gebhart/patrepeval huggingface dataset:
Synthetic Transcription Amplifier System for Orthogonal Control of Gene Expression in Saccharomyces cerevisiae (2016)

This work describes the development and characterization of a modular synthetic expression system that provides a broad range of adjustable and predictable expression levels in S. cerevisiae. The system works as a fixed-gain transcription amplifier, where the input signal is transferred via a synthetic transcription factor (sTF) onto a synthetic promoter, containing a defined core promoter, generating a transcription output signal. The system activation is based on the bacterial LexA-DNA-binding domain, a set of modified, modular LexA-binding sites and a selection of transcription activation domains. We show both experimentally and computationally that the tuning of the system is achieved through the selection of three separate modules, each of which enables an adjustable output signal: 1) the transcription-activation domain of the sTF, 2) the binding-site modules in the output promoter, and 3) the core promoter modules which define the transcription initiation site in the output promoter. The system has a novel bidirectional architecture that enables generation of compact, yet versatile expression modules for multiple genes with highly diversified expression levels ranging from negligible to very strong using one synthetic transcription factor. In contrast to most existing modular gene expression regulation systems, the present system is independent from externally added compounds. Furthermore, the established system was minimally affected by the several tested growth conditions. These features suggest that it can be highly useful in large scale biotechnology applications.
Supplementary Material from A Combined PD-1/C5a Blockade Synergistically Protects against Lung Cancer Growth and Metastasis (2023)

&lt;p&gt;Supplementary Methods: For the characterization of the L-aptamer AON-D21 Supplementary Results: Characterization of the L-aptamer AON-D21 Supplementary References Supplementary Figure S1: Pharmacokinetics of AON-D21 Supplementary Figure S2: Individual follow up of subcutaneous growth and rechallenge Supplementary Figure S3: Splenic leukocyte subpopulations in mice bearing 393P tumors Supplementary Figure S4: Scatter plots of CD8 T cells in treated 393P tumors Supplementary Figure S5: Tumor-infiltrating leukocyte subpopulations in 393P tumors Supplementary Figure S6: Splenic leukocyte subpopulations in mice bearing LLC tumors Supplementary Figure S7: Tumor-infiltrating leukocyte subpopulations and IL2 in LLC tumors Supplementary Figure S8: Flow cytometry gating strategy Supplementary Table S1: Rate constants and dissociation constant of AON-D21 Supplementary Table S2: mRNA expression of immune-related molecules in 393P tumors&lt;/p&gt;
Porphyrin molecular tweezers for fullerenes (2011)

Facing zinc bisporphyrins connected with diethanoanthracene and diethanonaphthacene (syn-1 and syn-2) are prepared by double [3+1] porphyrin synthesis of tripyrranedicarbaldehyde with syn-5,11-dimethoxy-4,6,10,12-tetrahydro-4,12;6,10-diethanoanthracene[2,3-c;7,8-c′]dipyrrole and syn-4,7,11,14- tetrahydro-4,14;7,11-diethanonaphthacene[2,3-c;8,9-c′]dipyrrole. These bisporphyrins contain large clefts with different sizes capable for complexation with fullerenes such as C 60 and C 70 . These designed syn-oriented bisporphyrins serve as effective and selective molecular tweezers for C 70 . Binding affinity of the zinc bisporphyrins, namely, syn-1 and syn-2, towards C 60 and C 70 in solution is determined by employing UV-vis spectrophotometric technique. Values of binding constants (K) in toluene for the non-covalent complexes of syn-1 with C 60 and C 70 are estimated to be 3.1(4) × 10 4 and 5.0(2) × 10 5 M -1 , respectively, and those of syn-2 with C 60 and C 70 are enumerated to be 2.1(4) × 10 4 and 1.70(13) × 10 5 M -1 , respectively. Binding of C 60 and C 70 in the clefts of syn-1 and syn-2 is clearly demonstrated by the crystal structures of C 60 /syn-1, C 70 /syn-1, C 60 /syn-2, and C 70 /syn-2 complexes. In the crystal structures with C 70 , the directions of the long axis of C 70 are found to be quite different: in the case of C 70 /syn-1 complex the axis lies perpendicularly to the line connecting two zinc atoms; however, for the C 70 /syn-2 complex, the axis occupies in-plane to the same line. Both the clefts of syn-1 and syn-2 are induced to fit the included fullerenes by domed out-of-plane distortion of porphyrin rings. Moreover, the bicyclo[2.2.2]octadiene moieties of syn-1 are widened by complexation with the fullerenes, while the same moieties of syn-2 are narrowed by the complexation. Therefore, syn-1 catches the fullerenes at the shallow part of the cleft. On the other hand, syn-2 catches the fullerenes at the bottom part of the cleft. NMR experiments of the complexes in THF-d 8 also support these orientations even in solution.
Molecular pharmacology of serotonin receptors (1994)

The serotonin system has long been thought to play a role at several steps in the cycle of alcohol abuse. Initial motivation may be triggered by anxiety, which may exhibit a serotonergic component (5-HT1A receptor). Alcohol can potentiate the opening of 5-HT3 receptor ion channels, and agents which elevate serotonergic tone, including serotonergic agonists, uptake inhibitors and releasers, have shown promise in assisting with recovery from alcoholism. In this review, recent advances in serotonin receptor research are presented, with a special emphasis on the impact and interpretation of molecular biological data. Genetic and pharmacological concepts of receptor subtypes are reviewed and related to a new classification system for the 14 currently recognized subtypes of serotonin receptors. The current and likely future impact on drug design of the molecular approach to serotonin receptors is discussed. Finally, the question of why there are so many serotonin receptor subtypes is examined, along with possible roles of multiple G protein and second messenger pathways, and their effect on conserved domains of these receptor proteins.
Mechanistic Understanding of Cr Poisoning on La0.6Sr0.4Co0.2Fe0.8O3-δ (LSCF) (2009)

The effects of Cr poisoning on the catalytic activity of La0.6Sr0.4Co0.2Fe0.8O3-δ (LSCF) and the poisoning mechanism was investigated. AC impedance spectroscopy and temperature programmed isotopic exchange (TPX) were consistent in proving poisoning mainly degraded the surface catalytic activity as a passive layer evolved on the surface or near-surface region. The formation of small particles was clearly observed in scanning electron microscopy when LSCF was heat treated in the presence of Crofer22APU. Low angle X-ray diffraction identified these were SrCrO4. As a result of Sr diffusion to form SrCrO4 particles, it was found that a Sr-deficient phase was formed and a phase transition from rhombohedral to cubic perovskite occurred in the near surface region. While previous Cr poisoning studies on LSCF mostly emphasized the effects of SrCrO4 formation, the Sr deficient surface layer also significantly degrades the catalytic activity of LSCF due to reduction of oxygen vacancies and surface Co/Fe concentration.
Distributed Intelligent Algorithm for Interdependent Electrified Transportation and Power Networks (2019)

Plug-in Electric Vehicles (PEVs) play a pivotal role in transportation electrification. The flexible nature of PEVs' charging demand can be utilized for reducing charging cost as well as optimizing the operating cost of power and transportation networks. Utilizing charging flexibility of geographically spread PEVs requires design and implementation of efficient optimization algorithms. To this end, we propose a fully distributed algorithm to solve the PEVs' Cooperative Charging with Power constraints (PEV-CCP). Our solution considers the electric power limits that originate from physical characteristics of charging station, such as on-site transformer capacity limit, and allows for containing charging burden of PEVs on the electric distribution network. Our approach also enables plug-and-play and valley-filling capabilities of PEV charge scheduling. It distributes computation among agents (PEVs) to solve the PEV-CCP problem in a distributed fashion through an iterative interaction between neighboring agents. The structure of each agent's update functions ensures an agreement on a price signal while enforcing individual PEV constraints. In addition to converging towards the globally-optimum solution, our algorithm ensures the feasibility of each PEV's decision at each iteration. We have tested performance of the proposed approach using a fleet of PEVs. Simulation results verify the plug-and-play capability of the proposed approach by efficiently tracking the changes in terms of arrival/depart of PEVs.
Subharmonic Excitation for Electrically Actuated Microbeams (2005)

We present analysis of the global dynamics of electrically actuated microbeams under subharmonic excitation. The microbeams are excited by a DC electrostatic force and an AC harmonic force with a frequency tuned near twice their fundamental natural frequencies. We show that the dynamic pull-in instability can occur in this case for an electric load much lower than that predicted with static analysis and the same order-of-magnitude as that predicted in the case of primary-resonance excitation. We show that, once the subharmonic resonance is activated, all frequency-response curves reach pull-in, regardless of the magnitude of the AC forcing. Our results show a limited influence of the quality factor on the frequency response. This result and the fact that the frequency-response curves have very steep passband-to-stopband transitions make the combination of a DC voltage and a subhormonic of order one-half a promising candidate for designing improved high-sensitive RF MEMS filters.
Watermarking integer linear programming solutions (2002)

Linear programming (LP) in its many forms has proven to be an indispensable tool for expressing and solving optimization problems in numerous domains. We propose the first set of generic watermarking techniques for integer-LP (ILP). The proof of authorship by watermarking is achieved by introducing additional constraints to limit the solution space and can be used as effective means of intellectual property protection (IPP) and authentication. We classify and analyze the types of constraints in the ILP watermarking domain and show how ILP formulations provide more degrees of freedom for embedding signatures than other existing approaches. To demonstrate the effectiveness of the proposed ILP watermarking techniques, the generic discussion is further concretized using two examples, namely satisfiability and scheduling.
On the mechanism of myocardial edema contrast in T2-STIR images (2010)

Acute myocardial infarcts (AMI) are typically discriminated with T2-STIR imaging [1], albeit with limited specificity [2]. Guided by the association that T2-STIR images identify AMI territories on the basis of edema-related T2 changes, even some of the recently proposed improvements [2,3] have relied on preferential sensitization of magnetization to T2-weighting. However, whether T2-STIR imaging itself may also be sensitive to other sources of contrast have not been fully investigated.
Doherty PAs for 5G Massive MIMO: Energy-Efficient Integrated DPA MMICs for Sub-6-GHz and mm-Wave 5G Massive MIMO Systems (2020)

To accommodate growing user demand for faster data rates and extensive connectivity, modern wireless communication systems must evolve to support a sharply increasing number of subscribers, all requesting service at the same time. This trend encourages the broad application of multiple input/multiple output (MIMO) systems. In fact, MIMO techniques can increase data rates, coverage of service areas, and communication reliability without additional RFs. In recent proposals for 5G systems, the required separate RF chains in massive MIMO RF front ends can reach up to 256, with bandwidths of up to 800 MHz per RF chain [1], [2]. Massive MIMO is a critical technology that helps significantly in increasing network capacity and spectral efficiency, while reducing wireless network interference, ultimately improving the end-user experience.
CDNA microarray gene expression analysis of B-cell chronic lymphocytic leukemia proposes potential new prognostic markers involved in lymphocyte trafficking (2001)

Human cancer is characterized by complex molecular perturbations leading to variable clinical behavior, often even in single-disease entities. We performed a feasibility study systematically comparing large-scale gene expression profiles with clinical features in human B-cell chronic lymphocytic leukemia (B-CLL). cDNA microarrays were employed to determine the expression levels of 1,024 selected genes in 54 peripheral blood lymphocyte samples obtained from patients with B-CLL. Statistical analyses were applied to correlate the expression profiles with a number of clinical parameters including patient survival and disease staging. We were able to identify genes whose expression levels significantly correlated with patient survival and/or with clinical staging. Most of these genes code either for cell adhesion molecules (L-selectin, integrin-beta2) or for factors inducing cell adhesion molecules (IL-1beta, IL-8, EGR1), suggesting that prognosis of this disease may be related to a defect in lymphocyte trafficking. This report demonstrates the feasibility of a systematic integration of large-scale gene expression profiles with clinical data as a general approach for dissecting human diseases.
Biocatalytic resolution of tertiary .alpha.-substituted carboxylic acid esters: efficient preparation of a quaternary asymmetric carbon center (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTBiocatalytic resolution of tertiary .alpha.-substituted carboxylic acid esters: efficient preparation of a quaternary asymmetric carbon centerChristopher Yee, Todd A. Blythe, Thomas J. McNabb, and Alan E. WaltsCite this: J. Org. Chem. 1992, 57, 13, 3525–3527Publication Date (Print):June 1, 1992Publication History Published online1 May 2002Published inissue 1 June 1992https://doi.org/10.1021/jo00039a004RIGHTS & PERMISSIONSArticle Views255Altmetric-Citations36LEARN 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 InReddit PDF (371 KB) Get e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Measurement of Slow Diffusion Coefficients of Molecules with Arbitrary Scalar Couplings via Long-Lived Spin States (2008)

New experiments are described for the determination of very slow diffusion constants by nuclear magnetic resonance (NMR) using long-lived (singlet) states. These experiments are suitable for molecules or conformations featuring a wide range of J-couplings.
Energy-Efficient Beam Coordination Strategies With Rate-Dependent Processing Power (2017)

This paper proposes energy-efficient coordinated beamforming strategies for multicell multiuser multiple-input single-output system. We consider a practical power consumption model, where part of the consumed power depends on the base station or user specific data rates due to coding, decoding, and backhaul. This is different from the existing approaches where the base station power consumption has been assumed to be a convex or linear function of the transmit powers. Two optimization criteria are considered, namely network energy efficiency maximization and weighted sum energy efficiency maximization. We develop successive convex approximation-based algorithms to tackle these difficult nonconvex problems. We further propose decentralized implementations for the considered problems, in which base stations perform parallel and distributed computation based on local channel state information and limited backhaul information exchange. The decentralized approaches admit closed-form solutions and can be implemented without invoking a generic external convex solver. We also show an example of the pilot contamination effect on the energy efficiency using a heuristic pilot allocation strategy. The numerical results are provided to demonstrate that the rate dependent power consumption has a large impact on the system energy efficiency, and, thus, has to be taken into account when devising energy-efficient transmission strategies. The significant gains of the proposed algorithms over the conventional low-complexity beamforming algorithms are also illustrated.
Optimizing 2 mode fibers with Aeff of 170µm2 for LP01 mode and studying a possibility of realizing endlessly 2 mode operation using holey fibers (2012)

Two mode fibers for mode division multiplexing were optimized and fabricated to realize Aeff of 170µm2 for fundamental mode. A possibility of realizing endlessly 2 mode operation using holey fibers will be also demonstrated.
Impact of Metabolism in on T-Cell Differentiation and Function and Cross Talk with Tumor Microenvironment (2017)

The immune system and metabolism are highly integrated and multilevel interactions between metabolic system and T lymphocyte signaling and fate exist. Accumulating evidence indicates that the regulation of nutrient uptake and utilization in T cells is critically important for the control of their differentiation and manipulating metabolic pathways in these cells can shape their function and survival. This review will discuss some potential cell metabolism pathways involved in shaping T lymphocyte function and differentiation. It will also describe show subsets of T cells have specific metabolic requirements and signaling pathways that contribute to their respective function. Examples showing the apparent similarity between cancer cell metabolism and T cells during activation are illustrated and finally some mechanisms being used by tumor microenvironment to orchestrate T-cell metabolic dysregulation and the subsequent emergence of immune suppression are discussed. We believe that targeting T-cell metabolism may provide an additional opportunity to manipulate T-cell function in the development of novel therapeutics.
Pulmonary Fibrosis, Bone Marrow Failure, and Telomerase Mutation (2012)

ning. Patients assigned to CAC had improvements in blood pressure (P = 0.02), cholesterol levels (P = 0.04), waist circumference (P
Vitreous levels of soluble vascular endothelial growth factor receptor (VEGFR)-1 in eyes with vitreoretinal diseases (2011)

Vitreous concentrations of sVEGFR-1 increase with advancing age and are associated with quiescent rather than active PDR even after adjustment for age.
Comparison of regional lung perfusion response on longitudinal MAA SPECT/CT in lung cancer patients treated with and without functional tissue-avoidance radiation therapy (2019)

This novel preliminary study reports differences in dose-response relationships between patients receiving functional lung avoidance radiation therapy (FLARE-RT) and those receiving conventionally planned radiation therapy (LUNG-RT). Following further validation and testing of these effects in larger patient populations, individualized estimation of regional lung perfusion dose-response may help refine future risk-adaptive strategies to minimize lung function deficits and toxicity incidence.
Lockup of a Client Object Cache and How to Avoid It (Student Paper) (1993)

I present the problem of client object cache lockup in a distributed object-oriented database system where storage is recovered by garbage collection. If garbage collection is augmented with the ability to discard reachable unmodified versions of persistent objects, cache lockup is greatly reduced. I outline some remaining questions about this technique for managing an object cache.
Synthesis of Fused Imidazo Azepine Derivatives by Sequential van Leusen/Enyne Metathesis Reactions. (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Curses or Cures: A Review of the Numerous Benefits Versus the Biosecurity Concerns of Conotoxin Research (2020)

Conotoxins form a diverse group of peptide toxins found in the venom of predatory marine cone snails. Decades of conotoxin research have provided numerous measurable scientific and societal benefits. These include their use as a drug, diagnostic agent, drug leads, and research tools in neuroscience, pharmacology, biochemistry, structural biology, and molecular evolution. Human envenomations by cone snails are rare but can be fatal. Death by envenomation is likely caused by a small set of toxins that induce muscle paralysis of the diaphragm, resulting in respiratory arrest. The potency of these toxins led to concerns regarding the potential development and use of conotoxins as biological weapons. To address this, various regulatory measures have been introduced that limit the use and access of conotoxins within the research community. Some of these regulations apply to all of the ≈200,000 conotoxins predicted to exist in nature of which less than 0.05% are estimated to have any significant toxicity in humans. In this review we provide an overview of the many benefits of conotoxin research, and contrast these to the perceived biosecurity concerns of conotoxins and research thereof.
Opportunity Detection for OFDMA Systems with Timing Misalignment (2008)

Accurate detection of spectrum opportunities within the frequency band of an orthogonal frequency division multiple access (OFDMA) system is a critical requirement for the realization of a coexisting cognitive radio. In this paper, we analyze the opportunity detection performances of energy detection and ESPRIT algorithms in the presence of timing misalignments in uplink (UL) OFDMA. For the energy detector, the statistics of subcarrier power are derived, and the accuracy of these derivations is verified through simulations. The feasibility of opportunity detection in an asynchronous UL-OFDMA system is proven. Also, it is shown that energy detection has a considerably better performance than the ESPRIT algorithm especially when the subcarrier assignments change frequently.
Spectral Clustering of Shape and Probability Prior Models for Automatic Prostate Segmentation in Ultrasound Images (2012)

International audience
Broadcasting in massive MIMO using OSTBC with reduced dimension (2015)

An analysis of broadcasting in massive MIMO (multiple-input and multiple-output) systems with a limited coherence interval is presented. When broadcasting common information, such as control signals, the base station does not have channel state information to the terminals. We propose that the base station broadcasts this common information using a low dimensional orthogonal space-time block code (OSTBC). This code is mapped onto the large antenna array with the use of a dimension reducing matrix, effectively “shrinking” the channel. The terminal can estimate the effective channel and decode the information, even when the coherence interval is short compared to the number of base station antennas. Different OSTBCs are compared in terms of outage capacity in practical scenarios using estimated CSI. In particular, the trade-off between diversity and rate, when little or no time/frequency diversity is available, is investigated.