gebhart/patrepeval huggingface dataset:
Tribeca (2009)

With continued advances in CMOS technology, parameter variations are emerging as a major design challenge. Irregularities during the fabrication of a microprocessor and variations of voltage and temperature during its operation widen worst-case timing margins of the design—degrading performance significantly. Because runtime variations like supply voltage droops and temperature fluctuations depend on the activity signature of the processor's workload, there are several opportunities to improve performance by dynamically adapting margins. This paper explores the power-performance efficiency gains that result from designing for typical conditions while dynamically tuning frequency and voltage to accommodate the runtime behavior of workloads. Such a design depends on a fail-safe mechanism that allows it to protect against margin violations during adaptation; we evaluate several such mechanisms, and we propose a local recovery scheme that exploits spatial variation among the units of the processor. While a processor designed for worst-case conditions might only be capable of a frequency that is 75% of an ideal processor with no parameter variations, we show that a fine-grained global frequency tuning mechanism improves power-performance efficiency (BIPS3/W) by 40% while operating at 91% of an ideal processor's frequency. Moreover, a per-unit voltage tuning mechanism aims to reduce the effect of within-die spatial variations to provide a 55% increase in power-performance efficiency. The benefits reported are clearly substantial in light of the ≪1% area overhead relative to existing global recovery mechanisms.
Chemical Evolution Reimagined (2022)

Some of the most interesting open questions about the origins of life and molecular sciences center on chemical evolution and the spontaneous generation of new complex and functional chemical species. The spectacular polymers that underlay biology demonstrate an untapped, by modern science, creative potential. We hypothesized that prebiotic chemical evolutionary processes leading to biopolymers were not idiosyncratic one-off events. We have developed an experimental platform that accomplishes chemical evolution in the laboratory. In this paper we describe this platform and report empirical outcomes, some of which were not foreseen. We have constructed experimental platform to study evolution of chemical systems that: (i) undergo continuous recursive change with transitions to new chemical spaces while not converging, (ii) demonstrate stringent chemical selection, during which combinatorial explosion is avoided, (iii) maintain synchronicity of molecular sub-populations, and (iv) harvest environmental energy that is invested in chemical reactions. We have established general guidelines for conducting chemical evolution. Our results suggest that chemical evolution can be adapted to produce a broad array of molecules with novel structures and functions.
<title>Efficient VLSI implementation of bit plane coder of JPEG 2000</title> (2001)

To overcome many drawbacks in the current JPEG standard for still image compression, a new standard, JPEG2000, is under development by the International Standard Organization. Embedded bit plane coding is the heart of the JPEG2000 encoder. This encoder is more complex and has significantly higher computational requirements compared to the entropy encoding in current JPEG standard. Because of the inherent bit-wise processing of the entropy encoder in JPEG2000, memory traffic is a substantial component in software implementation. However, in hardware implementation, the lookup tables can be mapped to logic gates and memory accesses for the state bit computation can be reduced significantly by careful design. In this paper, we present an efficient VLSI architecture for embedded bit-plane coding in JPEG2000 that reduces the number of memory accesses. To better understand the interaction of this architecture with the rest of the coder, we also present a system level architecture for efficient implementation of JPEG2000 in hardware.
A Multimodal CMOS MEA for High-Throughput Intracellular Action Potential Measurements and Impedance Spectroscopy in Drug-Screening Applications (2018)

Multi-electrode arrays (MEAs) are a candidate technology to screen cardiotoxicity <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">in vitro</i> because they enable noninvasive recording of cardiac beating rate, electrical field potential duration, and other parameters. In this paper, we present an active MEA chip featuring 16 384 electrodes, 1024 simultaneous readout channels, and 64 stimulation units (SUs) to enable six different cell-interfacing modalities: extracellular and intracellular recording, current and voltage stimulation, fast impedance motoring, and impedance spectroscopy (IS). The chip was designed and fabricated in a 0.13- <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\mu \text{m}$ </tex-math></inline-formula> Al CMOS technology, and the electrodes were fabricated on top of the silicon substrate using biocompatible TiN. Measurement results show a total input-referred noise of <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$7.5 \pm 0.6~\mu \text{V}_{\mathrm{rms}}$ </tex-math></inline-formula> and <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$12.0 \pm 2.4~\mu \text{V}_{\mathrm {rms}}$ </tex-math></inline-formula> for the action potential and full bands, respectively, with a total power consumption of 95 mW for 1024 readout channels. We have experimentally validated the CMOS MEA in <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">in vitro</i> experiments, demonstrating all the different modalities. This novel platform will potentially enable high-throughput electrical activity monitoring and drug screening of cardiomyocytes.
SF3B1 mutation and ATM deletion codrive leukemogenesis via centromeric R-loop dysregulation (2023)

RNA splicing factor SF3B1 is recurrently mutated in various cancers, particularly in hematologic malignancies. We previously reported that coexpression of Sf3b1 mutation and Atm deletion in B cells, but not either lesion alone, leads to the onset of chronic lymphocytic leukemia (CLL) with CLL cells harboring chromosome amplification. However, the exact role of Sf3b1 mutation and Atm deletion in chromosomal instability (CIN) remains unclear. Here, we demonstrated that SF3B1 mutation promotes centromeric R-loop (cen-R-loop) accumulation, leading to increased chromosome oscillation, impaired chromosome segregation, altered spindle architecture, and aneuploidy, which could be alleviated by removal of cen-R-loop and exaggerated by deletion of ATM. Aberrant splicing of key genes involved in R-loop processing underlay augmentation of cen-R-loop, as overexpression of the normal isoform, but not the altered form, mitigated mitotic stress in SF3B1-mutant cells. Our study identifies a critical role of splice variants in linking RNA splicing dysregulation and CIN and highlights cen-R-loop augmentation as a key mechanism for leukemogenesis.
The Role of Prolactin– and Endometriosis-Associated Infertility (2009)

After completion of this article, the reader should be able to explain the relationship between prolactin- and endometriosis-associated infertility, relate endometriosis with infertility, and summarize two ways in which prolactin and endometriosis may be linked in the pathophysiology of infertility.
Flow cytometric method to monitor the destruction of CD4+ cells following their fusion with HIV‐infected cells (1990)

Syncytium formation between HUT-78 cells persistently infected with human immunodeficiency virus type 1 (HIV-1) and uninfected CD4-bearing MOLT-4 or CEM cells results in a rapid destruction of the MOLT-4 or CEM cells. This syncytium formation is due to the interaction between the gp120 glycoprotein expressed by the persistently HIV-1-infected HUT-78 cells and the CD4 receptor present on MOLT-4 or CEM cells. A flow cytometric method has been applied to separate the infected (HUT-78) from the uninfected (MOLT-4, CEM) cell populations. This method is based on a modified DNA staining protocol which clearly shows the differences in DNA content between HUT-78 cells, on the one hand, and MOLT-4 or CEM cells, on the other hand. Using this flow cytometric method we have demonstrated that those compounds (i.e., sulfated polysaccharides, aurintricarboxylic acid) that interact with gp120 (of the HIV-infected cells) or CD4 (of the uninfected cells) suppress syncytium formation and concomitant destruction of the CD4+ cells.
Intraocular Pressure and Big Bubble Diameter in Deep Anterior Lamellar Keratoplasty: An Ex-Vivo Microscope-Integrated OCT With Heads-Up Display Study. (2017)

In this ex-vivo model of DALK, the BB technique guided by SS-MIOCT with HUD yielded bubbles of optimal diameters only at physiologic pressures (10‒20 mm Hg). Extremely high IOP (40 mm Hg) resulted in BBs of significantly smaller diameter than BBs obtained at physiologic and low (5 mm Hg) IOPs.
Investigation of NH3 input partial pressure for N-polarity InGaN growth on GaN substrates by tri-halide vapor phase epitaxy (2015)

Abstract The influence of NH 3 input partial pressure on N-polarity InGaN grown by tri-halide vapor phase epitaxy was investigated. It was found that surface morphology, solid composition and optical properties were affected by NH 3 input partial pressure. As shown in thermodynamic analyses, the indium content increased due to an increase in the driving force for InN deposition caused by increased NH 3 input partial pressure. In addition, the deep level emission around 2.1 eV in photoluminescence measurements drastically decreased at higher NH 3 input partial pressures. Ab initio calculations and subsequent secondary ion mass spectrometry measurements suggested the reduction of metal-vacancies and/or carbon impurity incorporation in the InGaN layers.
Targeted nanoagents for the detection of cancers (2010)

Nanotechnology has enabled a renaissance in the diagnosis of cancers. This is due, in part to the ability to develop agents bearing multiple functionalities, including those utilized for targeting, imaging, and therapy, allowing for the tailoring of the properties of the nanomaterials. Whereas many nanomaterials exhibit localization to diseased tissues via intrinsic targeting, the addition of targeting ligands, such as antibodies, peptides, aptamers, and small molecules, facilitates far more sensitive cancer detection. As such, this review focuses upon some of the most poignant examples of the utility of affinity ligand targeted nanoagents in the detection of cancer.
High-Throughput Quantitative and Qualitative Analysis of Microsomal Incubations by Cocktail Analysis with an Ultraperformance Liquid Chromatography-Quadrupole Time-Of-Flight Mass Spectrometer System (2014)

For the first time, a high-throughput quantitative-qualitative workflow was established using a cocktail approach for sample analysis with UPLC-HRMS in order to enable metabolite identification in early discovery projects.
The Role of HTS in Drug Discovery at the University of Michigan (2014)

High throughput screening (HTS) is an integral part of a highly collaborative approach to drug discovery at the University of Michigan. The HTS lab is one of four core centers that provide services to identify, produce, screen and follow-up on biomedical targets for faculty. Key features of this system are: protein cloning and purification, protein crystallography, small molecule and siRNA HTS, medicinal chemistry and pharmacokinetics. Therapeutic areas that have been targeted include anti-bacterial, metabolic, neurodegenerative, cardiovascular, anti-cancer and anti-viral. The centers work in a coordinated, interactive environment to affordably provide academic investigators with the technology, informatics and expertise necessary for successful drug discovery. This review provides an overview of these centers at the University of Michigan, along with case examples of successful collaborations with faculty.
Synthetic studies on polyether antibiotics. 6. Total synthesis of monensin. 3. Stereocontrolled total synthesis of monensin (1979)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthetic studies on polyether antibiotics. 6. Total synthesis of monensin. 3. Stereocontrolled total synthesis of monensinT. Fukuyama, K. Akasaka, D. S. Karanewsky, C. L. J. Wang, G. Schmid, and Y. KishiCite this: J. Am. Chem. Soc. 1979, 101, 1, 262–263Publication Date (Print):January 1, 1979Publication History Published online1 May 2002Published inissue 1 January 1979https://pubs.acs.org/doi/10.1021/ja00495a066https://doi.org/10.1021/ja00495a066research-articleACS PublicationsRequest reuse permissionsArticle Views1485Altmetric-Citations83LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Laser angiosurgery with spectral diagnostics (1986)

Laser angiosurgery is a potential powerful method for treating atherosclerosis in coronary and peripheral vessels. Treatment is based on ablating arterial plaque using laser light delivered via a catheter containing fiber optics. From an engineering point of view laser angiosurgery can be viewed as a problem in controlled tissue matching and can be attacked using the tools of spectroscopy and physics.
Investigation on the Drying Dynamics of Millimetric Water Droplets: Source of Watermarks on Silicon Wafers (2011)

Evaporation of unpinned sessile droplets with small contact angles (below 90°) is studied here extensively. We focused our work on the constant contact-angle mode in which the contact area of the droplet on the substrate decreases. A thorough understanding of droplet evaporation is of vital importance for examining the drying rate, the flow patterns observed inside drying drops, and the residual deposits. The concentration of each potential dissolved species (e.g. silica or silicic acid) can also be predicted and confronted to their solubility. We developed a theoretical model to predict the evaporation rate and the behavior of millimetric droplets taking into account the characteristics of the ambient and the substrate during the drying process. We discuss also the topology of watermarks on silicon wafers in the case of a predominant evaporation phenomenon.
Coal combustion aerosols: a field study (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCoal combustion aerosols: a field studyEsko I. Kauppinen and Tuomo A. PakkanenCite this: Environ. Sci. Technol. 1990, 24, 12, 1811–1818Publication Date (Print):December 1, 1990Publication History Published online1 May 2002Published inissue 1 December 1990https://pubs.acs.org/doi/10.1021/es00082a004https://doi.org/10.1021/es00082a004research-articleACS PublicationsRequest reuse permissionsArticle Views653Altmetric-Citations152LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Regional pest suppression associated with adoption of Cry1Ac soybean benefits pest management in tropical agriculture (2022)

We provide evidence for regional suppression of lepidopteran pests and reduced insecticide use with the widespread adoption of Cry1Ac soybean in Brazil, bringing economic, social and environmental benefits. © 2022 Society of Chemical Industry.
Development of predictive capability of cycle-to-cycle variation in dual-fuel engines using supercomputing-based computational fluid dynamics (2023)

Cycle-to-cycle variation (CCV) in internal combustion engines is expected due to variabilities in operating conditions such as in-cylinder fuel stratification, mixing behavior, manifold air pressure, injection timing etc. Generally, engine experimental studies provide averaged quantities such as cylinder pressure, emissions, indicated mean effective pressure (IMEP) from multiple cycles and their CCV of IMEP, and CCV of cylinder pressure from consecutive cycles for a given test condition. Capturing 3D spatial distributions of relevant measures such as fuel-air mixing, temperature, turbulence levels and emissions from such experiments is challenging. Computational Fluid Dynamics (CFD) is an alternative to experiments, that can be used effectively to understand the spatial and temporal distributions of parameters of interest.Quantitative understanding of CCV in dual-fuel (DF) engines will accelerate the development and deployment of engines that provide fuel flexibility, economic advantage and emission compliance. Earlier work [1] performed to develop an understanding of the physics of CCV in large-bore, medium-speed, dual-fuel engines was partially successful. That effort entailed a sparse design of experiment (DOE) of full-cylinder geometry, closed-cycle, dual-fuel CFD simulations in which variabilities within some of the identified global parameters were exercised. The Coefficient of Variation (COV) of cylinder pressure was promising compared with experimental COV. This reinforced the understanding of which global parameters are significant contributors to CCV in DF combustion.The authors have used several high-performance supercomputing facilities in the process of developing predicting capability of CCV in large-bore engines, while operating in dual-fuel, diesel and natural gas (NG), combustion mode [1, 2]. In the current study CCV influencing parameters in a diesel-natural gas dual-fuel engine was studied using a 4th order DOE consisting of 137 concurrent cases. These full-geometry, closed-cycle, CFD simulations were run on the Mira supercomputing facility at the Argonne National Laboratory (ANL). This paper describes key learnings of that study along with a validation of the DOE. Further, the CCV prediction methodology, which is applicable to simulation-based design and testing, is described.
Exploring the epigenetic drug discovery landscape (2017)

Epigenetic modification has been implicated in a wide range of diseases and the ability to modulate such systems is a lucrative therapeutic strategy in drug discovery. Areas covered: This article focuses on the concepts and drug discovery aspects of epigenomics. This is achieved by providing a survey of the following concepts: (i) factors influencing epigenetics, (ii) diseases arising from epigenetics, (iii) epigenetic enzymes as druggable targets along with coverage of existing FDA-approved drugs and pharmacological agents, and (iv) drug repurposing/repositioning as a means for rapid discovery of pharmacological agents targeting epigenetics. Expert opinion: Despite significant interests in targeting epigenetic modifiers as a therapeutic route, certain classes of target proteins are heavily studied while some are less characterized. Thus, such orphan target proteins are not yet druggable with limited report of active modulators. Current research points towards a great future with novel drugs directed to the many complex multifactorial diseases of humans, which are still often poorly understood and difficult to treat.
Novel Xanthomonas Species From the Perennial Ryegrass Seed Microbiome – Assessing the Bioprotection Activity of Non-pathogenic Relatives of Pathogens (2020)

The productivity of the Australian dairy industry is underpinned by pasture grasses, and importantly perennial ryegrass. The performance of these pasture grasses is supported by the fungal endophyte <i>Epichloë</i> spp. that has bioprotection activities, however, the broader microbiome is not well characterized. In this study, we characterized a novel bioprotectant <i>Xanthomonas</i> species isolated from perennial ryegrass (<i>Lolium perenne</i> L. cv. Alto). <i>In vitro</i> and <i>in planta</i> bioassays against key fungal pathogens of grasses (<i>Sclerotium rolfsii</i>, <i>Drechslera brizae</i> and <i>Microdochium nivale</i>) indicated strong bioprotection activities. A complete circular chromosome of ∼5.2 Mb was generated for three strains of the novel <i>Xanthomonas</i> sp. Based on the 16S ribosomal RNA gene, the strains were closely related to the plant pathogen <i>Xanthomonas translucens</i>, however, comparative genomics of 22 closely related xanthomonad strains indicated that these strains were a novel species. The comparative genomics analysis also identified two unique gene clusters associated with the production of bioprotectant secondary metabolites including one associated with a novel nonribosomal peptide synthetase and another with a siderophore. The analysis also identified genes associated with an endophytic lifestyle (e.g., Type VI secretion system), while no genes associated with pathogenicity were identified (e.g., Type III secretion system and effectors). Overall, these results indicate that these strains represent a novel, bioactive, non-pathogenic species of the genus <i>Xanthomonas</i>. Strain GW was the designated type strain of this novel <i>Xanthomonas</i> sp.
Macromolecular Regulation of Sepiapterin and Drosopterin Synthesis in the Purple Mutant of Drosophila (1983)

This study of the mechanism of genetic suppression revealed the existence of a macromolecule which exhibits an inhibitory effect on a mutant form of sepiapterin synthase (probably sepiapterin synthase A) but not on the wild type activity. This inhibitor may be related to the product of the su(s)/sup +/ locus. The possibility of purifying and characterizing this su(s)/sup +/ substance arises since a simple procedure was developed to measure the extent of inhibition as related to the concentration. (PSB)