gebhart/patrepeval huggingface dataset:
Sorbitol-6-Phosphate Dehydrogenase Expression in Transgenic Tobacco1 (1998)

We analyzed transgenic tobacco (Nicotiana tabacum L.) expressing Stpd1, a cDNA encoding sorbitol-6-phosphate dehydrogenase from apple, under the control of a cauliflower mosaic virus 35S promoter. In 125 independent transformants variable amounts of sorbitol ranging from 0.2 to 130 &mgr;mol g-1 fresh weight were found. Plants that accumulated up to 2 to 3 &mgr;mol g-1 fresh weight sorbitol were phenotypically normal, with successively slower growth as sorbitol amounts increased. Plants accumulating sorbitol at 3 to 5 &mgr;mol g-1 fresh weight occasionally showed regions in which chlorophyll was partially lost, but at higher sorbitol amounts young leaves of all plants lost chlorophyll in irregular spots that developed into necrotic lesions. When sorbitol exceeded 15 to 20 &mgr;mol g-1 fresh weight, plants were infertile, and at even higher sorbitol concentrations the primary regenerants were incapable of forming roots in culture or soil. In mature plants sorbitol amounts varied with age, leaf position, and growth conditions. The appearance of lesions was correlated with high sorbitol, glucose, fructose, and starch, and low myo-inositol. Supplementing myo-inositol in seedlings and young plants prevented lesion formation. Hyperaccumulation of sorbitol, which interferes with inositol biosynthesis, seems to lead to osmotic imbalance, possibly acting as a signal affecting carbohydrate allocation and transport.
A 23.5 GHz PLL With an Adaptively Biased VCO in 32 nm SOI-CMOS (2013)

A 23.5 GHz 32 nm SOI-CMOS PLL with 30% frequency tuning range features an adaptively biased VCO. The adaptive biasing scheme lowers the average PLL power consumption from 34 mW to 27.2 mW, while keeping the jitter below 1.3° RMS across all frequency bands.
Response to Zöller et al.'s critique on “Potential short‐term earthquake forecasting by farm‐animal monitoring” (2021)

Abstract Zöller et al. (Ethology, 2020) criticize our original publication (Wikelski et al., Ethology, 126(9), 2020, 931) for obvious reasons: we only observed the behavior of one group of farm animals before, during and after one earthquake series in one area of the world. It is clear that no earthquake predictions are possible, and should not be attempted, from this data set. However, what we show is that there is important information within this animal collective pertaining to potential future local forecasting of earthquakes when combined with traditional data sources. We maintain that combining Zöller et al.'s (2020) modeling tools with the adequate use of our data can stimulate novel ways of earthquake forecasting. Future studies should combine both approaches.
Optical damage of dielectrics down to 5 fs (1997)

Experiments have been carried out on a barium borosilicate glass and on fused silica using 800-nm-pulses from a kHz-rate Ti:sapphire amplifier system. The output pulses of the system have been broadened up to 5 ps by passing them through glass blocks of different path lengths. The damaged thresholds were determined by focusing a He-Ne laser exactly onto the interaction region and inspecting reflected and transmitted beam. The threshold fluence is by a factor of five higher than observed with the use of the 20-fs pulses directly from the amplifier output.
Conduction Mechanisms and Structure of Ionomeric Single-Ion Conductors (2015)

Our team has designed using DFT (Gaussian) and synthesized low glass transition temperature single-ion conductors that are either polyanions that conduct small cations Li+, Na+, Cs+ or polycations that conduct small anions F-, OH-, Br-. We utilize a wide range of complimentary experimental materials characterization tools to understand ion transport; differential scanning calorimetry, dielectric relaxation spectroscopy, infrared spectroscopy, nuclear magnetic resonance spectroscopy, linear viscoelasticity, X-ray scattering and molecular dynamics simulations. The glass transition temperature Tg needs to be as low as possible to facilitate ion transport, so the nonionic parts of the polymer need to be polar, flexible and have strong solvation interactions with the ions. The lowest Tg we have managed for polyanions conducting Li+ is -60 °C. In contrast, polysiloxanes with PEO side chains and tetrabutylphosphonium cationic side groups have Tg ≈ -75 °C that barely increases with ion content, as anticipated by DFT. A survey of all polyanions in the literature suggests that Tg < -80 °C is needed to achieve the 10-4 S/cm conductivity needed for battery separators.
The Effect of Refinements in Energetic Statistical Weighting on the Computed Chain Dimensions of Homopolypeptides (1978)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Effect of Refinements in Energetic Statistical Weighting on the Computed Chain Dimensions of HomopolypeptidesYvonne Paterson and Sydney J. LeachCite this: Macromolecules 1978, 11, 2, 415–418Publication Date (Print):March 1, 1978Publication History Published online1 May 2002Published inissue 1 March 1978https://pubs.acs.org/doi/10.1021/ma60062a025https://doi.org/10.1021/ma60062a025research-articleACS PublicationsRequest reuse permissionsArticle Views22Altmetric-Citations4LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Characterization of Quantum Dot/Conducting Polymer Hybrid Films and Their Application to Light‐Emitting Diodes (2009)

Quantum dot/conducting polymer hybrid films are used to prepare light-emitting diodes (LEDs). The hybrid films (CdSe@ZnS quantum dots excellently dispersed in a conducting polymer matrix, see figure) are readily prepared by various solution-based processes and are also easily micropatterned. The LEDs exhibit a turn-on voltage of 4 V, an external quantum efficiency greater than 1.5%, and almost pure-green quantum-dot electroluminescence.
Mammalian-Transmissible H5N1 Virus: Containment Level and Case Fatality Ratio (2012)

Dr. Casadevall serves on the NSABB, and the views expressed in this Editorial do not represent official policy or those of the NSABB. In addition, the views expressed in this Editorial do not necessarily reflect the views of the journal or of ASM .

The life sciences, and the field of microbiology in particular, are in the midst of an unprecedented debate regarding the risks posed by the publication of two studies that report the generation of mammalian-transmissible H5N1 virus in the laboratory. The controversy was precipitated when the National Science Advisory Board for Biosecurity (NSABB) advised the U.S. government that the best course of action was to seek a redaction of the manuscripts to delete important details that could be used for nefarious purposes (1, 2). In a recent issue, mBio published pro- and anti-NSABB decision commentaries (3–6) with the goal of informing the debate and the hope that airing these views would lead to the best decisions. At the time of this writing the issue remains unsettled, and a fierce debate is raging in government and academic circles on the best course of action. Even with the question of how to publish these studies unsettled, two …
Efficient Recovery in Harp (1992)

Harp is a replicated Unix file system accessible via the VFS interface. It provides highly available and reliable storage for files and guarantees that file operations are executed atomically in spite of concurrency and failures. Replication enables Harp to safely trade disk accesses for network communication and thus to provide good performance both during normal operation and during recovery. In this position statement, we focus on the techniques Harp uses to achieve efficient recovery.
Process Safety Considerations for the Supply of a High-Energy Oxadiazole IDO1-Selective Inhibitor (2019)

The development of a stereospecific synthesis of a IDO1-selective inhibitor is described. The synthetic strategy toward enabling early discovery efforts along with additional findings pertaining to process safety that limited scalability are outlined. A convergent approach that supported the synthesis of material suitable for early preclinical and/or good laboratory practice toxicology studies and avoided the formation of key high-energy intermediates is summarized.
Supplementary Figure 5 from Higher Frequencies of GARP<sup>+</sup>CTLA-4<sup>+</sup>Foxp3<sup>+</sup> T Regulatory Cells and Myeloid-Derived Suppressor Cells in Hepatocellular Carcinoma Patients Are Associated with Impaired T-Cell Functionality (2023)

&lt;p&gt;PDF file - 117K, Supplementary Figure 5. Plasmacytoid dendritic cells in HCC patients.&lt;/p&gt;
A Sensitive Method for Estimating the Linear Length of a System (2022)

An orthogonal decomposition-based method is proposed for estimating the linear length of a system. Through orthogonal spectrum analysis, a suitable linear length is determined to realize accurate nonlinear modeling and optimal linear equalization.
Advancing Laboratory Medicine through Innovation: A Tale of Six Inventors (2012)

In a recent issue of Science Translational Medicine (1), Yock and colleagues of Stanford University discuss the merits and challenges of developing a discipline of medical technology innovation. Innovation is defined as “inventiveness put to use”; a discovery that results in a commercial product or service. In this provocative article, the authors discuss two main streams of educational theory and practice that together form the basis for teaching innovation: design thinking and entrepreneurship education (Fig. 1). Design thinking focuses on identifying the opportunity and need, developing the idea to solve the problem, building the prototype, and testing the product, while entrepreneurship education provides an introduction to the skills and approaches required to take a product or a service and successfully commercialize it. The authors argue that medical technology innovation is the ideal environment for interdisciplinary team building combining physicians, engineers, scientists, and business professionals.



Fig. 1. Components of innovation as suggested in a recent review on biomedical technology innovation as a discipline [Yock et al. (1)]. 
Design thinking encompasses the creative roadmap toward innovation, including awareness of the opportunity or unsolved problem, an idea to fill the opportunity, development work to design and prototype the solution, and experimental testing as a reality check. Multiple cycles of ideas, prototyping, and testing may be required before a viable product emerges. Entrepreneurship assesses the feasibility of commercializing the product, including components of uniqueness (intellectual property) and market potential. Regulatory requirements and business strategy often suggest outcomes that may include in-house manufacturing, licensing, mergers/acquisitions, or an initial public offering (IPA).



In laboratory medicine, numerous scientists and physicians have been able to successfully launch their inventions into the marketplace; inventions that changed the practice of medicine. Six of those inventors were invited to share their success stories with the readers of Clinical Chemistry. How did they do it? What influenced most their success? What were the major drivers for their pursuits? Did they have formal training in …
Cylinder deactivation during dynamic diesel engine operation (2017)

Cylinder deactivation can be implemented at low loads in diesel engines to improve efficiency and aftertreatment thermal management through reductions in pumping work and airflow, respectively. The rate of increase of torque/power during diesel engine transients is limited by the engine’s ability to increase the airflow quickly enough to allow sufficient fuel addition to meet the desired torque/power. The reduced airflow during cylinder deactivation needs to be managed properly so as to not slow the torque/power response. This paper demonstrates that it is possible to operate a diesel engine at low loads in cylinder deactivation without compromising its transient torque/power capabilities, a key finding in enabling the practical implementation of cylinder deactivation in diesel engines.
Traces and Characteristic Classes in Infinite Dimensions (2014)

This paper surveys topological results obtained from characteristic classes built from the two types of traces on the algebra of pseudodifferential operators of nonpositive order. The main results are the construction of a universal $\hat A$-polynomial and Chern character that control the $S^1$-index theorem for all circle actions on a fixed vector bundle over a manifold, and $|π_1({\rm Diff}(M^5))| = \infty$, for ${\rm Diff}(M^5)$ the diffeomorphism group of circle bundles $M^5$ with large first Chern class over projective algebraic Kaehler surfaces.
Blocking eIF5A Modification in Cervical Cancer Cells Alters the Expression of Cancer-Related Genes and Suppresses Cell Proliferation (2013)

Cancer etiology is influenced by alterations in protein synthesis that are not fully understood. In this study, we took a novel approach to investigate the role of the eukaryotic translation initiation factor eIF5A in human cervical cancers, where it is widely overexpressed. eIF5A contains the distinctive amino acid hypusine, which is formed by a posttranslational modification event requiring deoxyhypusine hydroxylase (DOHH), an enzyme that can be inhibited by the drugs ciclopirox and deferiprone. We found that proliferation of cervical cancer cells can be blocked by DOHH inhibition with either of these pharmacologic agents, as well as by RNA interference-mediated silencing of eIF5A, DOHH, or another enzyme in the hypusine pathway. Proteomic and RNA analyses in HeLa cervical cancer cells identified two groups of proteins in addition to eIF5A that were coordinately affected by ciclopirox and deferiprone. Group 1 proteins (Hsp27, NM23, and DJ-1) were downregulated at the translational level, whereas group 2 proteins (TrpRS and PRDX2) were upregulated at the mRNA level. Further investigations confirmed that eIF5A and DOHH are required for Hsp27 expression in cervical cancer cells and for regulation of its key target IκB and hence NF-κB. Our results argue that mature eIF5A controls a translational network of cancer-driving genes, termed the eIF5A regulon, at the levels of mRNA abundance and translation. In coordinating cell proliferation, the eIF5A regulon can be modulated by drugs such as ciclopirox or deferiprone, which might be repositioned to control cancer cell growth.
SUSHI: Sparsity-Based Ultrasound Super-Resolution Hemodynamic Imaging (2018)

Identifying and visualizing vasculature within organs and tumors has major implications in managing cardiovascular diseases and cancer. Contrast-enhanced ultrasound scans detect slow-flowing blood, facilitating noninvasive perfusion measurements. However, their limited spatial resolution prevents the depiction of microvascular structures. Recently, super-localization ultrasonography techniques have surpassed this limit. However, they require long acquisition times of several minutes, preventing the detection of hemodynamic changes. We present a fast super-resolution method that exploits sparsity in the underlying vasculature and statistical independence within the measured signals. Similar to super-localization techniques, this approach improves the spatial resolution by up to an order of magnitude compared to standard scans. Unlike super-localization methods, it requires acquisition times of only tens of milliseconds. We demonstrate a temporal resolution of ~25 Hz, which may enable functional super-resolution imaging deep within the tissue, surpassing the temporal resolution limitations of current super-resolution methods, e.g., in neural imaging. The subsecond acquisitions make our approach robust to motion artifacts, simplifying in vivo use of super-resolution ultrasound.
Removal of thick (&gt;100nm) InGaN layers for optical devices using band-gap-selective photoelectrochemical etching (2004)

We report on band-gap-selective photoelectrochemical (PEC) etching of thick InGaN layers for use in optical devices, such as GaN microdisks, distributed Bragg reflectors, and two-dimensional photonic crystal membranes. Three InGaN sacrificial layer structures are studied: a 300nm InGaN layer, an InGaN∕GaN superlattice, and an InGaN∕InGaN superlattice. Calculated equilibrium band diagrams of the epitaxial structures are used to explain the observed etching behavior. The strong piezoelectric-induced fields within the InGaN sacrificial layers are found to greatly affect carrier confinement and etching behavior. As a demonstration of the etching technique, a free-standing GaN microdisk on an InGaN post is fabricated.
XArch (2008)

Database archiving is important for the retrieval of old versions of a database and for temporal queries over the history of data. We demonstrate XArch, a management system for maintaining, populating, and querying archives of hierarchical data. XArch is based on a nested merge approach that efficiently stores multiple versions of hierarchical data in a compact archive. By merging elements into one data structure, any specific version is retrievable from the archive in a single pass over the data and efficient tracking of object history is possible. XArch implements this approach and extends it in two important ways. First, in order to merge large hierarchical data sets, elements need to be sorted according to their key values. We developed an efficient algorithm for sorting hierarchical data in secondary storage and modified the nested merge algorithm accordingly. Second, we designed and implemented a declarative query language that enables one both to view data from particular versions and to track the history of objects. We demonstrate this using both molecular biology and demographic reference data as examples.
Self-extinguishing polymer–clay nanocomposites (2011)

Thermodynamically, the introduction of a solid particle into a polymer matrix either decreases or increases the interfacial energy, depending on the degree of interaction between polymer chains and solid surfaces. If strong absorption of the polymer chains on the surfaces takes place, the system can be approached through minimization of the interfacial energy, reducing the energy factors. Furthermore, the minimization of interfacial energy can be optimized by increasing the interfacial area of solid particles. Therefore, in order to maximize reduction of the interfacial energy, the solid particles need a large aspect ratio, making both layered silicates and carbon nanotubes (CNTs) good candidates. In particular, layered silicates cation-exchanged with organophilic surfactants can be delaminated into a single silicate sheet in a polymer matrix and remain as nanosheets with aspect ratio 100–1000. Because of this unique delamination of organophilic silicates, polymer–organoclay nanocomposites are of great interest in industry and academia. Numerous research groups have characterized and predicted the microstructures of polymer/organoclay nanocomposites using advanced techniques.
A rolling-shutter distortion-free 3D stacked image sensor with &#x2212;160dB parasitic light sensitivity in-pixel storage node (2013)

Conventional CMOS image sensors widely used in products currently on the market are mainly equipped with a rolling exposure function. This rolling exposure causes so-called “Jell-o effect” distortion when capturing a moving target. CMOS image sensors with a global-shutter function are one of the solutions to avoid this distortion. An in-pixel storage node is required to create a global-shutter CMOS image sensor. A floating diffusion and an additional capacitor can be used as an in-pixel storage node [1,2]. The light sensitivity of the in-pixel storage node is specified by the parasitic light sensitivity (PLS), which is the ratio of the light sensitivity of an in-pixel storage node and the light sensitivity of a photodiode. The PLS should be small enough so that the in-pixel storage is not light-sensitive. Artifacts are captured in an image from bright moving objects during read-out if the PLS is not small enough. The PLS of reported global-shutter CMOS image sensors is around -100dB. That would be small enough to use those image sensors in fields where the light source can be controlled. However, for DSC usage, users can easily encounter scenes with bright objects (e.g. sunlight or car headlights). Even if the in-pixel storage node is light-shielded, it is difficult to perfectly protect the in-pixel storage node from photo-generated carriers, as long as the in-pixel storage node and a photodiode are on the same silicon substrate. Meanwhile, 3D stacking technologies have been introduced for image sensors to give them more functionality and improved performance [3,4]. The reported minimum interconnection pitches for image sensors are over 20μm. These technologies do not fit the smaller pixel pitches of the image sensors in recent DSCs. In this paper, we report a rolling-shutter distortion-free 3D stacked image sensor with an in-pixel storage node of -160dB parasitic light sensitivity. The image sensor virtually achieves a global-shutter function using a 4-times frame-shutter operation. The image sensor has 2 semiconductor substrates, where 1 substrate has a backside-illuminated photodiode array and the other a storage-node array. The image sensor achieves a PLS level of -160dB. The image sensor has 8.6μm pitched interconnections, and an interconnection yield of over 99.9% is achieved.
A High-Throughput Microenvironment for Single-Cell Operations (2003)

This project was conducted as a feasibility study, in preparation for including this work in the forthcoming ''Instrumented Cell'' (IC) Strategic Initiative. The goal of the IC is to study individual cells; the goal of this feasibility study was to determine the best method for isolating large numbers of individual cells in a way that facilitates various types of environmental changes and intracellular measurements. We have the capability to do this with one cell, and sought to expand the number of cells that we could study simultaneously. Our specific goal for this feasibility study was to discover a way to isolate individual cells, and impale them on a nanopipette. This would enable samples to be introduced into and removed from a cell.