gebhart/patrepeval huggingface dataset:
Photo-induced changes in 157-nm optical coatings (2004)

The photo-induced degradation of 157-nm anti-reflective (AR) coatings, and the role of water vapor in the ambient, have been studied with in-situ spectroscopic ellipsometry, atomic force microscopy (AFM), and x-ray photoelectron spectroscopy. Using ellipsometric techniques, we find that MgF<sub>2</sub> thin films develop a surface roughness layer under laser irradiation at an incident dose of ~0.1 MJ/cm<sup>2</sup>. These thin film changes occur well before any changes in 157-nm transmission are observed. The findings are confirmed by ex-situ post-irradiation AFM measurements. LaF<sub>3</sub> does not exhibit this effect. Addition of ppm-levels of moisture suppresses surface roughness formation, suggesting that the surface roughness growth may be a precursor to the transmission degradation of full AR stacks that had been observed earlier.
Cre expression in primary spermatocytes: A tool for genetic engineering of the germ line (1998)

Transgenic mice were generated expressing a testicular Cre recombinase driven by promoter sequences derived from the gene encoding Synaptonemal Complex Protein 1 (Sycp1), expressed at an early stage of the male meiosis (leptotene to zygotene). Recombination at target LoxP sites was examined during germinal differentiation in mice harboring Sycp1-Cre and a second transgene where LoxP sites flank either the βgeo coding region, the Pgk1 promoter, or a tk-neo cassette inserted into the Rxrα locus. The LoxP-flanked transgenes were stably maintained in the somatic tissues of the double transgenic animals, as well as in the progeny of the females. Mice born after mating the double-transgenic males with normal females showed extensive deletions of the LoxP-flanked sequences. When the males were hemizygous for the Sycp1-Cre transgene, the deletions were observed even in the fraction of the offspring which had not inherited the Cre gene, thus demonstrating that expression occurred in the male parent during spermatogenesis. The high efficiency of excision at the LoxP sites makes the Sycp1-Cre transgenic males suitable for evaluating the role of defined gene functions in the germinal differentiation process. Mol. Reprod. Dev. 51:274–280, 1998. © 1998 Wiley-Liss, Inc.
Early bedside detection of ischemia and rejection in liver transplants by microdialysis (2012)

This study was performed to explore whether lactate, pyruvate, glucose, and glycerol levels sampled via microdialysis catheters in the transplanted liver could be used to detect ischemia and/or rejection. The metabolites were measured at the bedside every 1 to 2 hours after the operation for a median of 10 days. Twelve grafts with biopsy-proven rejection and 9 grafts with ischemia were compared to a reference group of 39 grafts with uneventful courses. The median lactate level was significantly higher in both the ischemia group [5.8 mM (interquartile range = 4.0-11.1 mM)] and the rejection group [2.1 mM (interquartile range = 1.9-2.4 mM)] versus the reference group [1.5 mM (interquartile range = 1.1-1.9 mM), P < 0.001 for both]. The median pyruvate level was significantly increased only in the rejection group [185 μM (interquartile range = 155-206 μM)] versus the reference group [124 μM (interquartile range = 102-150 μM), P < 0.001], whereas the median lactate/pyruvate ratio and the median glycerol level were increased only in the ischemia group [66.1 (interquartile range = 23.9-156.7) and 138 μM (interquartile range = 26-260 μM)] versus the reference group [11.8 (interquartile range = 10.6-13.6), P < 0.001, and 9 μM (interquartile range = 9-24 μM), P = 0.002]. Ischemia was detected with 100% sensitivity and greater than 90% specificity when a positive test was repeated after 1 hour. In 3 cases of hepatic artery thrombosis, ischemia was detected despite normal blood lactate levels. Consecutive pathological measurements for 6 hours were used to diagnose rejection with greater than 80% sensitivity and specificity at a median of 4 days before the activity of alanine aminotransferase, the concentration of bilirubin in serum, or both increased. In conclusion, bedside measurements of intrahepatic lactate and pyruvate levels were used to detect ischemia and rejection earlier than current standard methods could. Discrimination from an uneventful patient course was achieved. Consequently, intrahepatic graft monitoring with microdialysis may lead to the earlier initiation of graft-saving treatment.
Topology selection for stream mining systems (2009)

Multi-concept identification in high volume multimedia streams is critical for a number of applications, including large-scale multimedia analysis, processing, and retrieval. Content of interest is filtered using a collection of binary classifiers that are deployed on distributed resource-constrained infrastructure. In this paper, we design distributed algorithms for determining the optimal topology of single concept detectors (classifiers) to identify the multiple concepts of interest. These algorithms dynamically order individual classifiers into chain topologies to tradeoff accuracy against processing delay, based on underlying data characteristics, system resource constraints as well as the performance and complexity characteristics of each classifier
Data from Artificial Intelligence–Assisted Amphiregulin and Epiregulin IHC Predicts Panitumumab Benefit in <i>RAS</i> Wild-Type Metastatic Colorectal Cancer (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;High tumor mRNA levels of the EGFR ligands amphiregulin (AREG) and epiregulin (EREG) are associated with anti-EGFR agent response in metastatic colorectal cancer (mCRC). However, ligand RNA assays have not been adopted into routine practice due to issues with analytic precision and practicality. We investigated whether AREG/EREG IHC could predict benefit from the anti-EGFR agent panitumumab.&lt;/p&gt;Experimental Design:&lt;p&gt;Artificial intelligence algorithms were developed to assess AREG/EREG IHC in 274 patients from the PICCOLO trial of irinotecan with or without panitumumab (Ir vs. IrPan) in &lt;i&gt;RAS&lt;/i&gt; wild-type mCRC. The primary endpoint was progression-free survival (PFS). Secondary endpoints were RECIST response rate (RR) and overall survival (OS). Models were repeated adjusting separately for &lt;i&gt;BRAF&lt;/i&gt; mutation status and primary tumor location (PTL).&lt;/p&gt;Results:&lt;p&gt;High ligand expression was associated with significant PFS benefit from IrPan compared with Ir [8.0 vs. 3.2 months; HR, 0.54; 95% confidence interval (CI), 0.37–0.79; &lt;i&gt;P&lt;/i&gt; = 0.001]; whereas low ligand expression was not (3.4 vs. 4.4 months; HR, 1.05; 95% CI, 0.74–1.49; &lt;i&gt;P&lt;/i&gt; = 0.78). The ligand-treatment interaction was significant (&lt;i&gt;P&lt;/i&gt;&lt;sub&gt;interaction&lt;/sub&gt; = 0.02) and remained significant after adjustment for &lt;i&gt;BRAF&lt;/i&gt;-mutation status and PTL. Likewise, RECIST RR was significantly improved in patients with high ligand expression (IrPan vs. Ir: 48% vs. 6%; &lt;i&gt;P&lt;/i&gt; &lt; 0.0001) but not those with low ligand expression (25% vs. 14%; &lt;i&gt;P&lt;/i&gt; = 0.10; &lt;i&gt;P&lt;/i&gt;&lt;sub&gt;interaction&lt;/sub&gt; = 0.01). The effect on OS was similar but not statistically significant.&lt;/p&gt;Conclusions:&lt;p&gt;AREG/EREG IHC identified patients who benefitted from the addition of panitumumab to irinotecan chemotherapy. IHC is a practicable assay that may be of use in routine practice.&lt;/p&gt;&lt;/div&gt;
Exploration of the potential performance of polycrystalline silicon-based active matrix flat-panel imagers incorporating active pixel sensor architectures (2008)

Conventional active matrix flat-panel imagers (AMFPIs), employing amorphous silicon (a-Si:H) semiconductors, are based on a relatively simple pixel architecture, commonly taking the form of a single, thin-film transistor (TFT) coupled to a pixel storage capacitor. Although this semiconductor-architecture combination has led to the successful creation of x-ray imagers for many applications, a variety of significant performance limitations related to DQE, frame rate and charge trapping have also become apparent. While prospects for designing solutions to these restrictions based on a-Si:H TFTs are uncertain, progress in the development of high-quality polycrystalline silicon (poly-Si) TFTs is opening up new possibilities for large area x-ray imager design. Recently, initial prototype imagers have been developed using poly-Si TFTs in the form of 1-stage and 2-stage pixel amplifiers-ircuit architectures that can generally be referred to as active pixel sensors (APS). The insight gained from empirical evaluations of such prototypes, coupled with theoretical studies, can inspire increasingly sophisticated APS architectures that overcome the limitations, while preserving the advantages, of conventional AMFPIs. In this paper, cascaded systems analysis and circuit simulation are used to explore potential performance improvements enabled by APS architectures based on poly-Si TFTs. These studies suggest that it is possible to achieve significant improvements in DQE at low exposures or very small pixel sizes, higher maximum frame rates, and reduced charge trapping effects through implementation of such architectures.
New Diagnostic Assays for Differential Diagnosis Between the Two Distinct Lineages of Bovine Influenza D Viruses and Human Influenza C Viruses (2020)

Influenza D virus (IDV), a novel orthomyxovirus, is currently emerging in cattle worldwide. It shares >50% sequence similarity with the human influenza C virus (HICV). Two clades of IDV are currently co-circulating in cattle herds in the U.S. New assays specific for each lineage are needed for accurate surveillance. Also, differential diagnosis between zoonotic human influenza C virus and the two clades of IDV are important to assess the zoonotic potential of IDV. We developed an enzyme-linked immunosorbent assay (ELISA) based on two different epitopes HEF and NP and four peptides, and fluorescent focus neutralization assay to differentiate between IDV bovine and swine clades. Calf sera were obtained, and bovine samples underwent surveillance. Our results highlight the importance of position 215 with 212 in determining the heterogeneity between the two lineages. We needed IFA and FFN for tissue culture-based analysis and a BSL2 facility for analyzing virus interactions. Unfortunately, these are not available in many veterinary centers. Hence, our second aim was to develop an iELISA using specific epitopes to detect two lineages of IDVs simultaneously. Epitope-iELISA accurately detects neutralizing and non-neutralizing antibodies against the IDV in non-BSL2 laboratories and veterinary clinics and is cost-effective and sensitive. To differentiate between IDVs and HICVs, whole antigen blocking, polypeptides, and single-peptide ELISAs were developed. A panel of ferret sera against both viruses was used. Results suggested that both IDV and ICV had a common ancestor, and IDV poses a zoonotic risk to individuals with prior or current exposure to cattle. IDV peptides IANAGVK (286-292 aa), KTDSGR (423-428 aa), and RTLTPAT (448-455 aa) could differentiate between the two viruses, whereas peptide AESSVNPGAKPQV (203-215 aa) detected the presence of IDV in human sera but could not deny that it could be ICV, because the only two conserved influenza C peptides shared 52% sequence similarity with IDV and cross-reacted with IDV. However, blocking ELISAs differentiated between the two viruses. Diagnostic tools and assays to differentiate between ICV and IDV are required for serological and epidemiological analysis to clarify the complexity and evolution and eliminate misdiagnosis between ICV and IDV in human samples.
Supplementary Figure S4 from NAP1051, a Lipoxin A4 Biomimetic Analogue, Demonstrates Antitumor Activity Against the Tumor Microenvironment (2023)

&lt;p&gt;Figure S4 shows the gating strategy for analysis of myeloid cell subpopulations in the spleen or tumor.&lt;/p&gt;
THE PRECISE ROLE OF CD28 AND CD154 POSITIVE AND CTLA4 NEGATIVE SIGNALS IN THE ALLOGRAFT RESPONSE. (2000)

Zheng, Xin Xiao; Markees, Thomas A.; Weber, Martina; Li, Xian Chang; Li, Yongsheng; Tian, Yang; Rossini, Aldo A.; Strom, Terry B.
A Pedagogy of Digital Materiality: Integrated Design and Robotic Fabrication Projects of the Master of Advanced Studies in Architecture and Digital Fabrication (2022)

Abstract This paper illustrates the pedagogical approach to teaching computational design and digital fabrication in the Master of Advanced Studies in Architecture and Digital Fabrication. It demonstrates how the introduction of computational design and digital fabrication methods foster a holistic approach to integrate novel material and constructive systems into the design process. Such an integration allows the students to combine digital fabrication techniques with sustainable material processes, taking into account the questions of reversibility, recycling and reuse, and thus designing for a more sustainable construction. In the presented paper, the structure and the curriculum of the MAS programme is introduced and the pedagogical approach of the Integrated Design and Robotic Fabrication Project is demonstrated through four case studies, highlighting their respective teaching strategies in combination with the learning experiences of the students.
Polarization Transfer Solid-State NMR for Studying Surfactant Phase Behavior (2010)

The phase behavior of amphiphiles, e.g., lipids and surfactants, at low water content is of great interest for many technical and pharmaceutical applications. When put in contact with air having a moderate relative humidity, amphiphiles often exhibit coexistence between solid and liquid crystalline phases, making their complete characterization difficult. This study describes a (13)C solid-state NMR technique for the investigation of amphiphile phase behavior in the water-poor regime. While the (13)C chemical shift is an indicator of molecular conformation, the (13)C signal intensities obtained with the CP and INEPT polarization transfer schemes yield information on molecular dynamics. A theoretical analysis incorporating the effect of molecular segment reorientation, with the correlation time τ(c) and order parameter S, shows that INEPT is most efficient for mobile segments with τ(c) < 0.01 μs and S < 0.05, while CP yields maximal signal for rigid segments with τ(c) > 10 μs and/or S > 0.5 under typical solid-state NMR experimental conditions. For liquid crystalline phases, where τ(c) < 0.01 μs and 0 < S < 0.3, the observed CP and INEPT intensities serve as a gauge of S. The combination of information on molecular conformation and dynamics permits facile phase diagram determination for systems with solid crystalline, solid amorphous, anisotropic liquid crystalline, and isotropic liquid (crystalline) phases as demonstrated by experiments on a series of reference systems with known phase structure. Three solid phases (anhydrous crystal, dihydrate, gel), two anisotropic liquid crystalline phases (normal hexagonal, lamellar), and two isotropic liquid crystalline phases (micellar cubic, bicontinuous cubic) are identified in the temperature-composition phase diagram of the cetyltrimethylammonium succinate/water system. Replacing the succinate counterion with DNA prevents the formation of phases other than hexagonal and leads to a general increase of τ(c).
Deep Learning for Classification of Bone Lesions on Routine MRI (2021)

This work was funded by a Radiological Society of North America Research Medical Student Grant (#RMS2013) and supported by the Amazon Web Services Diagnostic Development Initiative.
Evaluation of Resist Capability for EUV Lithography (2006)

This study had three goals. One is an evaluation of the ultimate fine-pitch patterning performance of our high-numerical-aperture (NA = 0.3) small-field exposure system (HINA). Another is development of an EUV flood exposure tool for investigating the development characteristics of EUV resists. The third is an evaluation of the lithographic performance of molecular resists using HINA and the flood exposure tool. An investigation of the ultimate resolution of HINA using coherent illumination (σ = 0.0) revealed that the smallest patterns delineated were dense 27-nm-wide lines in a non-chemically-amplified resist, and the resolution obtained was nearly equal to the resolution limit of HINA for three-ray interference. A polymeric chemically-amplified (CA) resist based on acetal-protected poly(hydroxystyrene) provided the best performance, with 28-nm-wide lines and spaces being delineated at an exposure dose of 10 mJ/cm2. Two CA positive-tone molecular resists were also tested. One is based on a low-molecular-weight amorphous polyphenol, namely 4,4'-methylenebis[2-[di(2,5-dimehtyl-4-hydroxyphenyl)methyl] phenol (25X-MBSA-P), and the other is a cholate derivative, 1,4-bis(methyloxymethylcholate) cyrohexane (C2ChDM). CA polyphenol resist provided a high contrast, a resolution of 30 nm at an exposure dose of 10 mJ/cm2, and a low LER of 6.2 nm (3σ) at an inspection length of 2000 nm. Finally, the CA cholate-derivative resist provided a resolution of 50 nm at an exposure dose of 14 mJ/cm2. Unfortunately, both molecular resists exhibited severe pattern collapse in dense fine-pitch patterns.
Material effect on thermal stress of annular-trench-isolated through silicon via (TSV) (2020)

Abstract The material effect on the thermal stress of annular-trench-isolated (ATI) through silicon via (TSV) was investigated. The ATI TSV with two sets of materials as the Cu core with the BCB insulator and solder core with parylene-HT insulator were successfully fabricated. A lower stress level was observed for the ATI TSV with a solder core and parylene-HT insulator in experiments and finite element method (FEM) simulation. In order to reveal the origin of the lower stress, the ATI TSVs with different core materials were simulated. The Si ring with high Young’s modulus and low CTE value blocked the effect of the different core material of ATI TSV inside the Si ring and maintained the stress in the Si substrate at the same level. The origin of the lower stress level in the Si substrate was determined to be the lower Young’s modulus and CTE of insulator Parylene-HT than BCB. Due to the surrounding structure of the Si ring, the effect of different core material on thermal stress in the Si substrate became weak. The discussion of the material effect on the thermal stress of ATI TSV provided further understanding of the structure with the Si ring.
Supplemental Figures 1-7 from Bacterial SOS Genes <i>mucAB/umuDC</i> Promote Mouse Tumors by Activating Oncogenes <i>Nedd9/Aurkb</i> via a miR-145 Sponge (2023)

&lt;p&gt;Supplementary Fig. S1. Nedd9 and Aurkb seed match sequences in mucAB and umuDC.&lt;/p&gt;&lt;p&gt;Supplementary Fig. S2. Selection of cells expressing Tet-repressor protein.&lt;/p&gt;&lt;p&gt;Supplementary Fig. S3. Microarray analysis of deregulated oncogenes.&lt;/p&gt;&lt;p&gt;Supplementary Fig. S4. Suppression of cellular transformation with anti-mucAB shRNA.&lt;/p&gt;&lt;p&gt;Supplementary Fig. S5. Confirmation of interaction of miR-145 with anti-miR-145.&lt;/p&gt;&lt;p&gt;Supplementary Fig. S6. Microcolony formation over time.&lt;/p&gt;&lt;p&gt;Supplementary Fig. S7. Comparison of tumor incidence rates between males and females, and between presence and absence of Zn.&lt;/p&gt;
Thermal sensitivity of an rf SQUID (1985)

A well known limitation to the resolution of practical SQUID systems is set by the sensitivity of the SQUID output to temperature fluctuations. This is particularly serious in non-stationary systems where agitation of the helium bath inevitably results in temperature fluctuations of the SQUID. We have undertaken to characterize the thermal response of commercial RF SQUIDS and tried to understand the causes of this sensitivity. The measurements are done with the SQUID package mounted in a thermally isolated can with He exchange gas. The input coil is open-circuited, and the SQUID unit is placed inside a Nb shield, resulting in negligible sensitivity to external fields. The ambient magnetic field is reduced to less than 10/sup -2/ G with mu-metal shields. Our measurement procedure is to slowly cool the SQUID and Nb shield through their superconducting transition temperature in the presence of various externally applied magnetic fields, then observe the temperature dependence of the SQUID output ..delta.. /phi/ from 2K to the highest temperature at which it will operate. It is of course necessary to readjust the RF drive level to its optimum level at each temperature since the critical current of the weak link in the SQUID has a strongmore » temperature dependence. We find that near the optimum setting the SQUID output depends only weakly on RF level, so this is not a crucial adjustment.« less
Enzymatic Activation of Peptide Prodrugs by Prostate-Specific Membrane Antigen (PSMA) as Targeted Therapy for Prostate Cancer (2003)

Abstract : The majority of our present chemotherapeutic agents only kill cells effectively when they are proliferating; this may explain why these agents have been of such limited success in patients. In contrast to these ineffective agents, we have chemically modified a plant toxin, Thapsigargin (TG), to produce primary amine-containing analogs that are potent, cell proliferation independent, inducers of apoptosis in prostate cancer cells, These TG-analogs, however, are not prostate cancer-specific cytotoxins. The hypothesis is that a potent TG analog can be converted to an inactive prodrug by coupling to a peptide carrier that is a substrate for Prostate Specific Membrane Antigen (PSMA). Since PSMA is expressed in high levels only by prostate cancer cells and not by normal cells, this should allow specific targeting of the TG-analog's killing ability to prostate cancer cells thus minimizing toxicity to normal tissue. Two enzymatic activities for PSMA have been described: an N-acetyl-alpha linked acid dipeptidase (NAALADase) activity and a pteroyl poly-y-glutamyl carboxypeptidase (folate hydrolase) activity. On the basis of preliminary data, the ideal TG prodrug should consist of either an aspartate or glutamate containing TO analog coupled via to a peptide containing a series of alpha- and gamma-linked glutamates and ending in an alpha-linked aspartyl-glutamate cap. This substrate would be readily cleaved by PSMA but would be stable to hydrolysis by proteases such as gamma-glutamyl hydrolase present in serum and extracellular fluid of some normal tissue types.
diaphanous is required for cytokinesis in Drosophila and shares domains of similarity with the products of the limb deformity gene (1994)

We show that the Drosophila gene diaphanous is required for cytokinesis. Males homozygous for the dia1 mutation are sterile due to a defect in cytokinesis in the germline. Females trans-heterozygous for dia1 and a deficiency are sterile and lay eggs with defective eggshells; failure of cytokinesis is observed in the follicle cell layer. Null alleles are lethal. Death occurs at the onset of pupation due to the absence of imaginal discs. Mitotic figures in larval neuroblasts were found to be polyploid, apparently due to a defect in cytokinesis. The predicted 123 x 10(3) M(r) protein contains two domains shared by the formin proteins, encoded by the limb deformity gene in the mouse. These formin homology domains, which we have termed FH1 and FH2, are also found in Bni1p, the product of a Saccharomyces cerevisiae gene required for normal cytokinesis in diploid yeast cells.