gebhart/patrepeval huggingface dataset:
A 157-nm immersion microstepper (2005)

We have designed and constructed a microstepper for 157 nm immersion lithography. The lens, designed and fabricated at Newport, provides a numerical aperture of 1.3 and a field size of 60 &mu;m with immersion liquids of index n=1.38. Because of a lack of system interferometer, final alignment has been ongoing in the field using actuators incorporated into the lens design. Lithography down to 250 nm has been demonstrated but lens alignment has proved difficult. We are currently implementing an image monitoring system to provide real-time feedback on lens performance and to allow expedited alignment.
Ad-versarial: Defeating Perceptual Ad-Blocking (2018)

Perceptual ad-blocking is a novel approach that detects online advertisements based on their visual content. Compared to traditional filter lists, the use of perceptual signals is believed to be less prone to an arms race with web publishers and ad networks. We demonstrate that this may not be the case. We describe attacks on multiple perceptual ad-blocking techniques, and unveil a new arms race that likely disfavors ad-blockers. Unexpectedly, perceptual ad-blocking can also introduce new vulnerabilities that let an attacker bypass web security boundaries and mount DDoS attacks. We first analyze the design space of perceptual ad-blockers and present a unified architecture that incorporates prior academic and commercial work. We then explore a variety of attacks on the ad-blocker's detection pipeline, that enable publishers or ad networks to evade or detect ad-blocking, and at times even abuse its high privilege level to bypass web security boundaries. On one hand, we show that perceptual ad-blocking must visually classify rendered web content to escape an arms race centered on obfuscation of page markup. On the other, we present a concrete set of attacks on visual ad-blockers by constructing adversarial examples in a real web page context. For seven ad-detectors, we create perturbed ads, ad-disclosure logos, and native web content that misleads perceptual ad-blocking with 100% success rates. In one of our attacks, we demonstrate how a malicious user can upload adversarial content, such as a perturbed image in a Facebook post, that fools the ad-blocker into removing another users' non-ad content. Moving beyond the Web and visual domain, we also build adversarial examples for AdblockRadio, an open source radio client that uses machine learning to detects ads in raw audio streams.
Pulsed fiber lasers with over 12-kW peak power, bandwidth-limited spectrum, and M2 <1.1 beam for the 1064nm and 1550nm wavelength ranges (2005)

We have developed all fiber format pulsed lasers with bandwidth-limited emission and over 12kW peak power for the 1064nm and 1550nm wavelength ranges. The master oscillator followed by power fiber amplifier configurations were employed with operational frequencies from 100kHz to over 2MHz range and 2ns pulse duration. The pulse duration remains the same for all repetition rates. The designs of the low NA core fibers deployed ensure stable single spatial mode emission with 12&mu;m and 14&mu;m mode field diameter (MFD) for 1064nm and 1550nm correspondingly. The output emission bandwidth was below 0.1nm and pulse-to-pulse energy stability better than 1% were measured for all operational frequencies and output powers. Single mode fiber design of the fiber amplifiers ensured diffraction-limited output beam quality with M<sup>2</sup> less than 1.1. New lasers can be used for nonlinear frequency conversion to generate emission in the visible and UV parts of optical spectrum as well as in other applications.
Suppression of Raman scattering by controlling the angular momentum content of fiber modes (2020)

We demonstrate, for the first time, that Raman scattering can be suppressed, by as much as ~17 dB, just by controlling the angular momentum content of fiber modes, of identical mode area.
The relationship of potential G-quadruplex sequences in cis-upstream regions of the human genome to SP1-binding elements (2008)

We have carried out a survey of potential quadruplex structure sequences (PQSS), which occur in the immediate upstream region (500 bp) of human genes. By examining the number and distribution of these we have established that there is a clear link between them and the occurrence of the SP1-binding element 'GGGCGG', such that a large number of upstream PQSS incorporate the SP1-binding element.
Natural heteroclitic-like peptides are generated by SARS-CoV-2 mutations (2022)

ABSTRACT Mutations carried by SARS-CoV-2 spike protein variants may promote viral escape from immune protection. Humoral immunity is sensitive to evasion by SARS-CoV-2 mutants, but the impact of viral evolution on the interplay between virus and host CD8 T cell reactivity remains uncertain. By a systematic functional analysis of 30 spike variant mutations, we show that in vaccinated as well as convalescent subjects, mutated epitopes can have not only a neutral or abrogating effect on the recognition by CD8 T cells but can also enhance or even generate de novo CD8 T cell responses. Large pools of peptides spanning the entire spike sequence and comprising previously identified CD8 T cell epitopes were then used in parallel with variant peptides to define strength and multispecificity of total anti-spike CD8 responses. In some individuals, CD8 cells were narrowly focused on a few epitopes indicating that in this context of weak and oligospecific responses the overall antiviral protection can likely benefit of the function enhancing effect of heteroclitic-like mutations. In conclusion, appearance of mutated stimulatory epitopes likely reflects an epiphenomenon of SARS-CoV-2 evolution driven by antibody evasion and increased transmissibility, that might bear clinical relevance in a subset of individuals with weak and oligospecific CD8 T cell responses.
Estimation du potentiel infectieux en fonction du temps de porcs infectés par le virus du Syndrome Dysgénésique et Respiratoire Porcin (SDRP) : Corrélation avec les charges génomiques virales dans le sang, dans le mucus nasal et la réponse immunitaire humorale (2012)

National audience
Redox Control of Conformation and Luminescence of a Dinuclear Ruthenium(II) Complex with a Bis-dipyridophenazine Bridging Ligand (2002)

This spectroelectrochemical study deals with an interesting luminescent dinuclear complex [{Ru(bpy)2}2(µ-bdppz)]4+ (14+), where bpy stands for 2,2′-bipyridine and bdppz for 1,1′-dipyrido[3,2-a:2′,3′-c]phenazin-1,1′-yldipyrido[3,2-a:2′,3′- c]phenazine. The electronic coupling between the phenazine moieties through the central C−C bond can be easily modified as a function of the ligand oxidation state. Upon stepwise one-electron reduction in acetonitrile, complex 14+ is reversibly transformed into 13+ and 12+, with consequent major structural and electronic changes of the bridging ligand and with quenched MLCT emission of the excited Ru(bpy)2 moieties.
Intrinsic Depth: Improving Depth Transfer with Intrinsic Images (2015)

We formulate the estimation of dense depth maps from video sequences as a problem of intrinsic image estimation. Our approach synergistically integrates the estimation of multiple intrinsic images including depth, albedo, shading, optical flow, and surface contours. We build upon an example-based framework for depth estimation that uses label transfer from a database of RGB and depth pairs. We combine this with a method that extracts consistent albedo and shading from video. In contrast to raw RGB values, albedo and shading provide a richer, more physical, foundation for depth transfer. Additionally we train a new contour detector to predict surface boundaries from albedo, shading, and pixel values and use this to improve the estimation of depth boundaries. We also integrate sparse structure from motion with our method to improve the metric accuracy of the estimated depth maps. We evaluate our Intrinsic Depth method quantitatively by estimating depth from videos in the NYU RGB-D and SUN3D datasets. We find that combining the estimation of multiple intrinsic images improves depth estimation relative to the baseline method.
Using DNS-based Authentication of Named Entities (DANE) to validate TLS certificates for the Session Traversal Utilities for NAT (STUN) protocol (2015)

This document defines how DNS-based Authentication of Named Entities
(DANE) can be used to validate TLS certificates with the Session
Traversal Utilities for NAT (STUN) protocol.
Low-Noise Detection System using an InGaAs PIN Photodiode with a Charge Integrating Amplifier (1993)

We developed a low noise detection system using an InGaAs-PIN photodiode for near infrared spectroscopic measurement. Since no practical photomultipliers are available in near infrared region, a Ge PIN photodiode cooled at 77K with a transimpedance (TIA) circuit and lock-in amplifier is usually used. InGaAs PIN photodiodes are more suitable than Ge PIN photodiodes for detecting low level light in the view of dark current and quantum efficiency. The detection system consists of an InGaAs PIN photodiode with a charge integrating amplifier operated at 77K. The minimum detectable power of 10-16 W was achieved at the wavelength of 1.28μm. The integration time was 10s.The system performance was tested by the measurement of the spectrum of singlet oxygen.
Identification of a gene cluster for biosynthesis of the sesquiterpene antibiotic, heptelidic acid, in Aspergillus oryzae (2018)

Heptelidic acid (HA), a sesquiterpene lactone, is a known inhibitor of glyceraldehyde-3-phosphate dehydrogenase (GAPDH). Recently, we found that HA was produced by <i>Aspergillus oryzae</i> RIB40 and acted as the growth inhibitor of the salt-tolerant lactic acid bacteria in soy sauce brewing. Although several decades have passed since the discovery of HA, the genes involved in its biosynthesis and biosynthetic pathway have not yet been fully identified. In this study, we identified the HA biosynthetic gene cluster (HA cluster) using gene disruption and expression analysis. We also revealed that two transcription regulatory genes adjacent to the HA cluster were responsible for the expression of HA biosynthetic genes in <i>A. oryzae</i>. Interestingly, the HA cluster contained a gene encoding GAPDH (<i>gpdB</i>), which showed much higher resistance to HA than the GAPDH gene (<i>gpdA</i>) located at the other locus, but which did not seem to act as a self-resistant gene.
Biochemical analysis of acute and chronic wound environments (1996)

The process of wound healing involves a complex interaction between numerous cell types, extracellular matrix molecules, and soluble mediators including growth factors and cytokines. This complex milieu is under active investigation for the purposes of beginning to understand how this environment regulates tissue repair. Quantitation of growth factors, cytokines, and matrix metalloproteinases within surgical wound fluids may help to elucidate this regulatory network, not only in noncomplicated wound healing but also in pathologic lesions such as chronic ulcers.
Deployment and implementation strategies for massive MIMO in 5G (2014)

Massive MIMO has emerged as one technology enabler for the next generation mobile communications 5G. The gains promised by massive MIMO are augured to overcome the capacity crunch in today's mobile networks and to pave the way for the ambitious targets of 5G. The challenge to realize massive MIMO for 5G is a successful and cost-efficient integration in the overall network concept. This work highlights deployment and implementation strategies for massive MIMO in the context of 5G indoor small cell scenarios. Different massive MIMO deployment scenarios are analyzed for a standard 3GPP indoor office scenario. In particular stand-alone MIMO at a single location, distributed MIMO without cooperation and network MIMO with full cooperation are investigated for varying array configurations. For the performance analysis of the different MIMO configurations the ratio of total transmit antennas to spatial streams is varied stepwise from equality to a factor of ten. For implementation of massive MIMO in 5G networks trends in beamforming techniques, mutually coupled subarrays, over the calibration procedure and estimated ADC performance in 2020 time-frame are discussed. Based on the debate the paper indicates how to integrate large-scale arrays in future 5G networks.
Transcriptional profiling of Ivermectin resistant Cooperia punctata using deep sequencing. (2014)

Intestinal parasites pose a burden to the livestock industry throughout the world. Since the discovery of macrocyclic lactones, Ivermectin has been a popular choice to combat nematode (roundworm) infectious due to its broad spectrum of action and high efficacy. Widespread use of this drug has led to the development of resistance in many parasitic nematodes, including the highly prevalent cattle intestinal parasite <em>Cooperia punctata</em>. Ivermectin is known to bind and activate glutamate-gated chloride channels, thereby disrupting neurotransmission and paralyzing the worms. We hypothesize that Ivermectin treatment of drug-resistant <em>C. punctata</em> will lead to changes in the expression pattern of genes related to the drugs mode of action. We used high throughput sequencing to study the adult transcriptome of drugresistant <em>C. punctata</em> and to assess Ivermectin’s impact on gene expression. RNAseq datasets from treated and untreated Ivermectin resistant adult worms were assembled into 110,772 unique transcripts corresponding to 66,788 genetic loci. 18,585 loci showed evidence of alternative splicing, with an average of 4 transcripts per alternatively spliced locus. Fragmentation rate was estimated at 18.1% by comparison with <em>C. elegans</em> CDSs. 101,411 CDSs, representing some 69% of the complete <em>C. punctata</em> gene repertoire, were predicted from our dataset. The predicted CDSs are associated with 4,738 unique InterPro protein domains, 3,013 unique Kyoto Encyclopedia of Gene and Genomes (KEGG) terms, and 524 unique Gene Ontology (GO) terms. 5,308 predicted CDSs were up-regulated in Ivermectin treated worms while 4,047 were down-regulated. Thirteen GO terms were statistically over-represented among up-regulated CDSs, including gated channels and metabolism. This suggests that functions related to Ivermectin’s mode of action are up-regulated in response to treatment. These results provide insights into potential mechanisms of Ivermectin resistance and possible genetic markers that may be used to monitor the spread of resistant <em>C. punctata</em> in cattle and prevent treatment failures.
[Idiopathic spontaneous pneumomediastinum: a not to be mistaken diagnosis in chest pain]. (1995)

We report two cases of mediastinal emphysema occurring without etiologic factor. Chest pain and subcutaneous emphysema are the most prevalent symptoms. In the absence of oesophagus related symptoms, a single chest radiograph is usually sufficient to make the diagnosis. In this paper, we recall the main radiographic signs, physio-pathological mechanisms, and differential diagnosis of spontaneous pneumomediastinum.
Definition of the zebrafish genome using flow cytometry and cytogenetic mapping (2007)

The chromosomal mapping of the 575 large-insert DNA clones allows for these clones to be integrated into existing zebrafish mapping data. An accurately annotated zebrafish reference genome serves as a valuable resource for investigating the molecular basis of human diseases using zebrafish mutant models.
Supervised learning based model for predicting variability-induced timing errors (2015)

Circuit designers typically combat variations in hardware and workload by increasing conservative guardbanding that leads to operational inefficiency. Reducing this excessive guardband is highly desirable, but causes timing errors in synchronous circuits. We propose a methodology for supervised learning based models to predict timing errors at bit-level. We show that a logistic regression based model can effectively predict timing errors, for a given amount of guardband reduction. The proposed methodology enables a model-based rule method to reduce guardband subject to a required bit-level reliability specification. For predicting timing errors at bit-level, the proposed model generation automatically uses a binary classifier per output bit that captures the circuit path sensitization. We train and test our model on gate-level simulations with timing error information extracted from an ASIC flow that considers physical details of placed-and-routed single-precision pipelined floating-point units (FPUs) in 45nm TSMC technology. We further assess the robustness of our modeling methodology by considering various operating voltage and temperature corners. Our model predicts timing errors with an average accuracy of 95% for unseen input workload. This accuracy can be used to achieve a 0%-15% guardband reduction for FPUs, while satisfying the reliability specification for four error-tolerant applications.
Fatty acid oxidation and the regulation of malonyl-CoA in human muscle. (2000)

Questions concerning whether malonyl-CoA is regulated in human muscle and whether malonyl-CoA modulates fatty acid oxidation are still unanswered. To address these questions, whole-body fatty acid oxidation and the concentration of malonyl-CoA, citrate, and malate were determined in the vastus lateralis muscle of 16 healthy nonobese Swedish men during a sequential euglycemic-hyperinsulinemic clamp. Insulin was infused at rates of 0.25 and 1.0 mU x kg(-1) x min(-1), and glucose was infused at rates of 2.0 +/- 0.2 and 8.1 +/- 0.7 mg x kg(-1) x min(-1), respectively. During the low-dose insulin infusion, whole-body fatty acid oxidation, as determined by indirect calorimetry, decreased by 22% from a basal rate of 0.94 +/- 0.06 to 0.74 +/- 0.07 mg x kg(-1) x min(-1) (P = 0.005), but no increase in malonyl-CoA was observed. In contrast, during the high-dose insulin infusion, malonyl-CoA increased from 0.20 +/- 0.01 to 0.24 +/- 0.01 nmol/g (P < 0.001), and whole-body fatty acid oxidation decreased by an additional 41% to 0.44 +/- 0.06 mg x kg(-1) x min(-1) (P < 0.001). The increase in malonyl-CoA was associated with 30-50% increases in the concentrations of citrate (102 +/- 6 vs. 137 +/- 7 nmol/g, P < 0.001), an allosteric activator of the rate-limiting enzyme in the malonyl-CoA formation, acetyl-CoA carboxylase, and malate (80 +/- 6 vs. 126 +/- 9 nmol/g, P = 0.002), an antiporter for citrate efflux from the mitochondria. Significant correlations were observed between the concentration of malonyl-CoA and both glucose utilization (r = 0.53, P = 0.002) and the sum of the concentrations of citrate and malate (r = 0.52, P < 0.001), a proposed index of the cytosolic concentration of citrate. In addition, an inverse correlation between malonyl-CoA concentration and fatty acid oxidation was observed (r = -0.32, P = 0.03). The results indicate that an infusion of insulin and glucose at a high rate leads to increases in the concentration of malonyl-CoA in skeletal muscle and to decreases in whole-body and, presumably, muscle fatty acid oxidation. Furthermore, they suggest that the increase in malonyl-CoA in this situation is due, at least in part, to an increase in the cytosolic concentration of citrate. Because cytosolic citrate is also an inhibitor of phosphofructokinase, an attractive hypothesis is that changes in its concentration are part of an autoregulatory mechanism by which glucose modulates its own use and the use of fatty acids as fuels for skeletal muscle.
Dynamic weaving for aspect-oriented programming (2002)

When using Aspect Oriented Programming in the development of software components, a developer must understand the program units actually changed by weaving, how they behave, and possibly correct the aspects used. Support for rapid AOP prototyping and debugging is therefore crucial in such situations. Rapid prototyping is difficult with current aspect weaving tools because they do not support dynamic changes. This paper describes PROSE (PROgrammable extenSions of sErvices), a platform based on Java which addresses dynamic AOP. Aspects are expressed in the same source language as the application (Java), and PROSE allows aspects to be woven, unwoven, or replaced at run-time.
Abstract LB-303: Anti-IGF1R therapy with dalotuzumab is efficacious in pre-clinical models of erlotinib refractory NSCLC (2010)

Abstract Epidermal growth factor receptor (EGFR) is expressed in a majority of non-small cell lung carcinomas (NSCLC) and it has been an attractive target for the development of therapeutic agents. The small-molecule EGFR tyrosine kinase inhibitors (TKI), including gefitinib and erlotinib, are currently used in the treatment of late stage NSCLC. Activating mutations in the oncogene KRAS has been associated with resistance to EGFR targeted therapy. Cross-talk between EGFR and insulin like growth factor receptor (IGF1R) has been reported. MK-0646 (dalotuzumab), a monoclonal antibody targeting IGF1R is currently being developed for the treatment of various cancers. Pre-clinical studies suggest that response to EGFR inhibitors can be substantially increased by combining with an IGF1R inhibitor such as MK-0646, a hypothesis currently being tested in clinical studies. In this study, sensitivity to MK-0646 or erlotinib or their combination was compared in a panel of NSCLC cell lines harboring wild type or activating mutations in KRAS. Erlotinib sensitivity was observed in 3/26 (12%) cell lines, all of which harbored wild type KRAS. In contrast, MK-0646 sensitivity was observed in 4/26 (15%), two of which harbor activating mutations in RAS. Sensitivity to erlotinib/MK-0646 combination was observed in 11/26 (42%) cell lines. Activating mutations in KRAS did not confer resistance to MK-0646 treatment. To identify predictive biomarkers that would enrich responders to MK-0646 therapy, gene expression profiling and reverse phase protein array were performed in this panel of NSCLC cell lines. Analysis of reverse-phase protein arrays identified IGF1R levels as a predictive marker of response to MK-0646. In contrast, ERBB3 levels and a gene signature of epithelial mesenchymal transition (EMT) were predictive of sensitivity to erlotinib, but not response to MK-0646. Sensitivity to MK-0646 was observed in primary human tumors propagated in mice or cell line xenografts harboring activating mutations in KRAS. The activity of MK-0646 in KRAS mutant NSCLC models is associated with inhibition of the PI3K pathway and subsequent down-regulation of the “Growth factor associated gene-expression signature” (GFS). The parallel RAS-MAPK pathway was not significantly modulated by MK-0646 treatment. The results suggest that patients with high levels of IGF1R expression, independent of KRAS status, will benefit from MK-0646 therapy. Growing number of studies suggest that EGFR inhibitors is not efficacious in patients harboring tumors with activating mutations in KRAS. MK-0646 therapy may overcome this resistance. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr LB-303.
The role of the sonic hedgehog signalling pathway in patients with midline defects and congenital hypopituitarism (2014)

Our data suggest that mutations in SHH, GAS1 and SBE2 are not associated with hypopituitarism, although GLI2 is an important candidate for CH.
LOCOS process-induced stress effect on CMOS SOI characteristics (2002)

Process-induced stress effects on LOCOS SOI devices are reported. We show that as the field oxide thickness increases, degradation (enhancement) of NMOS (PMOS) I-V characteristics becomes increasingly pronounced. In addition, the linear relationship of transconductance vs. device width, typically seen in the bulk devices, becomes nonlinear. We attribute both phenomena to the LOCOS-induced stress effects on the SOI film.