gebhart/patrepeval huggingface dataset:
Transcriptional Regulation of Endothelial Cell Tissue Factor Expression during Rickettsia rickettsii Infection: Involvement of the Transcription Factor NF-κB (1998)

The vascular endothelial cell (EC) is a primary target of infection with Rickettsia rickettsii, the etiologic agent of Rocky Mountain spotted fever. Changes in gene transcription elicited by intracellular infection, including EC expression of the coagulation pathway initiator known as tissue factor (TF), may contribute to the vascular pathology observed during disease. Nuclear run-on analysis of uninfected and infected, cultured human endothelial cells revealed that the rate of TF mRNA transcription is enhanced more than twofold at 3 h following infection, thus coinciding with increased steady-state levels of TF mRNA. TF mRNA remained relatively unstable during infection, with a half-life of 1.6 h. The eukaryotic protein synthesis inhibitor cycloheximide did not block R. rickettsii-induced increase in TF mRNA levels and actually resulted in its superinduction, thus revealing that de novo synthesis of host cell protein was not prerequisite to this transcriptional response. Involvement of the transcription factor NF-kappaB in R. rickettsii-induced TF expression was demonstrated by using two unrelated inhibitors of NF-kappaB activation. The antioxidant pyrrolidinedithiocarbamate and the proteasome inhibitor N-tosyl-L-phenylalanine chloromethyl ketone blocked expression of TF mRNA and activity during infection. This study demonstrates that R. rickettsii infection results in transcriptional activation of the TF gene and that this response involves activation of the transcription factor NF-kappaB.
Effect of Neuraminidase Inhibitor–Resistant Mutations on Pathogenicity of Clade 2.2 A/Turkey/15/06 (H5N1) Influenza Virus in Ferrets (2010)

The acquisition of neuraminidase (NA) inhibitor resistance by H5N1 influenza viruses has serious clinical implications, as this class of drugs can be an essential component of pandemic control measures. The continuous evolution of the highly pathogenic H5N1 influenza viruses results in the emergence of natural NA gene variations whose impact on viral fitness and NA inhibitor susceptibility are poorly defined. We generated seven genetically stable recombinant clade 2.2 A/Turkey/15/06-like (H5N1) influenza viruses carrying NA mutations located either in the framework residues (E119A, H274Y, N294S) or in close proximity to the NA enzyme active site (V116A, I117V, K150N, Y252H). NA enzyme inhibition assays showed that NA mutations at positions 116, 117, 274, and 294 reduced susceptibility to oseltamivir carboxylate (IC(50)s increased 5- to 940-fold). Importantly, the E119A NA mutation (previously reported to confer resistance in the N2 NA subtype) was stable in the clade 2.2 H5N1 virus background and induced cross-resistance to oseltamivir carboxylate and zanamivir. We demonstrated that Y252H NA mutation contributed for decreased susceptibility of clade 2.2 H5N1 viruses to oseltamivir carboxylate as compared to clade 1 viruses. The enzyme kinetic parameters (V(max), K(m) and K(i)) of the avian-like N1 NA glycoproteins were highly consistent with their IC(50) values. None of the recombinant H5N1 viruses had attenuated virulence in ferrets inoculated with 10(6) EID(50) dose. Most infected ferrets showed mild clinical disease signs that differed in duration. However, H5N1 viruses carrying the E119A or the N294S NA mutation were lethal to 1 of 3 inoculated animals and were associated with significantly higher virus titers (P<0.01) and inflammation in the lungs compared to the wild-type virus. Our results suggest that highly pathogenic H5N1 variants carrying mutations within the NA active site that decrease susceptibility to NA inhibitors may possess increased virulence in mammalian hosts compared to drug-sensitive viruses. There is a need for novel anti-influenza drugs that target different virus/host factors and can limit the emergence of resistance.
Femtosecond Laser-Nanostructured Substrates for Surface-Enhanced Raman Scattering (2009)

We present a new type of surface-enhanced Raman scattering (SERS) substrate that exhibits extremely large and uniform cross-section enhancements over a macroscopic (greater than 25 mm2) area. The substrates are fabricated using a femtosecond laser nanostructuring process, followed by thermal deposition of silver. SERS signals from adsorbed molecules show a spatially uniform enhancement factor of approximately 107. Spectroscopic characterization of these substrates suggests their potential for use in few or single-molecule Raman spectroscopy.
Emerging molecular biology of pancreatic cancer. (2008)

Pancreatic cancer, like most other cancers, is fundamentally caused by mutations in specific genes. Many of the genes targeted in pancreatic cancer have been identified in the past decade, and an understanding of these genes and their function has helped identify familial forms of pancreatic cancer, define the precursor lesions from which invasive pancreatic cancers arise, and will soon lead to gene-specific therapies for this disease. This article reviews the tumor-suppressor genes, oncogenes, and DNA repair genes targeted in pancreatic cancer, and presents clinical applications based on our understanding of the genetic basis of pancreatic cancer.
Supplementary File 1 from Genome-Wide Functional Synergy between Amplified and Mutated Genes in Human Breast Cancer (2023)

Supplementary File 1 from Genome-Wide Functional Synergy between Amplified and Mutated Genes in Human Breast Cancer
Excursion Prevention Strategy to Increase Chip Performance by Photomask Tuning (2020)

Advanced process control in lithography and overall patterning is of tremendous importance for advanced semiconductor Fabs to ensure chip performance and yield. The final patterning result and thus yield depend on many process parameters such as lithography processes, exposure tool performance, etch process, CMP etc. To control these effects various knobs, e.g. on the scanner for both wafer inter- and intra-field process control have been introduced recently, including sophisticated in-line metrology. In this holistic lithography concept the metrology is supported by simulation and by inline data. Additionally, offline data such as the mask CDU data can be added as mask wafer interaction is also an important contribution to wafer intra-field performance. The metrology algorithm now looks for such locations where the simulation finds the weakest process features due to strong deviations of focus, dose, stage dynamics or other input parameters.These concepts are optimized to find the sites where the process may break. Our concept of “excursion preventions” is a complimentary approach. It concentrates pro-actively on the task to minimize the distributions of critical input parameters as much as possible, independently upon a certain pre-defined specification for that parameter is met or not. In our presentation, we will describe this concept by improving wafer intra-field CDU using CD Correction (CDC) by Mask Tuning (based on wafer Intra-Filed data). Mask Tuning by the ForTune system uses ultra-short pulse laser technology to locally change the mask transmission and hence improves CDU on wafer (CDC). To ensure a save patterning with a large enough process window without any negative yield or reliability impact, our concept looks for the tail of the final CD distribution instead of traditiona13sigma numbers. By using a calibrated 3-D resist model, we simulate the pattering result under all permutations of input parameter distributions like dose, focus and mask CDU and imaging stochastics. As a result of the simulation, we get thousands of CD-results. The tail of that CD distribution still needs to be larger the minimum CD needed for a safe etch transfer. The simulation will be additionally supported by experimental data. Secondly, we will show in detail how the pro-active optimization of wafer intra-field CDU by Mask Tuning using the ForTune CDC process will give us more patterning margin and process stability over any other process excursion (e.g. focus deviations). Furthermore, we will present the simulated yield improvement based on the weak points (hot spots) improvement.
A next-generation EUV Fresnel zoneplate mask-imaging microscope (2012)

We present the potential capabilities of a low-cost next generation EUV mask-imaging microscope, based on the proven optical principle of the SEMATECH Berkeley Actinic Inspection Tool (AIT), but surpassing it in every performance metric.The new tool design would enable research on multiple generations of EUV lithography technology, down to 8-nm or beyond, reaching to the year 2025's design rules.Owing to the wavelength-specific reflective properties of EUV reticles, imaging with EUV light is the only faithful way to understand the physical response of defects, repairs, and pattern optical proximity corrections.The wavelength-specific properties limit the effectiveness of all non-EUV inspection technologies, and the differences between EUV and non-EUV measurement technologies are likely to increase in future nodes.Therefore, the prolonged unavailability of an EUV microscopy tool could hamstring the commercialization of EUV lithography, and impede research into future nodes.
Chemical Vapor Deposition of Bernal‐Stacked Graphene on a Cu Surface by Breaking the Carbon Solubility Symmetry in Cu Foils (2017)

The synthesis of Bernal-stacked multilayer graphene over large areas is intensively investigated due to the value of this material's tunable electronic structure, which makes it promising for use in a wide range of optoelectronic applications. Multilayer graphene is typically formed via chemical vapor deposition onto a metal catalyst, such as Ni, a Cu-Ni alloy, or a Cu pocket. These methods, however, require sophisticated control over the process parameters, which limits the process reproducibility and reliability. Here, a new synthetic method for the facile growth of large-area Bernal-stacked multilayer graphene with precise layer control is proposed. A thin Ni film is deposited onto the back side of a Cu foil to induce controlled diffusion of carbon atoms through bulk Cu from the back to the front. The resulting multilayer graphene exhibits a 97% uniformity and a sheet resistance of 50 Ω sq<sup>-1</sup> with a 90% transmittance after doping. The growth mechanism is elucidated and a generalized kinetic model is developed to describe Bernal-stacked multilayer graphene growth by the carbon atoms diffused through bulk Cu.
Sensitivity of LWR and CD linearity to process conditions in active area (2011)

LWR and CD linearity are both a major concern in the interpretation of drawn devices to actual structures on Si, and even more when translating to expected currents (both driven current and leakage current). Both of them have long ago been shown to be sensitive to process (especially lithographic) conditions, but usually not comparatively and, even more seldom are the final (etched) results thus related to the lithography process. Following our previous work on the sensitivities of LER and LWR to layout, we set out to research whether these sensitivities are themselves sensitive to process changes which tend to affect LER and LWR. As a logical conclusion, we expected that process changes which tend to worsen roughness will increase the dependence of the roughness on layout effects - that the outcome will be addible. Measurements were done in Active Area (a.k.a. STI definition) layer. Results show very interesting dependence of roughness and CD linearity (dependence of measured CDs on drawn CDs) of long dense resistors. Process changes that tended to make roughness worse, also had significant impact on the linearity, making it surprisingly more accurate at the low CD regime, but with significantly more variance.
Outsider Perspectives (2018)

It can be hard for authors to know if what they write will be clear to their readers. While collaborators can provide expert feedback, their liMassachusetts Institute of Technologyed time and attention makes it costly for authors to continuously solicit detailed input from them. Via a study with ten graduate student authors, we find a clear need for more feedback. Our crowd-based approaches provide an outsider perspective that is timely and detailed, supplementing expert feedback.
Energy-Efficient Computing in Nanoscale CMOS (2016)

This Perspectives paper is on the ever-interesting topic of energy-efficient computing. It shows us that future goals are orders of magnitude higher energy efficiency (measured in Joule per operation) and a means to achieve that is operating at near-threshold voltage.
A Survey on Chirp Spread Spectrum-based Waveform Design for IoT (2022)

&lt;p&gt;Long Range (LoRa) is one of the most promising and widespread chirp spread spectrum (CSS)-based physical (PHY) layer technique for low-power wide-area networks (LPWANs). Using different spreading factors, LoRa can attain different spectral/energy efficiencies, and can target multitude of Internet-of-Thing (IoT) applications. However, one of the limiting factors for LoRa is the low bit rate. Little to no effort has been made in order to improve the achievable rate of LoRa, until recently, when a number of CSS-based PHY layer LoRa alternative are proposed for LPWANs. In this survey, for the first time, we present a comprehensive waveform design of these CSS-based schemes that have been proposed between 2019 to 2022. In total, fifteen alternatives to LoRa are compared. Other survey articles related to LoRa mostly tackle different issues, such as LoRa networking, LoRa deployment in massive IoT networks, and LoRa architectures, etc. This survey, on the other hand, comprehensively elucidates the waveform design of LoRa alternatives. The CSS schemes studied in this survey are divided into single chirp, multiple chirp, and index modulation based on the multiplexing pattern of the chirps. Complete transceiver architecture of these CSS schemes is studied, and performance is evaluated in terms of energy efficiency (EE), spectral efficiency (SE), bit-error rate (BER) performance in additive white Gaussian noise, BER in the presence of phase and frequency offsets. It has been observed that the EE, SE and robustness against the offsets is primarily linked to transmit symbol frame structure. The public versions of the MATLAB codes for the CSS schemes studied in this survey shall be provided to promote reproducible research.&lt;/p&gt;
CCR Translation for This Article from Genomic and Epigenomic Integration Identifies a Prognostic Signature in Colon Cancer (2023)

CCR Translation for This Article from Genomic and Epigenomic Integration Identifies a Prognostic Signature in Colon Cancer
Hyperabrupt-junction varactor for mmWave SiGe:C BiCMOS, enabling 77GHz VCO/TX with 13-15GHz tuning range (2010)

A millimeter-wave hyperabrupt-junction varactor (HAVAR) enabling 77 GHz VCO/TX with 13-15 GHz tuning range and better than -70 dBc/Hz phase noise at 100 kHz offset has been integrated in SiGe:C BiCMOS for automotive radar products. The HAVAR predominantly uses existing processes for low-cost integration and minimal process complexity. Optimization of TR-Q thru HAVAR width allows TR up to 2.7 and Q <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">min</sub> up to 10.
An improved method to determine MOSFET channel length (1982)

An accurate and simple method to determine channel length and parasitic drain/source series resistance is presented. This method is based on measured data of two identical devices with different channel lengths. Because of its simplicity, the technique is suitable for use in automatic parameter testing systems.
Improvement in the beam quality of large-mode-area fiber amplifier output through fiber tapering (2006)

It is shown that the introduction of an adiabatic taper at the output end of a large-mode-area fiber amplifier can greatly improve the beam quality factor of the single-mode output beam when the core refractive index profile departs from an ideal step-index distribution. The deleterious impact of higher-order modes is also analyzed.
Gene Defects in Congenital Factor XIII Deficiency (1996)

The knowledge of the molecular basis of factor XIII deficiency has improved significantly in recent years. Almost 20 different mutations have been described in the gene coding for the factor A-subunit and 3 mutations in the gene coding for the B-subunit. Half of the mutations in the factor XIIIa A-subunit gene are nonsense mutations that result in premature termination of translation. Three of them are frameshift mutations that are caused by minor deletions. Two of them are splicing mutations and 3 are stop mutations that are caused by single nucleotide substitutions. Ten of the mutations are missense mutations caused by nucleotide transitions leading to amino acid substitutions. In the factor XIII B-subunit gene, the 3 mutations are an amino acid substitution, a splicing mutation, and a trinucleotide insertion. These mutations explain the disease in the two families reported to have XIII B-subunit deficiency. In factor XIII A-subunit deficiency, the genetic defects have been characterized so far only in a minority of cases. In most of the reports of factor XIII A-subunit mutations, each family carries its own mutation/mutations. However, in some populations such as Finns and Arabs some enrichment of specific mutations has occurred. Some international migration of a few mutations has also been noted. The structural and functional effects of the mutations have been analyzed by studying the expression of the factor XIII subunits on mRNA and protein levels in vivo or in vitro, and by utilizing the three-dimensional model of crystallized factor XIII A-subunit in modeling of the missense mutations.
Picosecond optical limiting in reverse saturable absorbers: a theoretical and experimental study (2002)

We theoretically and experimentally study absorption of picosecond laser pulses in materials described by a four-level system that exhibit reverse saturable absorption (RSA). Using an approximate solution to the rate equations, we derive, analyze, and verify, numerically and experimentally, a single dynamical equation for the spatial evolution of the pulse fluence that includes both the rate equations and the propagation equation. This analytical approach considerably simplifies the study of optical limiting with picosecond pulses and helps to predict the behavior of the nonlinear transmittance, the level of output signal clamping, and a possible turnover from RSA to saturable absorption that restricts the performance of optical limiters based on RSA. The results obtained can also be used to characterize RSA materials by the pump–probe technique.
Clock synchronization using a linear process model (2005)

Abstract In this paper, we present a clock synchronization scheme based on a simple linear process model which describes the behaviors of clocks at a transmitter and a receiver. In the clock synchronization scheme, a transmitter sends explicit time indications or timestamps to a receiver, which uses them to synchronize its local clock to that of the transmitter. Here, it is assumed that there is no common network clock available to the transmitter and the receiver and, instead, the receiver relies on locking its clock to the arrival of the timestamps sent by the transmitter. The clock synchronization algorithm used by the receiver is based on a weighted least‐squares criterion. Using this algorithm, the receiver observes and processes several consecutive clock samples (timestamps) to generate accurate timing signals. This algorithm is very efficient computationally, and requires the storage of only a small number of clock samples in order to generate accurate timing signals. Copyright © 2006 John Wiley &amp; Sons, Ltd.
Supplementary Figure S2 from Clinical Acquired Resistance to RAF Inhibitor Combinations in <i>BRAF</i>-Mutant Colorectal Cancer through MAPK Pathway Alterations (2023)

&lt;p&gt;Supplementary Figure S2. KRAS mutation drives resistance to RAF inhibitor combinations.&lt;/p&gt;
Engineering Bioactive Dimeric Transcription Factor Analogs via Palladium Rebound Reagents (2021)

Transcription factors (TF), such as Myc, are proteins implicated in disease pathogenesis, with dysregulation of Myc expression in 50% of all human cancers. Still, targeting Myc remains a challenge due to the lack of small molecule binding pockets in the tertiary structure. Here, we report synthetic covalently linked TF mimetics that inhibit oncogenic Myc-driven transcription by antagonistic binding of the target DNA-binding site. We combined automated flow peptide chemistry with palladium(II) oxidative addition complexes (OACs) to engineer covalent protein dimers derived from the DNA-binding domains of Myc, Max, and Omomyc TF analogs. Palladium-mediated cross-coupling of synthesized protein monomers resulted in milligram quantities of seven different covalent homo- and heterodimers. The covalent helical dimers were found to bind DNA and exhibited improved thermal stability. Cell-based studies revealed the Max-Max covalent dimer is cell-penetrating and interfered with Myc-dependent gene transcription resulting in reduced cancer cell proliferation (EC<sub>50</sub> of 6 μM in HeLa). RNA sequencing and gene analysis of extracted RNA from treated cancer cells confirmed that the covalent Max-Max homodimer interferes with Myc-dependent transcription. Flow chemistry, combined with palladium(II) OACs, has enabled a practical strategy to generate new bioactive compounds to inhibit tumor cell proliferation.
Thomson Legal and Regulatory at NTCIR-5: Japanese and Korean Experiments (2005)

Thomson Legal and Regulatory participated in the CLIR task of the NTCIR-5 workshop. We submitted formal runs for monolingual retrieval in Japanese and Korean, as well as for bilingual English-to-Japanese retrieval. We employed enhanced tokenization for our Japanese and Korean runs and applied a novel selec-tive pseudo-relevance feedback scheme for Japanese. Our bilingual search participation was a straightfor-ward application of an off-the-shelf Machine Trans-lation system to transform an English query into a Japanese query. Unfortunately we cannot draw many conclusions from our participation, as our experiments were ham-pered by technical difficulties, particularly with our to-kenization and stemming components.
Polynomial-Complexity Optimal Resource Allocation Framework for Uplink SC-FDMA Systems (2011)

International audience
A network design technique for selective restoration (2011)

We outline a network design technique that exploits differences in the failure rate and impact of network elements to produce a more efficient design. We demonstrate its efficacy on a Tier-1 backbone network.