gebhart/patrepeval huggingface dataset:
Resist stripping in an O2+H2O plasma downstream (1991)

Characteristics are reported for a resist stripping process downstream of an oxygen plasma to which water vapor is added. The effects of additive water vapor are an increase in atomic oxygen concentration in the plasma, a decrease in activation energy of ashing reaction, and protection of semiconductor devices from the sodium contamination from the resist. The atomic oxygen concentration was approximately doubled by mixing 10% H2O into the oxygen plasma. The activation energy of the ashing reaction to the resist made from novolak resin decreased from about 0.5 to 0.39 eV by the addition of water vapor of more than 1%. The activation energy of hydrogen abstraction from hydrocarbon molecules by an OH radical was lower than that by a ground state oxygen atom [O(3P)], which was the dominant ashing species in the oxygen plasma downstream, and that by an atomic hydrogen was higher than that by the ground state oxygen atom. Moreover, the activation energy in the downstream ashing of the oxygen plasma added to which was 1% water vapor was lower than that of the oxygen plasma to which 3% hydrogen was added, even though the relative concentration of atomic hydrogen in each plasma was equal. Therefore the decrease in the activation energy was probably due to the OH radical generated in the plasma and the downstream. Sodium atoms in the resist were blocked from entering into the semiconductor devices in the stripping process by use of the O2+H2O plasma downstream. Thus sodium was not removed and remained on the wafer surface after resist stripping. Also, by adding N2 or CF4 to the O2+H2O plasma, we can increase the ashing rate without losing the above characteristics.
Adaptive electric potential sensors for smart signal acquisition and processing (2007)

Current applications of the Electric Potential Sensor operate in a strongly (capacitively) coupled limit, with the sensor physically close to or touching the source. This mode of operation screens the sensor effectively from the majority of external noise. To date however the full capability of these sensors operating in a remote mode has not been realised outside of a screened environment (Faraday cage). This paper describes the results of preliminary work in tailoring the response of the sensors to particular signals and so reject background noise, thereby enhancing both the dynamic range and signal to noise ratio significantly.
High-level interconnect model for the quantum logic array architecture (2008)

We summarize the main characteristics of the quantum logic array (QLA) architecture with a careful look at the key issues not described in the original conference publications: primarily, the teleportation-based logical interconnect. The design goal of the the quantum logic array architecture is to illustrate a model for a large-scale quantum architecture that solves the primary challenges of system-level reliability and data distribution over large distances. The QLA's logical interconnect design, which employs the quantum repeater protocol, is in principle capable of supporting the communication requirements for applications as large as the factoring of a 2048-bit number using Shor's quantum factoring algorithm. Our physical-level assumptions and architectural component validations are based on the trapped ion technology for implementing quantum computing.
A Clinical and Histological Comparison of Flashscanning versus Pulsed Technology in Carbon Dioxide Laser Facial Skin Resurfacing (1998)

Irradiated laser energy density in relation to time, and the way that it is delivered, should play an important role at the moment of producing collagen shrinkage. The SilkTouch delivers laser energy more aggressively, thereby producing a more intense inflammatory tissue reaction, which results in slower recovery of tissue, compared with the Coherent CPG. More active enhancement of vascularization found in the Sharplan is likely to be the reason for a more effective collagen proliferation and compaction. These changes, together with the increase in elastin in the dermis, may produce longer lasting effects in skin resurfacing.
GSK3α exhibits β‐catenin and tau directed kinase activities that are modulated by Wnt (2006)

In the presence of a Wnt signal beta-catenin is spared from proteasomal degradation through a complex mechanism involving GSK3beta, resulting in the transcription of Wnt target genes. In this study we have explored whether GSK3alpha, a related isoform, can also regulate nuclear beta-catenin levels and whether this and the tau-directed kinase activity of GSK3alpha are modulated by Wnt. GSK3alpha or GSK3beta and their substrates, beta-catenin and tau, were transiently expressed in mammalian cells. Immunoblotting revealed that GSK3alpha reduces nuclear levels of beta-catenin, whilst reporter gene assays demonstrated that GSK3alpha inhibits beta-catenin-directed Tcf/Lef-dependent transcription. Moreover, activation of the Wnt pathway was found to attenuate both the beta-catenin- and the tau-directed kinase activities of GSK3alpha and GSK3beta. By immunoprecipitation we also found that axin-1, the beta-catenin destruction complex scaffold protein, binds GSK3alpha. In the light of these findings GSK3alpha warrants further investigation regarding its involvement in Wnt signalling and tauopathies such as Alzheimer's disease.
High-dose combination chemotherapy with autologous bone marrow transplantation in adult solid tumors (1980)

In order to determine whether high-dose combination chemotherapy was active in chemotherapy resistant patients, 19 patients, (9 with small cell bronchogenic carcinoma, 6 with embryonal cell carcinoma, 2 with diffuse histiocytic lymphoma, 1 with Hodgkin's disease and 1 with chondrosarcoma), 18 of whom had had extensive prior chemotherapy and failed, received 23 courses of high-dose chemotherapy with autologous bone marrow infusion (ABMT). Three patients received four courses of cytoxan (2-6 g/m2) and VP-16 (500-600 mg/m2) and 16 patients received 19 courses of cytoxan and VP-16 in these doses plus BCNU (300 mg/m2). Activity was observed in 6 of 8 evaluable small cell bronchogenic carcinoma patients (1 complete response (CR), 4 partial responses (PR), 1 less than PR), in 6 embryonal cell carcinoma patients (3 CR, 2 PR, 1 less than PR), in both patients with diffuse histiocytic lymphoma (1 CR, 1 less than PR), in the patient with Hodgkin's disease (1 PR); and in the patient with chondrosarcoma (stable). Only 2 patients who had received prior cytoxan and VP-16 extensively showed resistance to these programs. The median response duration was 11 weeks (range = 4-55 + weeks). Major toxicity consisted of bacterial infections. Two patients died from treatment related causes. Neutrophils recovered to levels of greater than or equal to 1.5 x 10(9)/liter by days 20-42 (median, day 27) and platelets to levels of greater than 100 x 10(9)/liter by days 21-56 (median, day 32) without any delayed BCNU toxicity. High-dose combination chemotherapy with ABMT causes acceptable toxicity and high response rates of relatively short duration in tumors refractory to conventional chemotherapy.
Energy properties of an EMI-Im ionic liquid ion source (2005)

The identity and the energy distributions of positive and negative ions electrostatically extracted from the liquid phase in an ionic liquid ion source (ILIS) are analysed with a time-of-flight mass spectrometer and a multi-grid retarding potential analyzer. Accurate energy measurements using ionic liquids in an externally wetted configuration are reported for the first time. Droplet-free beams are produced using the ionic liquid 1-ethyl-3-methylimidazolium bis(triflouromethylsulfonyl)amide (EMI-Im) in which the solvated ions (EMI-Im)nEMI+ and (EMI-Im)nIm− with n = 0,1,2 are observed. The small ion source size and the energy distribution widths and deficits of a few electronvolts are quite similar to those of liquid metal ion sources, confirming that ILIS can be used in applications requiring highly focusable beams, e.g. sub-micron ion lithography. Measurements also suggest that solvated ions with n ⩾ 1 exhibit post-extraction fragmentation into lighter species at a rate increasing with their original degree of solvation. About 10% of the total beam current is carried away by metastable species that break up almost immediately after extraction while inside the emitter accelerating region.
The ideal SoC memory: 1T-SRAM/sup TM/ (2002)

The advances of process technology makes system-on-a-chip a reality and present major challenge to IC design. Integration of memory in SoC is further complicated by the incompatibility of memory process technology to the logic process. The simplicity of 1T-SRAM cell facilitates its easy porting to most processes. This helps alleviate the problem of process incompatibility. The simplicity of the cell structure also makes it extremely scalable and cost effective. The challenges of using this cell to satisfy the requirement of embedded SRAM are high-frequency operation, short latency, transparent refresh and soft-error rate. The use of multi-bank architecture and the leverage of multi-layer metal interconnect available in logic processes, allow these challenges to be met readily.
Expression of BLyS and its receptors in B-cell non-Hodgkin lymphoma: correlation with disease activity and patient outcome (2004)

BLyS, recently shown to be critical for survival of normal B cells, has been found to be elevated in a number of immune disease models. A role for BLyS in the survival of malignant B cells has also been revealed and we therefore sought to identify a role for BLyS and its receptors in non-Hodgkin lymphoma (NHL). We found that tumor cells from all NHL histologic subtypes expressed one or more of 3 known receptors (BCMA, TACI, and BAFF-R) for BLyS; however, the pattern of expression was variable. We provide evidence that BLyS is expressed in tumors from patients with NHL and that BLyS levels increase as tumors transform to a more aggressive phenotype. Additionally, we provide evidence that serum BLyS levels are elevated in a subgroup of patients with NHL. In patients with de novo large B-cell lymphoma, a high BLyS level correlated with a poorer median overall survival, the presence of constitutional symptoms, and elevated values of lactic dehydrogenase. When BLyS levels were correlated with response to therapy in all patients, responding patients had a significantly lower BLyS level than those with progressive disease. In summary, we found that BLyS and its receptors represent a potentially important therapeutic target in B-cell lymphoma.
A Nyquist folding analog-to-information receiver (2008)

Many radar and communications applications require detection and estimation of signal information across an extremely wide radio frequency (RF) bandwidth. In practice, however, direct digitization of this broadband RF environment is problematic. Physical limitations in analog-to-digital converter (ADC) technology restrict the total bandwidth that can be digitized, as well as the ability to digitize high RF signals directly. This paper describes a novel ldquoanalog-to-informationrdquo receiver, motivated by recent developments in compressed sensing (CS), which overcomes both of these challenges in certain settings. The proposed receiver performs frequency modulated pulsed sampling at sub-Nyquist/Shannon rates to compress a broadband RF environment into an analog interpolation filter. The RF sample clock modulation induces a Nyquist-zone dependent frequency modulation on the received signals, allowing separation and recovery of the signal information from a sparse broadband RF environment.
An Extensible Framework for Quantifying the Coverage of Defenses Against Untrusted Foundries (2019)

The transistors used to construct Integrated Circuits (ICs) continue to shrink. While this shrinkage improves performance and density, it also reduces trust: the price to build leading-edge fabrication facilities has skyrocketed, forcing even nation states to outsource the fabrication of high-performance ICs. Outsourcing fabrication presents a security threat because the black-box nature of a fabricated IC makes comprehensive inspection infeasible. Since prior work shows the feasibility of fabrication-time attackers' evasion of existing post-fabrication defenses, IC designers must be able to protect their physical designs before handing them off to an untrusted foundry. To this end, recent work suggests methods to harden IC layouts against attack. Unfortunately, no tool exists to assess the effectiveness of the proposed defenses---meaning gaps may exist. This paper presents an extensible IC layout security analysis tool called IC Attack Surface (ICAS) that quantifies defensive coverage. For researchers, ICAS identifies gaps for future defenses to target, and enables the quantitative comparison of existing and future defenses. For practitioners, ICAS enables the exploration of the impact of design decisions on an IC's resilience to fabrication-time attack. ICAS takes a set of metrics that encode the challenge of inserting a hardware Trojan into an IC layout, a set of attacks that the defender cares about, and a completed IC layout and reports the number of ways an attacker can add each attack to the design. While the ideal score is zero, practically, our experience is that lower scores correlate with increased attacker effort.
Genetic Elucidation of Human Hyperosmia to Isovaleric Acid (2007)

The genetic basis of odorant-specific variations in human olfactory thresholds, and in particular of enhanced odorant sensitivity (hyperosmia), remains largely unknown. Olfactory receptor (OR) segregating pseudogenes, displaying both functional and nonfunctional alleles in humans, are excellent candidates to underlie these differences in olfactory sensitivity. To explore this hypothesis, we examined the association between olfactory detection threshold phenotypes of four odorants and segregating pseudogene genotypes of 43 ORs genome-wide. A strong association signal was observed between the single nucleotide polymorphism variants in OR11H7P and sensitivity to the odorant isovaleric acid. This association was largely due to the low frequency of homozygous pseudogenized genotype in individuals with specific hyperosmia to this odorant, implying a possible functional role of OR11H7P in isovaleric acid detection. This predicted receptor-ligand functional relationship was further verified using the Xenopus oocyte expression system, whereby the intact allele of OR11H7P exhibited a response to isovaleric acid. Notably, we also uncovered another mechanism affecting general olfactory acuity that manifested as a significant inter-odorant threshold concordance, resulting in an overrepresentation of individuals who were hyperosmic to several odorants. An involvement of polymorphisms in other downstream transduction genes is one possible explanation for this observation. Thus, human hyperosmia to isovaleric acid is a complex trait, contributed to by both receptor and other mechanisms in the olfactory signaling pathway.
Identification of an insulin response element in the fatty acid synthase promoter. (1994)

We have previously reported that insulin increases fatty acid synthase (FAS) gene transcription, and that sequences responsible for positive regulation are located within the first 332 base pairs of the FAS promoter. To define minimal sequences required for insulin regulation within this region, chimeric constructs containing serial 5' deletions starting at -318 and extending through position +67 of the rat FAS gene ligated to the luciferase reporter gene were transfected into 3T3-L1 adipocytes. Insulin treatment at 10 nM increased luciferase activity 2-3-fold in 3T3-L1 adipocytes transfected with constructs containing progressive deletions from -318 to -67. This stimulation of the FAS promoter activity by insulin was dose-dependent. However, no effect of insulin was observed when fusion constructs containing FAS promoter sequences spanning from -25 or from -19 to +67 were transfected into adipocytes. These results suggest that the insulin response sequences of the FAS gene may be located in the region from -67 to -25. DNase I footprinting using liver nuclear extracts revealed a protected region spanning -71 and -50 in addition to a region near the putative TATA box. Gel mobility shift assays using the sequence from -71 to -50 as a probe revealed nuclear factor(s) from mouse liver and 3T3-L1 adipocytes that specifically complexed with this sequence. Mutational analysis of this region showed that sequences between -68 and -60 are essential for recognition and interaction with a trans-acting factor(s). Moreover, when three tandem repeats of the sequences spanning -68 to -52 were linked to the SV40 promoter and used for transfection, luciferase activity increased 3.6-fold in response to insulin treatment. Thus, we have identified novel cis-acting DNA sequences responsible for insulin regulation of the FAS gene, which interact with nuclear protein(s) from liver and adipocytes and which are found to share limited homology to insulin response sequences present in other genes.
Essential Role of IL-21 in B Cell Activation, Expansion, and Plasma Cell Generation during CD4+ T Cell-B Cell Collaboration (2007)

During T cell-B cell collaboration, plasma cell (PC) differentiation and Ig production are known to require T cell-derived soluble factors. However, the exact nature of the cytokines produced by activated T cells that costimulate PC differentiation is not clear. Previously, we reported that costimulation of purified human B cells with IL-21 and anti-CD40 resulted in efficient PC differentiation. In this study, we addressed whether de novo production of IL-21 was involved in direct T cell-induced B cell activation, proliferation, and PC differentiation. We found that activated human peripheral blood CD4(+) T cells expressed mRNA for a number of cytokines, including IL-21, which was confirmed at the protein level. Using a panel of reagents that specifically neutralize cytokine activity, we addressed which cytokines are essential for B cell activation and PC differentiation induced by anti-CD3-activated T cells. Strikingly, neutralization of IL-21 with an IL-21R fusion protein (IL-21R-Fc) significantly inhibited T cell-induced B cell activation, proliferation, PC differentiation, and Ig production. Inhibition of PC differentiation was observed even when the addition of IL-21R-Fc was delayed until after initial B cell activation and expansion had occurred. Importantly, IL-21 was found to be involved in PC differentiation from both naive and memory B cells. Finally, IL-21R-Fc did not inhibit anti-CD3-induced CD4(+) T cell activation, but rather directly blocked T cell-induced B cell activation and PC differentiation. These data are the first to document that B cell activation, expansion, and PC differentiation induced by direct interaction of B cells with activated T cells requires IL-21.
Enhanced Shear-Induced Platelet Aggregation in Acute Myocardial Infarction (1999)

Shear-induced platelet aggregation is enhanced in plasma in the presence of acute myocardial infarction, apparently as a result of increased vWF concentration. This may contribute to the onset of acute coronary artery thrombosis and early reocclusion after reperfusion treatment.
Building NVRAM-Aware Swapping Through Code Migration in Mobile Devices (2017)

Mobile applications are becoming increasingly feature-rich and powerful, but also dependent on large main memories, which consume a large portion of system energy, especially for devices equipped with 4/6 GB DRAM. Swapping inactive DRAM pages to byte-addressable, non-volatile memory (NVRAM) is a promising solution to this problem. However, most NVRAMs have limited write endurance and the current victim pages selecting algorithm does not aware it. Therefore, to make it practical, the design of an NVRAM based swapping system must also consider endurance. In this paper, we target at prolonging the lifetime of NVRAM based swap area in mobile devices by reducing the write activities to NVRAM based swap area. Different from traditional wisdom, such as wear leveling and hot/cold data identification, we propose to build a system called nCode, which exploits the fact that code pages are easy to identify, read-only, and therefore a perfect candidate for swapping. Utilizing NVRAM's byte-addressability, we support execute-in-place (XIP) of the code pages in the swap area, without copying them back to DRAM based main memory. Experimental results based on the Google Nexus 5 smartphone show that nCode can effectively prolong the lifetime of NVRAM under various workloads.
Functional Studies on Viable Circulating Tumor Cells (2015)

Functional analyses on CTCs offer the possibility to identify the biological properties of metastatic cells, including the identification of metastasis-initiating cells. Moreover, CTC-derived cell lines and xenografts might reveal new therapeutic targets and can be used for drug screening.
In vivo Effects of a Histone Deacetylase Inhibitor, FK228, on Human Acute Promyelocytic Leukemia in NOD/Shi‐scid/scid Mice (2001)

Histone acetylation and deacetylation are closely linked to transcriptional activation and repression, respectively. In acute promyelocytic leukemia (APL), histone deacetylase inhibitors (HDACIs) have a synergistic effect with all-trans retinoic acid (ATRA) in vitro to induce differentiation. Here we report in vitro and in vivo effects of a HDACI, FK228 (formerly FR901228 or depsipeptide), on the human APL cell line NB4. FK228 had a strong and irreversible cytotoxicity compared with another HDACI, trichostatin A. In vivo administration of ATRA or FK228 alone partly inhibited the growth of established tumors of NB4 subcutaneously transplanted in NOD / Shi-scid / scid mice, and the combination was synergistically effective. Histopathological examination revealed that the combination induced apoptosis and differentiation as well as histone acetylation. Intravenous injection of NB4 in NOD / Shi-scid / scid mice followed by combination treatment significantly prevented leukemia death, whereas single administration did not. These findings suggest that FK228 is a promising agent to enhance ATRA-sensitivity in the treatment of APL.
A sensitive transcriptome analysis method that can detect unknown transcripts (2003)

We have developed an AFLP-based gene expression profiling method called 'high coverage expression profiling' (HiCEP) analysis. By making improvements to the selective PCR technique we have reduced the rate of false positive peaks to approximately 4% and consequently the number of peaks, including overlapping peaks, has been markedly decreased. As a result we can determine the relationship between peaks and original transcripts unequivocally. This will make it practical to prepare a database of all peaks, allowing gene assignment without having to isolate individual peaks. This precise selection also enables us to easily clone peaks of interest and predict the corresponding gene for each peak in some species. The procedure is highly reproducible and sensitive enough to detect even a 1.2-fold difference in gene expression. Most importantly, the low false positive rate enables us to analyze gene expression with wide coverage by means of four instead of six nucleotide recognition site restriction enzymes for fingerprinting mRNAs. Therefore, the method detects 70-80% of all transcripts, including non-coding transcripts, unknown and known genes. Moreover, the method requires no sequence information and so is applicable even to eukaryotes for which there is no genome information available.