gebhart/patrepeval huggingface dataset:
Mesoscale modeling: a study of particle generation and line-edge roughness (2014)

A lattice-type Monte Carlo–based mesoscale model and simulation of the lithography process have been adapted to study the insoluble particle generation that arises from statistically improbable events. These events occur when there is a connected pathway of soluble material that envelops a volume of insoluble material due to fluctuations in the deprotection profile. The simulation shows that development erodes the insoluble material into the developer stream and produces a cavity on the line edge that can be far larger than a single polymer molecule. The insoluble particles can coalesce to form aggregates that deposit on the wafer surface. The effect of the resist formulation, exposure, postexposure bake, and development variables on particle generation was analyzed in both low- and high-frequency domains. It is suggested that different mechanisms are dominant for the formation of line-edge roughness (LER) at different frequencies. The simulations were used to assess the commonly proposed measures to reduce LER such as the use of low molecular weight polymers, addition of quenchers, varying acid diffusion length, etc. The simulation can be used to help set process variables to minimize the extent of particle generation and LER.
REGIONAL CEREBRAL BLOOD FLOW (rCBF) MEASURED BY MULTIPLE SPECT ACQUISITIONS FOLLOWING A SINGLE INJECTION OF 99MTC-HMPAO WITH AND WITHOUT ACETAZOLAMIDE (ACZ). (1999)

Scientific Abstracts And Posters From The 44Th Annual Meeting Of The Southwestern Chapter Of The Society Of Nuclear Medicine, And From The 12Th Northeastern Regional Scientific Meeting Of The New England And New York Chapters Of The Society Of Nuclear Medicine
An endogenous retrovirus derived from human melanoma cells. (2003)

We show that human melanoma cells produce retrovirus-like particles that exhibit reverse transcriptase activity, package sequences homologous to human endogenous retrovirus K (HERV-K), and contain mature forms of the Gag and Env proteins. We also demonstrate expression of the pol gene and of Gag, Env, and Rec proteins in human melanomas and metastases but not in melanocytes or normal lymph nodes. The data suggest that expression of retroviral genes and production of retroviral particles is activated during development of melanoma.
Gemmatimonadetes (2015)

Abstract Gem.ma.ti.mo.na.de'tes. N.L. fem. pl. n. Gemmatimonadales type order of the class; N.L. fem. pl. n. Gemmatimonadetes the class of the order Gemmatimonadales . Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the class Gemmatimonadetes is: misspelling (last update, February 2025) * . Correct name: Gemmatimonadia LPSN classification: Bacteria / Pseudomonadati / Gemmatimonadota / Gemmatimonadia The class Gemmatimonadetes can also be recovered in the Genome Taxonomy Database (GTDB) as c__Gemmatimonadetes (version v220) ** . GTDB classification: d__Bacteria / p__Gemmatimonadota / c__Gemmatimonadetes * Meier‐Kolthoff et al. ( 2022 ). Nucleic Acids Res , 50 , D801 – D807 ; DOI: 10.1093/nar/gkab902 ** Parks et al. ( 2022 ). Nucleic Acids Res , 50 , D785 – D794 ; DOI: 10.1093/nar/gkab776
Home Networking Middleware Infrastructure for Improved Audio/Video Appliance Functionality and Interoperability (2005)

A software architecture is described which significantly improves the accessability of multiple home appliances on a heterogeneous home network. Methods for aggregating devices into virtual clusters on a local middleware server are described. These metadevices combine the functionalities of multiple devices but are presented to the user as a single device with a single user interface. Some practical examples of working A/V metadevices are given
Coherently-Shaped Free Electrons as High-Resolution Probes of Coherence in Quantum Systems (2021)

We propose a novel technique that leverages free electrons coherently-shaped by laser pulses to measure quantum coherence in materials, opening the way toward the full characterization of the state of quantum systems at atomic-scale resolution.
Saccharification of Lignocelluloses by Carbohydrate Active Enzymes of the White Rot Fungus Dichomitus squalens (2015)

White rot fungus Dichomitus squalens is an efficient lignocellulose degrading basidiomycete and a promising source for new plant cell wall polysaccharides depolymerizing enzymes. In this work, we focused on cellobiohydrolases (CBHs) of D. squalens. The native CBHI fraction of the fungus, consisting three isoenzymes, was purified and it maintained the activity for 60 min at 50°C, and was stable in acidic pH. Due to the lack of enzyme activity assay for detecting only CBHII activity, CBHII of D. squalens was produced recombinantly in an industrially important ascomycete host, Trichoderma reesei. CBH enzymes of D. squalens showed potential in hydrolysis of complex lignocellulose substrates sugar beet pulp and wheat bran, and microcrystalline cellulose, Avicel. Recombinant CBHII (rCel6A) of D. squalens hydrolysed all the studied plant biomasses. Compared to individual activities, synergistic effect between rCel6A and native CBHI fraction of D. squalens was significant in the hydrolysis of Avicel. Furthermore, the addition of laccase to the mixture of CBHI fraction and rCel6A significantly enhanced the amount of released reducing sugars from sugar beet pulp. Especially, synergy between individual enzymes is a crucial factor in the tailor-made enzyme mixtures needed for hydrolysis of different plant biomass feedstocks. Our data supports the importance of oxidoreductases in improved enzyme cocktails for lignocellulose saccharification.
Towards the Industrialization of New MDO Methodologies and Tools for Aircraft Design (2017)

An overall summary of the
Bone healing and mineralization, implant corrosion, and trace metals after nickel-titanium shape memory metal intramedullary fixation (1999)

Its shape memory effect, superelasticity, and good wear and damping properties make the NiTi shape memory alloy a material with fascinating potential for orthopedic surgery. It provides a possibility for making self-locking, self-expanding, and self-compressing implants. Problems, however, may arise because of its high nickel content. The purpose of this work was to determine the corrosion of NiTi in vivo and to evaluate the possible deleterious effects of NiTi on osteotomy healing, bone mineralization, and the remodeling response. Femoral osteotomies of 40 rats were fixed with either NiTi or stainless steel (StSt) intramedullary nails. The rats were killed at 2, 4, 8, 12, 26, and 60 weeks. Bone healing was examined with radiographs, peripheral quantitative computed tomography, (pQCT) and histologically. The corrosion of the retrieved implants was analyzed by electron microscopy (FESEM). Trace metals from several organs were determined by graphite furnace atomic absorption spectrometry (GF-AAS) or by inductively coupled plasma-atomic emission spectrometry (ICP-AES). There were more healed bone unions in the NiTi than in the StSt group at early (4 and 8 weeks) time points. Callus size was equal between the groups. The total and cortical bone mineral densities did not differ between the NiTi and StSt groups. Mineral density in both groups was lower in the osteotomy area than in the other areas along the nail. Density in the nail area was lower than in the proximal part of the operated femur or the contralateral femur. Bone contact to NiTi was close. A peri-implant lamellar bone sheet formed in the metaphyseal area after 8 weeks, indicating good tissue tolerance. The FESEM assessment showed surface corrosion changes to be more evident in the StSt implants. There were no statistically significant differences in nickel concentration between the NiTi and StSt groups in any of the organs. NiTi appears to be an appropriate material for further intramedullary use because it has good biocompatibility in bone tissue.
Impact of Running Slope and Cross Slope on the Difficulty Level of Outdoor Pathways (2003)

This pilot study examined proposed accessibility guidelines for running slope and cross slope and the perceived difficulty ratings of individuals with mobility limitations. Participants were 23 men and women, 23 to 67 years, with vision or mobility limitations who walked at their preferred pace before rating the path difficulty (1 to 10 scale). Paths meeting the proposed accessibility guidelines were rated as either easy or moderate for difficulty of use. Slopes exceeding the guidelines may also be acceptable for very short distances or on hard/paved surfaces. Future research should include a large representative population, evaluate surface firmness, and examine different perceptions between ambulatory individuals and wheelchair users.
Pharmacologic transglutaminase inhibition attenuates drug‐primed liver hypertrophy but not Mallory body formation (2006)

Mallory bodies (MBs) are characteristic of several liver disorders, and consist primarily of keratins with transglutaminase-generated keratin crosslinks. We tested the effect of the transglutaminase-2 (TG2) inhibitor KCC009 on MB formation in a mouse model fed 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC). KCC009 decreased DDC-induced liver enlargement without affecting MB formation or extent of liver injury. TG2 protein and activity increased after DDC feeding and localized within and outside hepatocytes. KCC009 inhibited DDC-induced hepatomegaly by affecting hepatocyte cell size rather than proliferation. Hence, TG2 is a potential mediator of injury-induced hepatomegaly via modulation of hepatocyte hypertrophy, and KCC009-mediated TG2 inhibition does not affect mouse MB formation.
Pilot-scale in situ water electrolyzer with an improved fluid flow and modified electrodes for upscaling hybrid biological–inorganic systems (2021)

Anthropogenic emissions of CO2 and other greenhouse gases have increased since the pre-industrial era, driven largely by economic and population growth, and are now higher than ever. In this scope, hybrid biological–inorganic systems represent a sustainable and versatile chemical synthesis platform using CO2 as a feedstock which realizes the idea of ’Cleaner Production’. Practical implementation of hybrid biological–inorganic systems for the production of value-added chemical products requires development of scalable and robust electrobioreactors with a high energy efficiency and an adequate size. This work reports an in situ water electrolyzer stack design as part of an electrobioreactor system required for the pilot-scale operation of the hybrid biological–inorganic process approaching the aforementioned requirements. The electrolyzer is designed by applying fluid dynamics simulation tools to model the electrolyte flow. The design takes into consideration the problem of leakage currents, reported in the previous works, which is tackled by applying an electrically insulating coating. Different electrode surface modification approaches, such as coating with electrocatalysts and etching, are used to further enhance the performance and energy efficiency of the electrolyzer. The performance of the electrolyzer stack was evaluated in a pH-neutral solution required for the hybrid biological–inorganic processes. The in situ water electrolyzer developed in this study showed a high Faraday efficiency close to 90% and acceptable specific energy consumption below 90 kWh kgH2−1. The obtained energy-efficiency values are the highest reported for similar applications with a similar scale which emphasizes the successful design of the in situ water electrolyzer stack. All data collected during experimental work might be applied to further investigation, simulation, and optimization of electrobioreactors operating at neutral pH. Overall, the results achieved in this study are promising and represent a crucial step toward the industrial implementation of hybrid biological–inorganic systems.
Low Frequency Noise Reduction of Super-Resolution Near-Field Structre Disc with Platinum-Oxide Layer (2005)

The low frequency noise of super-resolution near-field structure disc with platinum oxide layer was analyzed and reduced. The origin of the noise at low frequency region was found to be from the blank state, and the noise becomes high due to the high readout power for the super-resolution readout. We succeeded in reducing the low frequency noise from 25 dB to 20 and 16 dB by the reduction of super-resolution readout power from 2.6 mW to 2.2 and 1.4 mW. As a result signal uniformity of super-resolution signal was greatly improved. The reduction of readout power was achieved just by the optimization of film thickness without a major material change in the structure.
IGBT operation at cryogenic temperatures: non-punch-through and punch-through comparison (2004)

Detailed experimental data taken for punch through (PT) and non punch through (NPT) IGBTs are presented. The test program covered IGBT devices rated for 100-600 A and 600-1200 V from different manufacturers. The forward conduction drops and switching behavior of the IGBTs are examined over a temperature range of 4.2 to 295 K. Physical behavior at low junction temperatures is analyzed. Different behavior of the two structures at cryogenic temperatures is highlighted and the better performances of the NPT technology are shown.
Fungal endophytes of barley roots (2013)

SUMMARY Fungal infections of barley have tremendous agricultural significance, and can be detrimental or beneficial. Beneficial root infections often involve endophytic fungi, but endophytic associations do not always confer benefits on their hosts. Endophyte infection can be negative, positive or neutral for the host. Benefits to barley and other plants infected with endophytic root fungi include an increase in seed yield, enhanced resistance to pathogens and improved stress tolerance. Even if an endophyte is never pathogenic, it is not always beneficial. The most important factors that determine the nature of the relationship are the specific combination of partner genotypes and developmental stage, and the ecological and environmental setting. The nutrient status of the plant and the availability of soil nutrients may have little effect on the degree of beneficial endophyte colonization and, unlike mycorrhizae, there is no apparent increase in endophyte-associated phosphorous transfer. There are indications of an association between successful endophyte colonization and high soil pH and clay content. The greatest benefits to the barley plant resulting from the associations seem to be obtained in abiotically stressed environments. Fungal infection may give the plant a greater ability to cope with the stress if the partners are in a balanced relationship. Each new study reveals an increasing diversity of beneficial fungal root endophytes and the full potential of these organisms is still to be determined. Further studies are urgently required to develop specific beneficial root–endophyte associations, or combination of them, that are tailored to individual barley varieties for maximum impact in agriculture.
Synthesis and Antiviral Evaluation of 3'-Deoxy-β-L-erythro-pentofuranosyl Nucleosides of the Five Naturally Occurring Nucleic Acid Bases (1995)

Abstract The hitherto unknown title compounds were stereospecifically synthesized by glycosylation of pyrimidine and purine aglycons with a suitably peracylated 3′-deoxy-β-L-erythro-pentofuranose, followed by removal of the protecting groups. All the prepared compounds were tested for their ability to inhibit the replication of a variety of DNA and RNA viruses (including HIV), but they did not show significant antiviral activity.
Supplementary Table 1, Figures 1-7 from CXCR4 Signaling Regulates Metastasis of Chemoresistant Melanoma Cells by a Lymphatic Metastatic Niche (2023)

Supplementary Table 1, Figures 1-7 from CXCR4 Signaling Regulates Metastasis of Chemoresistant Melanoma Cells by a Lymphatic Metastatic Niche
Integrated network analysis reveals a novel role for the cell cycle in 2009 pandemic influenza virus-induced inflammation in macaque lungs (2012)

Our findings suggest that the enhanced pathology is the result of a prolonged immune response, despite successful virus clearance. Most interesting, we identify a mechanism which normally suppresses immune cell signaling and inflammation is ineffective in the pH1N1 virus infection; a dyregulatory event also associated with arthritis. This dysregulation offers several opportunities for developing strain-independent, immunomodulatory therapies to protect against future pandemics.
Design, synthesis and characterization of helical opioid glycopeptides and fluorescent derivatives including optimization of serine glycosylation utilizing sugar acetates (2010)

Our effort to provide an efficient route to serine glycosides with utility in glycopeptide synthesis has led to the identification of two particularly effective promoters of O-glycosylation. Indium(III) bromide and scandium(III) triflate were shown to be superior promoters of microwave accelerated O-glycosylation utilizing peracetyl carbohydrate donors. These Lewis acids afforded several advantages over previously described promoters including, increased yields, tolerance to moisture, decreased environmental toxicity, ease of work up, and increased reproducibility. Both affected the microwave accelerated glycosylation of Fmoc-ser-OH with sugar peracetates providing superior yields to previously reported methods. For larger scale work the two step route involving the glycosylation of Fmoc-Ser-OBn followed by removal of the benzyl protecting group via hydrogenolysis was preferred. Of the two Lewis acids, the minimally active indium (III) bromide was preferred, as it afforded slightly higher yields and was effective in catalytic quantities. Three groups of helical DAMGO glycopeptide analogs were synthesized in order to provide a better understanding of the structure activity relationships of these opioid peptides. Although the introduction of the amphipathic helix significantly affected binding of the DAMGO message, there was no correlation between binding affinity at the individual opioid receptors and the degree of helicity. In general, addition of the helical address imparted increased affinity for the kappa receptor. The nature of the linker connecting the N-terminal DAMGO sequence and the C-terminal helical address effected binding affinity only slightly. Successive addition of positive charges to the address increased binding at all three opioid receptors until a maximum was reached at a positive two address charge. Although, the amphipathic helix was shown to moderate receptor selectivity, the native mu preference of the DAMGO message was retained. Two groups of fluorescent analogs of the mixed δ/μ opioid agonist MD100 were prepared. Within the first series, the fluorescent label was attached to the interior of the address sequence employing the pNZ moiety as a secondary protecting group. The second series of analogs was based on NovaTag™ resin, and allowed for attachment of the fluorophore at the carboxy terminus. The influence on helicity imparted by fluorophore conjugation depended on the nature and point of attachment of the label. The disruption of secondary structure associated with attachment of the fluorescent correlated with decreased binding affinity at the individual opioid receptors. Preliminary in vivo results were encouraging. The least parent like of the MD100 fluorescent analogs was shown to be taken up into endothelial cells. This suggests that the labeled glycopeptides are likely to cross the blood-brain barrier.
System-Size Independence of Directed Flow Measured at the BNL Relativistic Heavy-Ion Collider (2008)

We measure directed flow (v_{1}) for charged particles in Au+Au and Cu+Cu collisions at sqrt[s_{NN}]=200 and 62.4 GeV, as a function of pseudorapidity (eta), transverse momentum (p_{t}), and collision centrality, based on data from the STAR experiment. We find that the directed flow depends on the incident energy but, contrary to all available model implementations, not on the size of the colliding system at a given centrality. We extend the validity of the limiting fragmentation concept to v_{1} in different collision systems, and investigate possible explanations for the observed sign change in v_{1}(p_{t}).
Equivalent Elmore delay for RLC trees (2000)

Closed-form solutions for the 50% delay, rise time, overshoots, and settling time of signals in an RLC tree are presented. These solutions have the same accuracy characteristics of the Elmore delay for RC trees and preserves the simplicity and recursive characteristics of the Elmore delay. Specifically, the complexity of calculating the time domain responses at all the nodes of an RLC tree is linearly proportional to the number of branches in the tree and the solutions are always stable. The closed-form expressions introduced here consider all damping conditions of an RLC circuit including the underdamped response, which is not considered by the Elmore delay due to the nonmonotone nature of the response. The continuous analytical nature of the solutions makes these expressions suitable for design methodologies and optimization techniques. Also, the solutions have significantly improved accuracy as compared to the Elmore delay for an overdamped response. The solutions introduced here for RLC trees can be practically used for the same purposes that the Elmore delay is used for RC trees.
Electricity from lignocellulosic substrates by thermophilic Geobacillus species (2020)

Given our vast lignocellulosic biomass reserves and the difficulty in bioprocessing them without expensive pretreatment and fuel separation steps, the conversion of lignocellulosic biomass directly into electricity would be beneficial. Here we report the previously unexplored capabilities of thermophilic Geobacillus sp. strain WSUCF1 to generate electricity directly from such complex substrates in microbial fuel cells. This process obviates the need for exogenous enzymes and redox mediator supplements. Cyclic voltammetry and chromatography studies revealed the electrochemical signatures of riboflavin molecules that reflect mediated electron transfer capabilities of strain WSUCF1. Proteomics and genomics analysis corroborated that WSUCF1 biofilms uses type-II NADH dehydrogenase and demethylmenaquinone methyltransferase to transfer the electrons to conducting anode via the redox active pheromone lipoproteins localized at the cell membrane.
Non‐Steroidal Aromatase Inhibitors Based on a Biphenyl Scaffold: Synthesis, in vitro SAR, and Molecular Modelling (2008)

The synthesis and in vitro biological evaluation (JEG-3 cells) of a series of novel and potent aromatase inhibitors, prepared by microwave-enhanced Suzuki cross-coupling methodology, are reported. These compounds possess a biphenyl template incorporated with the haem-ligating triazolylmethyl moiety, either on its own or in combination with other substituent(s) at various positions on the phenyl rings. The most potent aromatase inhibitor reported herein has an IC(50) value of 0.12 nM, although seven of its congeners are also highly potent (IC(50)<or=0.5 nM). They all bear the (5-triazolylmethyl-2-cyano)biphenyl structural motif. Docking of representative compounds into a homology model of human aromatase assists in the rationalisation of the SAR derived from the in vitro biological results and supports a crucial role for a cyano group on the "A" phenyl ring, which is accessible to hydrogen bond interactions with Ser 478. Further development of these compounds as potential therapeutic agents for the treatment of hormone-dependent breast cancer is warranted given the high level of potency observed for this class of aromatase inhibitor in vitro.