gebhart/patrepeval huggingface dataset:
Combinatorial promoter design for engineering noisy gene expression (2007)

Understanding the behavior of basic biomolecular components as parts of larger systems is one of the goals of the developing field of synthetic biology. A multidisciplinary approach, involving mathematical and computational modeling in parallel with experimentation, is often crucial for gaining such insights and improving the efficiency of artificial gene network design. Here we used such an approach and developed a combinatorial promoter design strategy to characterize how the position and multiplicity of tetO(2) operator sites within the GAL1 promoter affect gene expression levels and gene expression noise in Saccharomyces cerevisiae. We observed stronger transcriptional repression and higher gene expression noise as a single operator site was moved closer to the TATA box, whereas for multiple operator-containing promoters, we found that the position and number of operator sites together determined the dose-response curve and gene expression noise. We developed a generic computational model that captured the experimentally observed differences for each of the promoters, and more detailed models to successively predict the behavior of multiple operator-containing promoters from single operator-containing promoters. Our results suggest that the independent binding of single repressors is not sufficient to explain the more complex behavior of the multiple operator-containing promoters. Taken together, our findings highlight the importance of joint experimental-computational efforts and some of the challenges of using a bottom-up approach based on well characterized, isolated biomolecular components for predicting the behavior of complex, synthetic gene networks, e.g., the whole can be different from the sum of its parts.
Novel Synthesis of Indoles via Palladium-Catalyzed Reductive N-Heterocyclization of <i>o</i>-Nitrostyrene Derivatives (1992)

Abstract Indole derivatives were readily prepared from the reductive N-heterocyclization of o-nitrostyrene derivatives in the presence of a catalytic amount of PdCl2(PPh3)2–SnCl2 under carbon monoxide pressure (20 kg/cm2) at 100 °C for 16 h. With o-nitrostilbene, 2-phenylindole was obtained in 75% yield.
P‐37: Room Temperature Top‐Gate Self‐Aligned Amorphous InGaZnO TFTs Fabricated on Colorless Polyimide Substrate (2010)

Abstract Room temperature top‐gate self‐aligned amorphous InGaZnO TFTs were successfully fabricated on colorless polyimide plastic substrates for the first time. All these thin films were deposited by sputtering system at room temperature. The maximum field‐effect mobility is 48.5 cm 2 /V‐s, the subthreshold swing is 0.1 V/decade, and the threshold voltage is −1V.
Inter-Cell Interference Coordination in OFDMA Networks: A Novel Approach Based on Integer Programming (2010)

We study a dynamic inter-cell interference coordination scheme formulated using a novel binary integer linear programming optimization technique. The scheme aims to maximize utility, where different utility measures have been defined to model varying levels of user fairness. The formulated problem is decomposed into a number of smaller sub-problems and solved iteratively to ease the computational complexity. We observe the cell-edge and sector throughput as well as user fairness and compare with a reference scheme, where interference coordination is not used. It is observed that the proposed scheme always outperforms the reference scheme in terms of cell-edge and sector throughput as well as in fairness.
Convergent Synthesis of the Polyene Macrolide (-)-Roxaticin (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTConvergent Synthesis of the Polyene Macrolide (-)-RoxaticinScott D. Rychnovsky and Rebecca C. HoyeCite this: J. Am. Chem. Soc. 1994, 116, 5, 1753–1765Publication Date (Print):March 1, 1994Publication History Published online1 May 2002Published inissue 1 March 1994https://pubs.acs.org/doi/10.1021/ja00084a017https://doi.org/10.1021/ja00084a017research-articleACS PublicationsRequest reuse permissionsArticle Views1512Altmetric-Citations89LEARN 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 (2)»Supporting Information Supporting Information Get e-Alerts
Beat-to-beat heart rate estimation fusing multimodal video and sensor data (2015)

Coverage and accuracy of unobtrusively measured biosignals are generally relatively low compared to clinical modalities. This can be improved by exploiting redundancies in multiple channels with methods of sensor fusion. In this paper, we demonstrate that two modalities, skin color variation and head motion, can be extracted from the video stream recorded with a webcam. Using a Bayesian approach, these signals are fused with a ballistocardiographic signal obtained from the seat of a chair with a mean absolute beat-to-beat estimation error below 25 milliseconds and an average coverage above 90% compared to an ECG reference.
Security Extension for OSPFv2 When Using Manual Key Management (2015)

The current OSPFv2 cryptographic authentication mechanism as defined
in RFCs 2328 and 5709 is vulnerable to both inter-session and intra-
session replay attacks when using manual keying. Additionally, the
existing cryptographic authentication mechanism does not cover the IP
header. This omission can be exploited to carry out various types of
attacks. This document defines changes to the authentication sequence
number mechanism that will protect OSPFv2 from both inter-session and
intra- session replay attacks when using manual keys for securing
OSPFv2 protocol packets. Additionally, we also describe some changes
in the cryptographic hash computation that will eliminate attacks
resulting from OSPFv2 not protecting the IP header.
Optical properties of Ag conic helical nanostructures (2012)

The optical properties of an Ag conic helical nanostructure have been studied and compared with a similar corresponding normal helix by calculating the extinction spectra and the near electric field distributions. For most polarizations of the incident light, a number of resonance peaks appear in the extinction spectra of the conic helix, making the spectra more broadband. The peaks are originated from different radii of the conic helix pitches. The smaller side of the conic is more related to the optical properties at low wavelengths and the larger side to the high wavelength.
Ground Transportation for the 21st Century (1999)

This book reviews the status of vehicles powered by electric batteries, fuel cells and alternative fuels. The book discusses the development of hybrid electric vehicles and high-efficiency gasoline and diesel engines and provides an overview of public transportation technologies and asses the potential of telecommuting and intelligent transportation. A great deal of research on vehicle propulsion and transportation systems is in progress. This book presents a status report at the close of this century. The findings and conclusions should be reevaluated periodically to incorporate the results of research and development efforts that are currently under way.
Layer-by-Layer Assembly of Aquaporin Z-Incorporated Biomimetic Membranes for Water Purification (2015)

We fabricated a biomimetic nanofiltration (NF) membrane by immobilizing an Aquaporin Z (AqpZ)-incorporated supported lipid bilayer (SLB) on a layer-by-layer (LbL) complex polyelectrolyte membrane to achieve excellent permeability and salt rejection with a high stability. The polyelectrolyte membranes were prepared by LbL assembly of poly(ethylenimine) (PEI) with positive charges and poly(sodium 4-styrenesulfonate) (PSS) with negative charges alternately on a porous hydrolyzed polyacrylonitrile (H-PAN) substrate. AqpZ-incorporated 1,2-dioleloyl-sn-glycero-3-phosphocholine (DOPC)/1,2-dioleoyl-3-trimethylammo-nium-propane (chloride salt) (DOTAP) vesicles with positive charges were deposited on the H-PAN/PEI/PSS polyelectrolytes membrane surface. The resulting biomimetic membrane exhibited a high flux of 22 L·m(-2)·h(-1) (LMH), excellent MgCl2 rejection of ∼97% and NaCl rejection of ∼75% under an operation pressure of 0.4 MPa. Due to the attractive electrostatic interaction between SLB and the polyelectrolyte membrane, the biomimetic membrane showed satisfactory stability and durability as well as stable NF flux and rejection for at least 36 h. In addition, the AqpZ-containing biomimetic membrane was immersed in a 0.24 mM (critical micellar concentration, CMC) Triton X-100 solution for 5 min. The flux and rejection were slightly influenced by the Triton X-100 treatment. The current investigation demonstrated that the AqpZ-incorporated biomimetic membranes fabricated by the LbL method led to excellent separation performances and robust structures that withstand a high operation pressure for a relatively long time.
A New Newton's Method with Diagonal Jacobian Approximation for Systems of Nonlinear Equations (2010)

Problem statement: The major weaknesses of Newton method for nonlinear equations entail computation of Jacobian matrix and solving systems of n linear equations in each of the iterations. Approach: In some extent function derivatives are quit costly and Jacobian is computationally expensive which requires evaluation (storage) of nn matrix in every iteration. Results: This storage requirement became unrealistic when n becomes large. We proposed a new method that approximates Jacobian into diagonal matrix which aims at reducing the storage requirement, computational cost and CPU time, as well as avoiding solving n linear equations in each iterations. Conclusion/Recommendations: The proposed method is significantly cheaper than Newton's method and very much faster than fixed Newton's method also suitable for small, medium and large scale nonlinear systems with dense or sparse Jacobian. Numerical experiments were carried out which shows that, the proposed method is very encouraging.
Automatic segmentation of heart sound signals using hidden markov models (2005)

The monitoring of respiration rates using impedance plethysmography is often confused by cardiac activity. This paper proposes using the phonocardiogram as an alternative, since the process of respiration affects heart sounds. As part of this research, a technique is developed to segment heart sounds into its component segments, using hidden Markov models. The heart sounds data is preprocessed into feature vectors, where the feature vectors are comprised of the average Shannon energy of the heart sound signal, the delta Shannon energy, and the delta-delta Shannon energy. The performance of the segmentation system is validated using eight-fold cross-validation
Effects of dietary fat on androgen secretion and metabolism. (2006)

In humans and animals, food composition, especially dietary fat, affects androgen secretion and metabolism. On the other hand, disturbances of sex steroid metabolism play an important role in the etiology of hormone-related cancers. In this report the roles of dietary fat, its quantity, fatty acid composition and feeding period on androgens metabolism was described. In conclusion, it should be stated that the amount of dietary fat, and its composition, (i.e. the content of individual fatty acids and/or their groups), as well as the period during which the nutrient is fed to animals affect significantly the secretion and metabolism of androgens.
Fuzzy systems as universal approximators (1994)

An additive fuzzy system can uniformly approximate any real continuous function on a compact domain to any degree of accuracy. An additive fuzzy system approximates the function by covering its graph with fuzzy patches in the input-output state space and averaging patches that overlap. The fuzzy system computes a conditional expectation E|Y|X| if we view the fuzzy sets as random sets. Each fuzzy rule defines a fuzzy patch and connects commonsense knowledge with state-space geometry. Neural or statistical clustering systems can approximate the unknown fuzzy patches from training data. These adaptive fuzzy systems approximate a function at two levels. At the local level the neural system approximates and tunes the fuzzy rules. At the global level the rules or patches approximate the function.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Highly efficient asymmetric reduction of .alpha.-tertiary alkyl ketones with diisopinocampheylchloroborane (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHighly efficient asymmetric reduction of .alpha.-tertiary alkyl ketones with diisopinocampheylchloroboraneHerbert C. Brown, J. Chandrasekharan, and P. V. RamachandranCite this: J. Org. Chem. 1986, 51, 17, 3394–3396Publication Date (Print):August 1, 1986Publication History Published online1 May 2002Published inissue 1 August 1986https://pubs.acs.org/doi/10.1021/jo00367a037https://doi.org/10.1021/jo00367a037research-articleACS PublicationsRequest reuse permissionsArticle Views576Altmetric-Citations53LEARN 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
Anti-CD3 + interleukin-2 stimulation of marrow and blood: comparison of proliferation and cytotoxicity (1992)

The proliferation and in vitro cytolytic activity of interleukin-2 (IL- 2)-activated and anti-CD3 + IL-2-stimulated marrow mononuclear cells (MMC) and peripheral blood mononuclear cells (PBMC) were studied. Samples from 8 normal donors, 15 patients with acute lymphoblastic leukemia (ALL), and 7 patients with non-Hodgkin's lymphoma (NHL) in remission were cultured in IL-2 (100 U/mL) or IL-2 (100 U/mL) plus anti- CD3 (10 ng/mL). MMC as well as PBMC samples demonstrated significant synergy between IL-2 and anti-CD3 in the promotion of proliferation as measured by 3H thymidine incorporation on day 5 (P less than .001) or fold increase in cell number on day 14. Cryopreserved marrow specimens had equally rapid proliferation as fresh MMC when cultured in the presence of anti-CD3 + IL-2. Anti-CD3 concentrations of 3, 11, 33, and 100 ng/mL augmented proliferation similarly in the presence of IL-2 (0.1 to 100 U/mL). Mean fold increases in cell number of both marrow- and blood-derived cultures after 14 days were significantly higher for anti-CD3 + IL-2-stimulated cultures compared with cultures stimulated with IL-2 only (50- to 200-fold increase in cell number; P = .01). Comparison of remission MMC and PBMC from ALL and NHL patients with normal controls showed equivalent growth rates of activated cultures at 7, 14, and 21 days. Marrow purging with immunotoxin anti-CD19 pokeweed antiviral protein plus 4HC had no significant effect on proliferation of anti-CD3 + IL-2-stimulated MMC cultures in patients with ALL. Cytolytic activity of IL-2- and IL-2 + anti-CD3-activated PBMC and MMC cultures was assessed in 51Cr release assays using K562 (natural killer ([NK]-sensitive), Daudi (Burkitt's lymphoma-, NK-resistant), and Nalm-6 (ALL-, lymphokine-activated killer [LAK]-resistant) cell lines and cryopreserved ALL blasts. Cytolytic activity on a per-cell basis (percent cytotoxicity at an effector:target ratio of 30:1) was similar in IL-2-activated PBMC- and MMC-derived cultures from ALL patients. MMC activated with anti-CD3 plus IL-2 killed Daudi significantly less well than IL-2-activated cultures on days 12 and 19 (P = .03); no significant differences were observed in lysis of LAK-resistant Nalm-6 or cryopreserved ALL blast targets. Dose response of anti-CD3 augmentation of Daudi and Nalm-6 killing was different in IL-2- and IL- 2 + anti-CD3-stimulated cultures.
Sterols. LIII. The Structure of the Side Chain of Sarsasapogenin (1939)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSterols. LIII. The Structure of the Side Chain of SarsasapogeninRussell E. Marker and Ewald. RohrmannCite this: J. Am. Chem. Soc. 1939, 61, 4, 846–851Publication Date (Print):April 1, 1939Publication History Published online1 May 2002Published inissue 1 April 1939https://pubs.acs.org/doi/10.1021/ja01873a020https://doi.org/10.1021/ja01873a020research-articleACS PublicationsRequest reuse permissionsArticle Views243Altmetric-Citations57LEARN 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
A multivariate approach to QSAR (1986)

Quantitative structure-activity relationships (OSAR) constitute empirical analogy models connecting chemical structure and biological activity. The analogy approach to QSAR assume that the factors important in the biological system also are contained in chemical model systems. The development of a QSAR can be divided into subproblems: 1. to quantify chemical structure in terms of latent variables expressing analogy, 2. to design test series of compounds, 3. to measure biological activity and 4. to construct a mathematical model connecting chemical structure and biological activity. In this thesis it is proposed that many possibly relevant descriptors should be considered simultaneously in order to efficiently capture the unknown factors inherent in the descriptors. The importance of multivariately and multipositionally varied test series is discussed. Multivariate projection methods such as PCA and PLS are shown to be appropriate far QSAR and to closely correspond to the analogy assumption. The multivariate analogy approach is applied to a beta- adrenergic agents, b haloalkanes, c halogenated ethyl methyl ethers and d four different families of peptides.
An efficient algorithm for exhaustive template matching based on normalized cross correlation (2004)

This work proposes a novel technique aimed at improving the performance of exhaustive template matching based on the normalized cross correlation (NCC). An effective sufficient condition, capable of rapidly pruning those match candidates that could not provide a better cross correlation score with respect to the current best candidate, can be obtained exploiting an upper bound of the NCC function. This upper bound relies on partial evaluation of the crosscorrelation and can be computed efficiently, yielding a significant reduction of operations compared to the NCC function and allows for reducing the overall number of operations required to carry out exhaustive searches. However, the bounded partial correlation (BPC) algorithm turns out to be significantly data dependent. In this paper we propose a novel algorithm that improves the overall performance of BPC thanks to the deployment of a more selective sufficient condition which allows for rendering the algorithm significantly less data dependent. Experimental results with real images and actual CPU time are reported.
Kraft Lignin-Based Rigid Polyurethane Foam (2012)

Abstract Kraft pine lignin was derivatized to a liquid polyol through oxypropylation. The resulting polyol was characterized by GPC, FT-IR, H1, C13, and P31 NMR and was compared to commercial polyols in view of the mechanical property of the corresponding rigid polyurethane foams for the first time. A series of lignin-based PU was synthesized by replacing varying weight percentages of the amount of sucrose polyol and glycerol polyol, two commonly used commercial polyols employed in the control foam preparation. All foams had a low density of ∼30 Kg m−3 and showed typical linkages of PU in the FT-IR spectra. The diameter of closed-cells was ∼650 μm for most of the foams as revealed by SEM images. The optimal compressive property of rigid PU foams was obtained using lignin polyol without the addition of any other commercial polyols primarily attributed to the rigidity of lignin aromatic structure and the high functionality of lignin hydroxyl groups.
Rapid Loss of Vertebral Mineral Density after Renal Transplantation (1991)

Osteopenia associated with renal transplantation remains a problem in the cyclosporine era. The loss of vertebral bone in our subjects was due to an imbalance in bone remodeling consistent with a toxic effect of glucocorticoids.