gebhart/patrepeval huggingface dataset:
Metallic Impurities Segregation at the Interface Between Si Wafer and Liquid during Wet Cleaning (1992)

It is crucial to make Si wafer surfaces ultraclean in order to realize low‐temperature processing and high‐selectivity in ultralarge scale integrated production. The ultraclean wafer surface must be perfectly free from particles, organic materials, metallic impurities, native oxides, surface microroughness, and adsorbed molecular impurities. Metallic contamination, the major type of contaminants to be overcome, has a fatal effect on device characteristics and must be suppressed to at least below 1010 atom/cm2. The current dry processes, such as reactive ion etching or ion implantation, cause metallic contamination as high as 1012–1013 atom/cm2. The wet process becomes increasingly important to remove these metallic impurities introduced during dry processing. Employing a new evaluation method, the metallic impurity segregation at the interface between the Si wafer and the liquid in the wet cleaning process was studied. It has been found that metals, such as Cu having higher electronegativity than Si, are directly adsorbed on the Si surface by taking an electron from the Si. On the other hand, metals, such as Fe and K having lower electronegativity than Si, are not adsorbed on the Si surface. In the normal wet cleaning process when a native oxide is formed on the Si surface, metals such as Fe and K that are oxidized more easily than Si, are preferentially included into the native oxide. When the metals are in ultrapure water or chemicals with a concentration of 1 ppb, they are included into the Si surface, and native oxide with evaluation was 1012–1013 atom/cm2. Therefore, to decrease the metallic contamination level on the Si surface to levels less than , the metallic impurities must be suppressed to at least below the 1 ppt level in ultrapure water and high‐purity , which are employed in the final step of the cleaning process. To prevent the metallic contamination on the wafer surface, it was found that it is important to maintain an inert atmosphere, such as or Ar, to suppress native oxide growth and to reduce metallic impurities in the ultrapure water rinse. Moreover, it has been found that the diluted cleaning is effective in removing metals such as Cu, having high electronegativity, from the Si surface at room temperature and that it does not induce surface microroughness. This means the diluted cleaning, which has been employed in the final step of the conventional wet cleaning process to remove the native oxide, needs to be replaced with the diluted cleaning. It was also found that surfactants added to improve the wettability of chemicals on the Si surface were also able to prevent metallic impurity precipitation on the wafer surface.
X-ray Lithography with Environmentally Stable Chemical Amplification Positive Resist (1996)

Synchrotron x-ray lithography of a new environmentally stable chemically amplified positive resist (ESCAP) is described. The resist consists of a thermally and hydrolytically stable resin and acid generator and employs high temperature bake processes to achieve resistance to airborne contamination. The resist is environmentally stable due to reduction of the free volume by annealing and affords true single layer x-ray lithography, eliminating a need for a protective overcoat. Its design concept and x-ray lithographic performance are discussed.
A thermoreversible, photocrosslinkable collagen bio-ink for free-form fabrication of scaffolds for regenerative medicine (2017)

As a biomaterial, collagen has been used throughout tissue engineering and regenerative medicine. Collagen is native to the body, is highly biocompatible, and naturally promotes cell adhesion and regeneration. However, collagen fibers and the inherent weak mechanical properties of collagen hydrogels interfere with further development of collagen as a bio-ink. Herein, we demonstrate the use of a modified type-I collagen, collagen methacrylamide (CMA), as a fibril-forming bio-ink for free-form fabrication of scaffolds. Like collagen, CMA can self-assemble into a fibrillar hydrogel at physiological conditions. In contrast, CMA is photocrosslinkable and thermoreversible, and photocrosslinking eliminates thermoreversibility. Free-form fabrication of CMA was performed through self-assembly of the CMA hydrogel, photocrosslinking the structure of interest using a photomask, and cooling the entire hydrogel, which results in cold-melting of unphotocrosslinked regions. Printed hydrogels had a resolution on the order of ~350 μm, and can be fabricated with or without cells and maintain viability or be further processed into freeze-dried sponges, all while retaining pattern fidelity. A subcutaneous implant study confirmed the biocompatibility of CMA in comparison to collagen. Free-form fabrication of CMA allows for printing of macroscale, customized scaffolds with good pattern fidelity and can be implemented with relative ease for continued research and development of collagen-based scaffolds in tissue engineering.
Carbon Nanotube‐Based Impedimetric Biosensors for Bone Marker Detection (2015)

Current bone mass and density monitoring imaging technology for detection and evaluation of abnormal bone metabolism is not only bulky, cumbersome, and expensive but also involves complex equipment exhibiting slow response to detection of bone pathological changes. In this study, we report the development of an inexpensive, and simpler carbon nanotube (CNT) based impedimetric immunosensor for bone marker sensing, particularly, the detection of C-terminal telopeptide (CTx) bone resorption marker. These metal-coated CNT array electrodes were further functionalized to facilitate immobilization of CTx specific antibodies, and tested against various CTx antigen concentrations. Overall, the developed biosensor was not only facile, and exhibited good sensitivity comparable to ELISA assays, but could also detect a clinically relevant range of CTx antigen concentrations (0.00 ng/mL-0.60 ng/mL). Single frequency testing with and without protein interference (at f = 18.75 Hz) further demonstrated the feasibility and promise of the novel CNT based impedimetric biosensor for ex-situ point of care applications.
Synthesis of Tetrabenzoporphyrins Fused with Fluoranthenes (2010)

Tetrabenzoporphyrins fused with fluoranthenes were prepared by the retro Diels-Alder reaction of the precursors composed of a porphyrin and four fluoranthenes connected with bicyclo[2.2.2]octadiene (BCOD).These porphyrins exhibited the Soret (480-494 nm,  = 243,000-277,000) and intense Q bands (739-760 nm,  = 375,000-509,000).Free bases and Zn complexes of them fluoresce at 760 nm and 746 nm with small Storks shifts and high quantum yields of 30 and 10 %, respectively.
Evaluation of SCSI over TCP/IP and SCSI over fibre channel connections (2001)

This study explores the performance implications of an IP storage protocol (iSCSI) in a storage network. The results are compared with the characteristics of the fibre channel protocol. We set up a test-bed consisting of Linux PCs connected together with both fibre channel and Gigabit Ethernet adapters. We conducted experiments on user and kernel level TCP/IP communication and iSCSI data transfers over TCP/IP. By instrumenting the network and iSCSI device drivers on the initiator and target machines, we have collected performance data on various aspects of the protocols. Using a prototype SCSI target mode driver on the target machine, we were able to conduct similar experiments with the Fibre Channel protocol and interconnects. We present preliminary performance data for iSCSI and ways to improve the underlying TCP/IP bandwidth on Gigabit Ethernet.
Targeting the p27Kip1 E3 Ubiquitin Ligase for the Treatment of Multiple Myeloma and Other Hematological Malignancies. (2006)

Abstract Introduction: The proteasome inhibitor bortezomib (VELCADE®; formerly PS-341) has been approved for therapy of relapsed/refractory multiple myeloma but may be limited in its effectiveness by activation of an anti-apoptotic heat shock protein response. In contrast, targeting a unique E3 ubiquitin ligase could selectively stabilize specific cellular proteins whose ubiquitination is regulated by this E3, reducing the likelihood of any unwanted pro-survival effects on other pathways. Methods: To this end, we sought to identify a small molecule that preferentially stabilized the tumor suppressor proteins p21Cip1 and p27Kip1. Results: Here we report the identification of CC-125007, a small molecule that stabilized p21Cip1, p27Kip1, and p57 in models of multiple myeloma. Unlike bortezomib, CC-125007 did not induce accumulation of other cell cycle regulatory proteins such as p53. CC-125007 reduced viability in a time- and concentration-dependent fashion and, again unlike bortezomib, which induced arrest at G2/M, CC-125007 induced cell cycle arrest at the G1/S phase. Decreased viability due to CC-125007 was not accompanied by caspase-mediated apoptosis, however, since it could not be blocked by pre-incubation with a pan-caspase inhibitor. Instead, a puncate monodansylcadaverine staining pattern was observed, demonstrating the formation of autophagic vacuoles consistent with activation of autophagy, or type II programmed cell death. Further supporting this possibility, combination of the autophagy inhibitor bafilomycin A1 and CC-125007 diminished autophagic vacuole formation. Furthermore, Western blotting demonstrated that CC-125007 induced conversion of microtubule-associated protein light chain 3 form I to II, a biochemical marker for autophagy. Meanwhile, Western blotting also showed that CC-125007 did not activate the anti-apoptotic heat shock response proteins 27, 70, and 90, which would be typical of bortezomib. CC-125007 overcame melphalan and bortezomib resistance in multiple myeloma cell lines, and a combination of low dose bortezomib and CC-125007 triggered synergistic anti-myeloma activity. Importantly, in freshly isolated bone marrow mononuclear cells purified from multiple myeloma patients, CC-125007 decreased the viability of the CD138+ population to a much greater extant than that of the CD138− cells. CC-125007 also stabilized p27Kip1 in samples from patients with acute myeloid leukemia, and enhanced bortezomib-induced apoptosis. Studies to elucidate the mechanism by which CC-125007 stabilized p27Kip1 indicate direct targeting of the E3 ligase. Conclusions: Together, these data suggest that p27Kip1 E3 ligase inhibition with agents such as CC-125007 is a rational strategy for the treatment of multiple myeloma and other hematological malignancies, providing a framework for further development of this novel class of agents.
Geometric variations in high index-contrast waveguides, coupled mode theory in curvilinear coordinates (2002)

Perturbation theory formulation of Maxwell's equations gives a theoretically elegant and computationally efficient way of describing small imperfections and weak interactions in electro-magnetic systems. It is generally appreciated that due to the discontinuous field boundary conditions in the systems employing high dielectric contrast profiles standard perturbation formulations fail when applied to the problem of shifted material boundaries. In this paper we developed a novel coupled mode and perturbation theory formulations for treating generic non-uniform (varying along the direction of propagation) perturbations of a waveguide cross-section based on Hamiltonian formulation of Maxwell equations in curvilinear coordinates. We show that our formulation is accurate and rapidly converges to an exact result when used in a coupled mode theory framework even for the high index-contrast discontinuous dielectric profiles. Among others, our formulation allows for an efficient numerical evaluation of induced PMD due to a generic distortion of a waveguide profile, analysis of mode filters, mode converters and other optical elements such as strong Bragg gratings, tapers, bends etc., and arbitrary combinations of thereof. To our knowledge, this is the first time perturbation and coupled mode theories are developed to deal with arbitrary non-uniform profile variations in high index-contrast waveguides.
A Hybrid Three-Way Valve for Gas Chromatography Systems (2018)

This paper reports a three-way valve that combines a lithographically microfabricated silicon substrate and valve seats with prefabricated piezoelectric actuators and polyimide valve membranes. The microvalve is designed for low dead volume and flow channel chemical resistance, as needed for gas chromatography systems. In contrast with valves that use microfabricated valve membranes, the incorporation of prefabricated membranes significantly simplifies manufacturing and improves the structural robustness. Further, this three-way valve provides independent open-close control for each flow path, rather than simply switching the flow from one path to the other, which is the case for most three-way valves. The overall footprint of the device is 3×3×1.S cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> , Each flow path of the three-way valve provides an open-state flow conductance of 4.42 sccmlkPa, a leakage flow conductance of 0.0012 sccmlkPa, and an overall open-close ratio of 3.68×10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> . In preliminary tests, the valve had been switched 1900 times over 24 hours without showing any performance variation.
Primary structure and androgen regulation of a 20-kilodalton protein specific to rat ventral prostate (1989)

Nuclear and cytosolic forms of a 20-kdalton rat ventral prostate protein were purified and partially sequenced from their N-termini. Isolated nuclei were treated with micrococcal nuclease and extracted in 0.6 M NaCl, and proteins were separated by affinity chromatography on Matrex gel green A, ammonium sulfate fractionation, and fast protein liquid chromatography on Superose 12. The 43 amino acid N-terminal sequence of the nuclear 20-kdalton protein was identical with the cytosolic protein except it lacked 7 N-terminal amino acids present in the cytosolic form. The DNA sequence of a full-length complementary DNA clone isolated from a ventral prostate gt11 library extended the N-terminal sequence of the cytosolic form by an additional nine amino acids from the predicted initiation methionine. The cDNA included the nucleotide sequence for the 43 amino acid N-terminal sequence of the purified 20-kdalton protein and predicted molecular weights of 16,686, 17,521, and 18,650, respectively, for the nuclear, cytoplasmic, and nonprocessed proteins. Northern blot analyses of reproductive tract tissue RNAs using the 20-kdalton protein cDNA as probe revealed a single mRNA species of 0.92 kb detectable only in extracts of rat ventral prostate. Expression of the 0.92-kb mRNA was androgen dependent since the mRNA was undetectable in extracts obtained 4 days after castration and was restored 16 h after restimulation with androgen.
Discovery of Potent, Selective Triazolothiadiazole-Containing c-Met Inhibitors (2021)

Herein, we report a novel series of highly potent and selective triazolothiadiazole c-Met inhibitors. Starting with molecule <b>5</b>, we have applied structure-based drug design principles to identify the triazolothiadiazole ring system. We successfully replaced the metabolically unstable phenolic moiety with a quinoline group. Further optimization around the 5,6 bicyclic moiety led to the identification of <b>21</b>. Compound <b>21</b> suffered from PDE3 selectivity issues and subsequent, structurally informed design led to the discovery of compound <b>23</b>. Compound <b>23</b> has exquisite kinase selectivity, excellent potency, favorable ADME profile, and showed dose-dependent antitumor efficacy in a SNU-5 gastric cancer xenograft model.
Semi-Supervised Normalized Cuts for Image Segmentation (2015)

Since its introduction as a powerful graph-based method for image segmentation, the Normalized Cuts (NCuts) algorithm has been generalized to incorporate expert knowledge about how certain pixels or regions should be grouped, or how the resulting segmentation should be biased to be correlated with priors. Previous approaches incorporate hard must-link constraints on how certain pixels should be grouped as well as hard cannot-link constraints on how other pixels should be separated into different groups. In this paper, we reformulate NCuts to allow both sets of constraints to be handled in a soft manner, enabling the user to tune the degree to which the constraints are satisfied. An approximate spectral solution to the reformulated problem exists without requiring explicit construction of a large, dense matrix, hence, computation time is comparable to that of unconstrained NCuts. Using synthetic data and real imagery, we show that soft handling of constraints yields better results than unconstrained NCuts and enables more robust clustering and segmentation than is possible when the constraints are strictly enforced.
[PP.22.07] RELATIONSHIPS OF SYMMETRICAL AND ASYMMETRICAL AMBULATORY ARTERIAL STIFFNESS INDEX (AASI) WITH PRECLINICAL RENAL DAMAGE IN UNTREATED HYPERTENSIVE PATIENTS (2016)

Objective: The ambulatory arterial stiffness index (AASI), derived from the 24-h diastolic vs systolic blood pressure (BP) regression line, has been proposed as a surrogate measure of arterial stiffness and has been shown to predict stroke in some studies and meta-analyses. An association between AASI and early signs of renal damage has been described. It has been suggested that Symmetric AASI (symAASI) may provide a better clinical approach to evaluate arterial stiffness than the previously proposed asimmetrical AASI (aAASI) The aim of our study was to evaluate the relationships of aAASI and symAASI with preclinical markers of renal damage in hypertensive patients without severe renal dysfunction. Design and method: A total of 226 subjects (mean age 47 ± 14 years, men 54%) with never treated arterial hypertension were enrolled. Urinary albumin excretion rate (AER) and creatinine clearance (CrCl) were measured by 24-h urine collection, Glomerular filtration rate (eGFR) was estimated using CKD-EPI equation (CKD-EPI eGFR) and CrCl corrected for body surface area (BSA). The ambulatory BP was measured for 24-h by the Spacelab 90207 devices. Results: Statistical univariate analyses disclosed significant correlations of symAASI with Log (AER) (r = 0.16; p = 0.017), with CKD-EPI eGFR (r = −0.30; p < 0.0001) and with CrCl/BSA (see figure),while aAASI showed an inverse relationship only with CKD-EPI eGFR (r = − 0.16; p = 0.017). SymAASI (p = 0.005) and aAASI (p = 0.026) were significantly higher in patients with CKD-EPI eGFR < 90 ml/min71.73 m2 than in those with greater values of eGFR. In two multiple regression models in which aAASI and symAASI were regarded separately as outcome variables only symAASI showed an association with Log (AER) (beta: 0.14; p < 0.05) and with CKD-EPI eGFR (beta: −0.14; p < 0.05), independently of various confounding factors. When in this model CKD-EPI eGFR was replaced by CrCl/BSA this latter maintained its negative association with symAASI (beta = −0.21; p = 0.001). Conclusions: Our results seem to suggest that in patients with untreated arterial hypertension symAASI correlate better with preclinical markers of renal damage than do aAASI.
Decentralizing Computation with Edge Computing (2021)

Edge computing promises to bring computation close to the end-users to support emergent applications such as virtual reality. However, the computational capacity at the edge of the network is currently limited. To become a pervasive paradigm, edge computing needs highly dispersed decentralized deployments, that, contrary to cloud, cannot benefit from economies of scale. In this situation, crowdsourcing appears attractive - there are plenty of computing devices at the disposal of the general public, and these devices are located exactly where computing power is needed the most - at the edge of the network. Crowdsourcing has been a success maker for scientific computing projects, e.g., [email protected], or distributed ledger systems empowering decentralized finance. However, as of now, there is no crowdsourced system that addresses the needs of edge computing. In this position paper, we aim to identify the causes of this shortcoming, analyze the potential ways to overcome it, and outline future directions.
Correlated oxide Dirac semimetal in the extreme quantum limit (2021)

Quantum materials (QMs) with strong correlation and nontrivial topology are indispensable to next-generation information and computing technologies. Exploitation of topological band structure is an ideal starting point to realize correlated topological QMs. Here, we report that strain-induced symmetry modification in correlated oxide SrNbO<sub>3</sub> thin films creates an emerging topological band structure. Dirac electrons in strained SrNbO<sub>3</sub> films reveal ultrahigh mobility (μ<sub>max</sub> ≈ 100,000 cm<sup>2</sup>/Vs), exceptionally small effective mass (<i>m</i>* ~ 0.04<i>m</i><sub>e</sub>), and nonzero Berry phase. Strained SrNbO<sub>3</sub> films reach the extreme quantum limit, exhibiting a sign of fractional occupation of Landau levels and giant mass enhancement. Our results suggest that symmetry-modified SrNbO<sub>3</sub> is a rare example of correlated oxide Dirac semimetals, in which strong correlation of Dirac electrons leads to the realization of a novel correlated topological QM.
Downstream promoter interactions of TFIID TAFs facilitate transcription reinitiation (2017)

TFIID binds promoter DNA to recruit RNA polymerase II and other basal factors for transcription. Although the TATA-binding protein (TBP) subunit of TFIID is necessary and sufficient for in vitro transcription, the TBP-associated factor (TAF) subunits recognize downstream promoter elements, act as coactivators, and interact with nucleosomes. In yeast nuclear extracts, transcription induces stable TAF binding to downstream promoter DNA, promoting subsequent activator-independent transcription reinitiation. In vivo, promoter responses to TAF mutations correlate with the level of downstream, rather than overall, Taf1 cross-linking. We propose a new model in which TAFs function as reinitiation factors, accounting for the differential responses of promoters to various transcription factor mutations.
Demonstration of a common indole-based aromatic core in natural and synthetic eumelanins by solid-state NMR (2014)

Despite the essential functions of melanin pigments in diverse organisms and their roles in inspiring designed nanomaterials for electron transport and drug delivery, the structural frameworks of the natural materials and their biomimetic analogs remain poorly understood. To overcome the investigative challenges posed by these insoluble heterogeneous pigments, we have used l-tyrosine or dopamine enriched with stable (13)C and (15)N isotopes to label eumelanins metabolically in cell-free and Cryptococcus neoformans cell systems and to define their molecular structures and supramolecular architectures. Using high-field two-dimensional solid-state nuclear magnetic resonance (NMR), our study directly evaluates the assumption of structural commonality between synthetic melanin models and the corresponding natural pigments, demonstrating a common indole-based aromatic core in the products from contrasting synthetic protocols for the first time.