bound with a K(D) of 10.3 nmol/L, suggesting that the high-affinity binding site in MSP β-chain was properly formed. LNCaP prostate cancer cells overexpressing hepsin on the cell surface efficiently activated pro-MSP, which was blocked by a specific anti-hepsin antibody. Incubation of pro-MSP with hepsin led to robust RON-mediated phosphorylation of mitogen-activated protein kinase, ribosomal S6 protein, and Akt in human A2780 ovarian carcinoma cells stably expressing RON protein. In macrophages, pro-MSP with hepsin induced chemotaxis and attenuated lipopolysaccharide-dependent production of nitric oxide. These findings suggest that the MSP/RON signaling pathway may be regulated by hepsin in tissue homeostasis and in disease pathologies, such as in cancer and immune disorders.
Synthesis and properties of new anionic photoacid generators bound polymer resists for e-beam and EUV lithography (2008)

A new series of methacrylate substituted benzene sulfonic photoacid generators (PAGs) and a perfluoro alkanesulfonic PAG, bound polymeric resists based on hydroxystyrene (HS) and 2-ethyl-2-adamantyl methacrylate (EA) were prepared and characterized. The acid yield of these PAG bound polymer resists was among the range of 54-81% under deep ultraviolet exposure (254 nm) that agrees well with the electron withdrawing effect of the substituents on the PAG anion for enhancing acid generation efficiency. The intrinsic lithography performance of these polymer-bound PAG resists showed sub-50 nm half-pitch resolution and < 5 nm LER (3σ).
A Disposable Multi-Functional Air Filter: Paper Towel/Protein Nanofibers with Gradient Porous Structures for Capturing Pollutants of Broad Species and Sizes (2017)

Highly polluted air is usually concentrated with particles of broad sizes and species of gaseous toxic chemicals. Filtration of these pollutants simply relying on size effects is not sufficient; instead, strong interactions between filtering materials and pollutants are in critical need. Moreover, to reduce or even avoid further pollution to the environment from disposing of the massive amount of used air filters demands the development of “green” air filtering materials. Here, we report a high-performance hybrid cellulose/protein air filter with nanofiber structures. Interestingly, it was discovered that textured cellulose paper towel can not only act as a flexible mechanical support but also as a type of air flow regulator that can improve pollutant–nanofilter interactions. Therefore, the high-performance natural protein-based nanofabrics are promoted both mechanically and functionally by textured cellulose paper towel. Study results indicate that this hybrid filtering material possesses excellent removal efficiency for particulate matter with a broad size range, in particular for small pollutants, the most challenging for air filtration, and multiple species of toxic chemicals. This study indicates that the protein/cellulose hybrid system can be used in high-performance air filters and are disposable due to the abundance and environmental friendliness of the original materials.
Siglec induction of B cell tolerance by recognition of sialic acids as self (359.1) (2014)

The sialic acid binding immunoglobulin lectin family of cell adhesion receptors called siglecs are differentially expressed on most white blood cells of the immune system, with regulatory motifs in their cytoplasmic domains that modulate the activity of cell signaling receptors. A challenge in elucidating their functions has been to define the context in which they modulate immune cell functions. Exemplary are the B cell siglecs CD22 and Siglec‐10 (Siglec‐G in mouse), which participate in negative regulation of the B cell receptor. Evidence suggests that B cell siglecs mediate peripheral tolerance to membrane self‐antigens by their recruitment to the site of contact by sialic acid ligands on the same cell. The impact of the siglec is to activate a tolerogenic circuit, resulting in apoptosis of the antigen reactive B cell. This toleragenic mechanism can be exploited to induce tolerance to any desired antigen using Siglec Tolerizing Antigenic Liposomes (STALs), comprised of liposomal nanoparticles displaying both the antigen and high affinity siglec ligands. Engagement of a B cell with its cognate antigen and siglec ligands results CD22 mediated apoptosis of the B cell [J. Clin. Invest (2013) 123, 3074]. Such tolerization technology has potential for eliminating unwanted antibodies in the areas of autoimmunity, allergies, and biotherapeutics. (NIH grants AI050143, AI099141 and HFSP LT001099/2010‐L).
Development of a Low-Cost Optical Sensor for Cupric Reducing Antioxidant Capacity Measurement of Food Extracts (2010)

A low-cost optical sensor using an immobilized chromogenic redox reagent was devised for measuring the total antioxidant level in a liquid sample without requiring sample pretreatment. The reagent, copper(II)-neocuproine (Cu(II)-Nc) complex, was immobilized onto a cation-exchanger film of Nafion, and the absorbance changes associated with the formation of the highly colored Cu(I)-Nc chelate as a result of reaction with antioxidants was measured at 450 nm. The sensor gave a linear response over a wide concentration range of standard antioxidant compounds. The trolox equivalent antioxidant capacity (TEAC) values of various antioxidants reported in this work using the optical sensor-based "cupric reducing antioxidant capacity" (CUPRAC) assay were comparable to those of the standard solution-based CUPRAC assay, showing that the immobilized Cu(II)-Nc reagent retained its reactivity toward antioxidants. Common food ingredients like oxalate, citrate, fruit acids, and reducing sugars did not interfere with the proposed sensing method. This assay was validated through linearity, additivity, precision, and recovery, demonstrating that the assay is reliable and robust. The developed optical sensor was used to screen total antioxidant capacity (TAC) of some commercial fruit juices without preliminary treatment and showed a promising potential for the preparation of antioxidant inventories of a wide range of food plants.
Internal heat integration – the key to an energy‐conserving distillation column (2003)

Abstract This paper illustrates the thermal energy conservation potential of the so‐called heat integrated distillation column (HIDiC), which combines advantages of direct vapour recompression and diabatic operation at half of the normal column height. In a typical close boiling mixture separation, compared with a column utilising the usual vapour recompression scheme, HIDiC halved the consumption of exergy at approximately the same capital cost, indicating a strikingly short pay‐off time. The complexities of integrating the heat transfer equipment in the stripping section with proven gas/liquid contacting devices, which may work adversely to practical implementation of HIDiC concept, are also addressed. © 2003 Society of Chemical Industry
Producing human ceramide-NS by metabolic engineering using yeast Saccharomyces cerevisiae (2015)

Ceramide is one of the most important intercellular components responsible for the barrier and moisture retention functions of the skin. Because of the risks involved with using products of animal origin and the low productivity of plants, the availability of ceramides is currently limited. In this study, we successfully developed a system that produces sphingosine-containing human ceramide-NS in the yeast Saccharomyces cerevisiae by eliminating the genes for yeast sphingolipid hydroxylases (encoded by SUR2 and SCS7) and introducing the gene for a human sphingolipid desaturase (encoded by DES1). The inactivation of the ceramidase gene YDC1, overexpression of the inositol phosphosphingolipid phospholipase C gene ISC1, and endoplasmic reticulum localization of the DES1 gene product resulted in enhanced production of ceramide-NS. The engineered yeast strains can serve as hosts not only for providing a sustainable source of ceramide-NS but also for developing further systems to produce sphingosine-containing sphingolipids.
Abstract B028: Transcriptional and epigenetic signatures of ex vivo propagated three distinct TCR Vδ1, TCR Vδ2 and TCR Vδ3 cell subtypes with broad specificity for malignancies (2016)

Abstract Functionally pleiotropic human γδ T cells are a unique set of immune cells that exhibit qualities of both innate and adaptive immune responses. In contrast to αβ T cells, γδ T cells recognize their ligands independent of MHC and are infrequent (1%–5% of T cells) in peripheral blood. Studies have shown that γδ T cells exhibit endogenous cytotoxicity towards tumor cells by directly recognizing a diverse array of Tumor Associated Antigen (TAA) and have the ability to present TAA to elicit an antitumor response. This broad recognition of antitumor activity is achieved because these cells express a diverse TCR γδ repertoire (combination of Vδ1, Vδ2, or Vδ3 with one of fourteen Vγ chains). Because of their characteristics γδ T cells are attractive targets for clinical manipulation and tumor immunotherapy. To obtain clinically significant numbers of cells for immunotherapy current ex vivo γδ T cells expansion protocol uses Zoledronic acid, an aminobisphosphonate that results only in selective propagation of Vγ9Vδ2. These cells however, showed clinical response against both solid and hematologic tumors. We have previously shown a novel ex vivo expansion protocol using artificial antigen presenting cells (aAPC), IL2 and IL21 assist aAPC in activating and expanding polyclonal γδ T-cells (Vδ1, Vδ2 and Vδ1neg Vδ2neg T cell subtypes) to clinically significant numbers. These expanded cell subsets secrete proinflammatory cytokines, lysed a broad range of malignancies and improved survival in ovarian cancer xenograft model. To better define the role of the subsets and their application in immunotherapy here we present high-resolution transcriptome, microRNA and secreted cytokine-chemokine signatures of ex vivo expanded subsets. Our data provide an atlas of transcriptional, epigenetic and secretome of three defined subsets, and subset-specific signatures. The data presented here will have a broader impact in understanding the immunobiology of γδ T cell subsets and facilitate improving the human application of these cells in cancer immunotherapy. Citation Format: Sourindra Maiti, Drew Deniger, Jianliang Dai, Laurence Cooper. Transcriptional and epigenetic signatures of ex vivo propagated three distinct TCR Vδ1, TCR Vδ2 and TCR Vδ3 cell subtypes with broad specificity for malignancies. [abstract]. In: Proceedings of the CRI-CIMT-EATI-AACR Inaugural International Cancer Immunotherapy Conference: Translating Science into Survival; September 16-19, 2015; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(1 Suppl):Abstract nr B028.
Immunoreactive S-antigen in cerebrospinal fluid: a marker of pineal parenchymal tumors? (1989)

This investigation evaluated the possibility that the occurrence of S-antigen in cerebrospinal fluid (CSF) might be used as a preoperative marker of pineal parenchymal tumors (pineoblastoma and pineocytoma). Such a marker could provide a means of preoperatively differentiating these neoplasms from pineal region tumors of other origin. The S-antigen, also known as the 48-kD protein or arrestin, is a highly antigenic protein originally found in the retina and pineal gland. In the retinal photoreceptors and submammalian pineal photoreceptors the protein is thought to be involved in phototransduction; its function in the mammalian pinealocyte is unknown. S-Antigen immunoreactivity also occurs in certain neoplastic cells of retinoblastomas, pineocytomas, pineoblastomas, and cerebellar medulloblastomas. This study included a group of 13 patients with tumors of the pineal region. Samples of CSF were obtained preoperatively and analyzed for the S-antigen using western blot technology. Tumor biopsy material was classified according to conventional neurohistological criteria and was also examined by immunocytochemical techniques for the presence of the S-antigen. S-Antigen immunoreactivity was found in the preoperative CSF of the one patient found to have pineocytoma; tumor tissue removed from this patient was the only neoplastic tissue examined in this study which contained S-Antigen immunoreactive tumor cells. Furthermore, hydroxyindole-O-methyltransferase activity was detectable in the pineocytoma but not in three other pineal tumors, and melatonin levels in the CSF of the pineocytoma patient were the highest in the patient group examined. These preliminary results suggest that testing for S-antigen in CSF might be useful in characterizing and treating tumors of the pineal region and, when identified in conjunction with other markers, it might also help to better define pineal parenchymal tumors. This study needs confirmation with a larger number of patients. If this approach is eventually found to be a reliable predictor of pineal cell tumors, it may supplant the need for surgical biopsies before initiating appropriate adjunctive therapy.
Biotechnological Process for Production of β-Dipeptides from Cyanophycin on a Technical Scale and Its Optimization (2008)

A triphasic process was developed for the production of beta dipeptides from cyanophycin (CGP) on a large scale. Phase I comprises an optimized acid extraction method for technical isolation of CGP from biomass. It yielded highly purified CGP consisting of aspartate, arginine, and a little lysine. Phase II comprises the fermentative production of an extracellular CGPase (CphE(al)) from Pseudomonas alcaligenes strain DIP1 on a 500-liter scale in mineral salts medium, with citrate as the sole carbon source and CGP as an inductor. During optimization, it was shown that 2 g liter(-1) citrate, pH 6.5, and 37 degrees C are ideal parameters for CphE(al) production. Maximum enzyme yields were obtained after induction in the presence of 50 mg liter(-1) CGP or CGP dipeptides for 5 or 3 h, respectively. Aspartate at a concentration of 4 g liter(-1) induced CphE(al) production with only about 30% efficiency in comparison to that with CGP. CphE(al) was purified utilizing its affinity for the substrate and its specific binding to CGP. CphE(al) turned out to be a serine protease with maximum activity at 50 degrees C and at pH 7 to 8.5. Phase III comprises degradation of CGP to beta-aspartate-arginine and beta-aspartate-lysine dipeptides with a purity of over 99% (by thin-layer chromatography and high-performance liquid chromatography), employing a crude CphE(al) preparation. Optimum degradation parameters were 100 g liter(-1) CGP, 10 g liter(-1) crude CphE(al) powder, and 4 h of incubation at 50 degrees C. The overall efficiency of phase III was 91%, while 78% (wt/wt) of the used CphE(al) powder with sustained activity toward CGP was recovered. The optimized process was performed with industrial materials and equipment and is applicable to any desired scale.
New insights into the ORF2 capsid protein, a key player of the hepatitis E virus lifecycle (2018)

Abstract Hepatitis E Virus (HEV) genome encodes three proteins including the ORF2 protein that is the viral capsid protein. Recently, we developed an efficient HEV cell culture system and demonstrated that this virus produces three different forms of its capsid protein: (i) the ORF2i form (infectious/intracellular) which is the form associated with the infectious particles, (ii) the ORF2g (glycosylated ORF2) and ORF2c (cleaved ORF2) forms that are massively secreted glycoproteins not associated with infectious particles, but are the major antigens present in HEV-infected patient sera. The ORF2 protein sequence contains three highly conserved potential N-glycosylation sites (N1, N2 and N3). Although ORF2 protein is the most characterized viral protein, its glycosylation status and the biological relevance of this post-translational modification is still unclear. In the present study, we constructed and extensively characterized a series of ORF2 mutants in which the three N-glycosylation sites were mutated individually or in combination. We demonstrated that the ORF2g/c protein is N-glycosylated on N1 and N3 sites but not on the N2 site. We showed that N-glycosylation of ORF2 protein does not play any role in replication and assembly of infectious HEV particles. We found that glycosylated ORF2g/c forms are very stable proteins which are targeted by patient antibodies. During our study, we also demonstrated that the ORF2i protein is translocated into the nucleus of infected cells. In conclusion, our study led to new insights into the molecular mechanisms of ORF2 expression.
NOVEL ALKYLPHOSPHOCHOLINE ANALOGS FOR BROAD SPECTRUM CANCER IMAGING AND THERAPY (2014)

BACKGROUND: We present in vitro and in vivo imaging and therapeutic studies using a novel alkylphosphocholine (APC)-based molecular scaffold (CLR1404) that combines selective targeting of cancer (including cancer stem cells) with broad-spectrum activity against many different cancer types. CLR1404 APC analogs were created to exploit the finding that phospholipid ethers selectively accumulate in many cancers versus normal cells. METHODS: Depending on the iodine isotope used, radioiodinated CLR1404 is either a PET imaging (124I) or molecular radiotherapeutic agent (131I), with fluorescence analogs created by replacing iodide with various fluorophores. Standard tissue culture, xenograft and molecular biology protocols were used for these studies. RESULTS: CLR1404 displayed preferential uptake and retention in cancer and cancer stem cells compared to normal cells in vitro and in vivo. After 24 hours, selective uptake of fluorescent or radioiodinated CLR1404 analogs by multiple human cancer cell lines in vitro compared to patient-matched normal human fibroblasts was observed (2.3-2.8x). CLR1404 showed highly specific labeling of both human patient-matched glioblastoma stem cells and serum-cultured glioblastoma cells (3x over minimal labeling of control normal human astrocytes and neural stem cells). Lipid raft disruption reduced in vitro CLR1404 analog uptake.In vivo, CLR1404 analogs displayed prolonged tumor-selective retention in 55 different rodent and human cancer models (including triple-negative breast, lung, pancreatic, colorectal, prostate, renal, melanoma, GBM). Tumor accumulation was seen by 24 hours with continued normal tissue clearance between 48-120 hours. In vivo cancer stem cell labeling was also demonstrated. CLR1404 analogs do not visualize inflammatory or premalignant lesions (unlike currently used 18F-fluorodeoxy glucose (FDG)-PET tumor imaging).131I-CLR1404 also displayed therapeutic efficacy (tumor growth suppression, survival extension) especially in renal, colorectal, ovarian, prostate and triple-negative breast cancer, GBM models. CONCLUSIONS: The novel APC CLR1404 analogs potentially offer a powerful multi- modality strategy to detect, treat and follow primary and metastatic cancers in humans. Initial clinical trials strongly suggest CLR1404 has similar broad tumor targeting and retention properties in animals and humans. The pathological correlation between CLR1404 imaging and GBM is being tested in an ongoing multi-institutional Phase II clinical trial. SECONDARY CATEGORY: Preclinical Experimental Therapeutics.