gebhart/patrepeval huggingface dataset:
Algorithmic co-optimization of genetic constructs and growth conditions: application to 6-ACA, a potential nylon-6 precursor (2015)

Optimizing bio-production involves strain and process improvements performed as discrete steps. However, environment impacts genotype and a strain that is optimal under one set of conditions may not be under different conditions. We present a methodology to simultaneously vary genetic and process factors, so that both can be guided by design of experiments (DOE). Advances in DNA assembly and gene insulation facilitate this approach by accelerating multi-gene pathway construction and the statistical interpretation of screening data. This is applied to a 6-aminocaproic acid (6-ACA) pathway in Escherichia coli consisting of six heterologous enzymes. A 32-member fraction factorial library is designed that simultaneously perturbs expression and media composition. This is compared to a 64-member full factorial library just varying expression (0.64 Mb of DNA assembly). Statistical analysis of the screening data from these libraries leads to different predictions as to whether the expression of enzymes needs to increase or decrease. Therefore, if genotype and media were varied separately this would lead to a suboptimal combination. This is applied to the design of a strain and media composition that increases 6-ACA from 9 to 48 mg/l in a single optimization step. This work introduces a generalizable platform to co-optimize genetic and non-genetic factors.
T Cell Receptor Immunotherapy Drives Human Immunodeficiency Virus Evolution in Humanized Mice (2019)

Summary T cell receptor mediated immunotherapy using engineered Hematopoietic Stem/Progenitor Cells leads to durable partial suppression of HIV in humanized mice. Sustained viral suppression is accompanied by viral evolution under selection pressure. This study highlights the potential for TCR immunotherapy and the need to target multiple epitopes. Abstract Effective CD8+ T cell responses targeted to the KK10 epitope of HIV presented by HLA-B*27:05, a protective HLA allele, correlate with the ability to control infection without antiretroviral therapy (ART). Here, we report an immunotherapy approach using two B*27:05-KK10-specific T Cell Receptors (TCRs) isolated from HIV controllers. Immunocompromised mice engrafted with human Hematopoietic Stem/Progenitor Cells (HSPCs) encoding for the TCRs showed differentiation into functionally active engineered T cells. Following infection with HIV, both TCRs showed sustained, albeit modest, viral suppression over 32 weeks, accompanied by a concomitant increase in CD4+ T cells. Sequencing of viral quasi-species from the plasma of infected mice demonstrated clear evidence for viral evolution under selection pressure from the TCRs. The most commonly observed mutation in the KK10 epitope was L6M, which preserved viral fitness but showed attenuated recognition by the TCRs. These studies show that TCR-immunotherapy was able to suppress HIV infection long-term while driving HIV evolution in humanized mice.
Potassium channel opening drugs prevent cardioplegic solution-induced intracellular Ca2+ loading in cardiac cells. (1996)

Clinical Pharmacology & Therapeutics (1996) 59, 175–175; doi: 10.1038/sj.clpt.1996.198
Multilayer Line Micropatterning Using Convective Self-Assembly in Microfluidic Channels (2003)

A new approach to create layer-by-layer assembled multilayer ultrathin films with well-defined micropatterns in a short process time is introduced. To achieve such micropatterns with high line resolution in organic multilayer films, microfluidic channels were combined with the convective self-assembly process employing both hydrogen bonding and electrostatic intermolecular interactions. The channels were initially filled with polymer solution by capillary pressure, and the residual solution was then removed by the spinning process. Micropatterns with clear line boundaries were obtained, and small ridges were also observed at the edges of the patterned lines.
Post‐column derivatization in narrow‐bore capillaries for the analysis of amino acids and proteins by capillary electrophoresis with fluorescence detection (1994)

Abstract The construction and performance of a post‐column reactor for capillary electrophoresis with laser‐induced fluorescence detection in 10 μm i.d. capillaries is described. The post‐column reactor is based on a gap design and relies primarily on diffusion for addition and mixing of derivatizing reagents. Reactors with gaps of 4 to 160 μm are easily built with minimal micromanipulation between two 10 μm i.d. capillaries. Optimal separation efficiencies and sensitivities are obtained with gaps of less than 10 μm. Separations of amino acids and proteins with o ‐phthaldialdehyde/2‐mercaptoethanol post‐column derivatization and laser‐induced fluorescence detection are shown. Linear detector response is found for amino acids and proteins, and peak efficiencies as high as 230,000 theoretical plates are obtained for some analytes. The use of relatively small columns for capillary electrophoresis results in a separation and detection system that produces very low mass detection limits for biological molecules from picoliter sample injections. Mass detection limits of 130 and 5.2 attomoles are obtained for glycine and human transferrin, respectively.
Tailored macromolecules by living carbocationic techniques (1992)

Abstract This presentation concerns our latest results for the controlled synthesis of various homopolymers, blocks, random copolymers, networks, by living carbocationic polymerization (LC ⊕ Pzn). We start with an analysis of the Winstein ionicity spectrum, a roadsign toward LC ⊕ Pzn systems. Living isobutylene (IB) homopolymerization can be effected by the addition of common anion salts to conventional polymerization charges, e.g., by adding nBu 4 NCl to a 2‐chloro‐2,4,4‐trimethylpentane (TMPCl)/TiCl 4 /IB system. Various AB diblocks have been prepared by sequential monomer addition. The first clean svnthesis of an AB poly(olefin‐b‐alkyl vinyl ether) diblock, ie., poly(isobutylene‐b‐methyl vinyl ether), by sequential monomer addition was accomplished. These novel amphiphilic diblocks promise to be excellent nonionic detergents. The field of linear A‐B‐A triblocks and three‐arm star blocks where A = glassy and B = rubbery (polyisobutylene) segment, is vigorously expanding. Several new thermoplastic elastomers (TPEs) have been prepared, characterized and tested, e.g., poly‐(indene‐b‐isobutylene‐b‐indene). The synthesis of random copolymers, e.g., isobutylene/2,4,4‐dimethyl‐1,3‐pentadiene, by living reactivity leveling has been demonstrated. Transformation of the polyisobutylene cations PIB ⊕ and ⊕ PIB ⊕ yielded the corresponding anions PIB ⊖ and ⊖ PIB ⊖ , which upon block polymerization of butadiene (Bd) and methyl methacrylate (MMA), respectively, gave rise to the new diblock PIB‐PBd and triblock PMMA‐PIB‐PMMA. In the latter, the largely syndiotactic sPMMA endblocks were stereocomplexed with isotactic iPMMA and thus the upper use‐temperature of these novel TPEs was enhanced. Novel amphiphilic networks comprising hydrophilic polymethacrylates (e.g., dimethylaminoethyl methacrylate (DMAEMA) or hydroxyethyl methacrylate (HEMA)) crosslinked by methacrylate‐telechelic PIBs were prepared and their potential usefulness for biomedical applications has been studied.
Pultruded fiber reinforced thermoplastic poly(methyl methacrylate) composites. Part I. Correlation of processing parameters for optimizing the process (1991)

Abstract The effect of processing parameters on the properties (tensile, flexural strength and modulus and impact strength, etc.) of pultruded fiber reinforced poly(methyl methacrylate) (PMMA) composites has been studied. The processing parameters investigated included pulling rate, die temperature, and postcure. Wetting of fibers by PMMA resin was complete, and the fiber bundles were evenly distributed in the PMMA matrix. The conversion, molecular weight and viscosity of MMA prepolymer were studied by 1 H‐NMR, GPC and Brookfield viscometer. The optimum die temperature was determined from DSC diagram, molecular weight measurement and from the polymerization rate. The mechanical properties increased with the increasing postcure temperature and decreasing pulling rate and die temperature.
ChemInform Abstract: Recent Synthetic Additions to the Visible Light Photoredox Catalysis Toolbox (2015)

Abstract Review: [93 refs.
Iridium Metal as Potential Substrates for Experiments in Space (2006)

Due to its unique properties, Iridium is currently being considered by NASA as a substrate (optically thick Ir on ultra-smooth fused silica) for the study of contamination layers deposited in the space environment. Extremely smooth thin films of iridium were deposited in this work onto super-polished fused silica substrates, using DC magnetron sputtering in an argon plasma. The influence of deposition process parameters on film micro-roughness was investigated. Moreover, Ir film optical constants were determined using variable angle spectroscopic ellipsometry, over the spectral range from vacuum ultraviolet to middle infrared (140 nm-35 μm). Because the Ir films were optically thick and the surface roughness were measured by atomic force microscopy, and then accounted for in the optical model, the as-determined film optical constants are expected to be the best available for Ir bulk metals, minimally affected by surface over-layers or microstructure.
Airway-centered Interstitial Fibrosis (2004)

We describe 12 patients with a form of interstitial lung disease characterized pathologically by small airway-centered interstitial fibrosis and metaplastic bronchiolar epithelium extending around and often linking fibrotic and sometimes heavily muscularized bronchioles. Clinically, patients presented with chronic cough and progressive dyspnea. One was a current light smoker and two were ex-smokers. In 8 patients, a history of possible inhalational exposures, including wood smoke, birds, cotton, pasture, chalk dust, agrochemical compounds, and cocaine use, was elicited. Pulmonary function tests showed moderate to severe physiologic abnormalities, in most instances indicating a restrictive lung disease with decreased peripheral flow rates. Chest radiographs revealed predominantly diffuse reticulonodular infiltrates in the central lung fields, with thickening of the bronchial walls and decreased lung volumes. Chest computed tomography demonstrated peribronchovascular fibrosis and interstitial thickening. Bronchoalveolar lavage showed a mild increase in lymphocytes in 4 subjects. Patients were treated with corticosteroids and bronchodilators. Follow-up data were available in 10 patients. In 5 patients, the disease progressed and 4 of them died. Two patients remained stable and 3 improved or healed. We propose that these findings represent a distinct airway-centered disease that mostly behaves as an interstitial lung disease and may exhibit a poor outcome.
Scalable, Shape-Specific, Top-Down Fabrication Methods for the Synthesis of Engineered Colloidal Particles (2020)

The search for a method to fabricate non-spherical colloidal particles from a variety of materials is of growing interest. As the commercialization of nanotechnology continues to expand, the ability to translate particle fabrication methods from a laboratory to an industrial scale is of increasing significance. In this article, we examine several of the most readily scalable top-down methods for the fabrication of such shape specific particles and compare their capabilities with respect to particle composition, size, shape and complexity as well as the scalability of the method. We offer an extensive examination of Particle Replication In Non-wetting Templates (PRINT®) with regards to the versatility and scalability of this technique. We also detail the specific methods used in PRINT particle fabrication, including harvesting, purification and surface modification techniques, with examination of both past and current methods.
Variable Digital Filter With Group Delay Flatness Specification or Phase Constraints (2008)

In this paper, we consider the design of finite-impulse response variable digital filters (VDFs) with variable cutoff frequency or variable fractional delay. We propose the design of VDFs with minimum integral squared error and constraints on the maximum error deviation in conjunction with flatness group delay specification or phase constraints. These specifications allow the VDFs to have approximately linear phase, especially in the passband. As these specifications are required to be satisfied for all the filters generated by the VDF with controllable spectral characteristics, the linear constraints resulting from the flatness specification are relaxed to inequality constraints. To make the optimization problem tractable for the phase constrained problem, suitable approximations are employed in the paper. The design problem is formulated as an optimization problem with a quadratic cost function and infinite number of constraints. A numerical scheme with adaptive grid step size is proposed for solving the optimization problem.
Improved Spontaneous Activity Maps of Resting Skeletal Musculature by surface EMG-based Contraction Pattern Classification (2018)

Reliable assessment and analysis of spontaneous mechanical activities in musculature (SMAM) visible in repetitive DWI is a relatively new technique for non-invasive characterization of skeletal musculature. To correct for data corrupted by intentional contractions, a surface electromyography-based contraction state analysis was investigated to reject undesired DWI data. It is demonstrated that the presented method enables a more reliable quantification of SMAMs and improved spontaneous activity maps.
Vibrational spectroscopic examination of the formation of mordenite crystals (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTVibrational spectroscopic examination of the formation of mordenite crystalsJen Twu, Prabir K. Dutta, and Charles T. KresgeCite this: J. Phys. Chem. 1991, 95, 13, 5267–5271Publication Date (Print):June 1, 1991Publication History Published online1 May 2002Published inissue 1 June 1991https://pubs.acs.org/doi/10.1021/j100166a064https://doi.org/10.1021/j100166a064research-articleACS PublicationsRequest reuse permissionsArticle Views281Altmetric-Citations60LEARN 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 options Get e-Alerts
Next-Generation Proteomics: Toward Customized Biomarkers for Environmental Biomonitoring (2014)

Because of their ecological representativeness, invertebrates are commonly employed as test organisms in ecotoxicological assessment; however, to date, biomarkers employed for these species were the result of a direct transposition from vertebrates, despite deep evolutionary divergence. To gain efficiency in the diagnostics of ecosystem health, specific biomarkers must be developed. In this sense, next-generation proteomics enables the specific identification of proteins involved in key physiological functions or defense mechanisms, which are responsive to ecotoxicological challenges. However, the analytical investment required restricts use in biomarker discovery. Routine biomarker validation and assays rely on more conventional mass spectrometers. Here, we describe how proteomics remains a challenge for ecotoxicological test organisms because of the lack of appropriate protein sequences databases, thus restricting the analysis on conserved and ubiquitous proteins. These limits and some strategies used to overcome them are discussed. These new tools, such as proteogenomics and targeted proteomics, should result in new biomarkers specific to relevant environmental organisms and applicable to routine ecotoxicological assessment.
Enhancing Safety with a Mutual Assistance System for Automobile (2015)

Recently, a number of safety assistance systems for automobiles have been proposed. Most systems, such as adaptive cruise control systems (ACC), attempt to assist in improving driving safety for individual drivers. The authors&#39; study focuses on a new type of safety assistance system, by which drivers are able to mutually assist each other based on a &ldquo;Mutual Assistance&rdquo; paradigm. The authors&#39; previous study examined the effectiveness of the mutual assistance system from both the recipient and assister side with a driving simulator. In this paper, the effectiveness of a mutual assistance system is examined with a more detailed analysis. The results of experiments from the assistance recipient side indicate that early warning from a mutual assistance system statistically decreases the risks of collision by increasing the margin of collision avoidance. The results from the assister side indicate that a mutual assistance system brings positive attitude changes and enhances self-efficacy, particularly by including some voluntary actions. From the results of experiments the authors&#39; proposed system is expected to contribute to a much safer driving environment by reducing the target level of risk.
Deriving divide-and-conquer dynamic programming algorithms using solver-aided transformations (2016)

We introduce a framework allowing domain experts to manipulate computational terms in the interest of deriving better, more efficient implementations.It employs deductive reasoning to generate provably correct efficient implementations from a very high-level specification of an algorithm, and inductive constraint-based synthesis to improve automation. Semantic information is encoded into program terms through the use of refinement types. In this paper, we develop the technique in the context of a system called Bellmania that uses solver-aided tactics to derive parallel divide-and-conquer implementations of dynamic programming algorithms that have better locality and are significantly more efficient than traditional loop-based implementations. Bellmania includes a high-level language for specifying dynamic programming algorithms and a calculus that facilitates gradual transformation of these specifications into efficient implementations. These transformations formalize the divide-and conquer technique; a visualization interface helps users to interactively guide the process, while an SMT-based back-end verifies each step and takes care of low-level reasoning required for parallelism. We have used the system to generate provably correct implementations of several algorithms, including some important algorithms from computational biology, and show that the performance is comparable to that of the best manually optimized code.
Assessing the Impact of Ureteral Stent Design on Patient Comfort (2009)

Although it was not statistically significant, patients stented with the short loop tail had lower questionnaire pain scores on day 4 after placement and lower pain medication use on day 1 after placement when pain peaked in all stent groups, suggesting that ureteral stent comfort, especially pain, may be improved by less material in situ. The Ureteral Stent Symptoms Questionnaire may be better suited for longer term comparisons in stented vs nonstented patients, rather than in this short-term ureteral stent trial.
40-GHz optical pulse generation using strong external light injection of a gain-switched high-speed DBR laser diode (2003)

We demonstrate a compact 40-GHz repetition rate optical pulse source using a gain-switched distributed Bragg reflector laser diode with strong external light injection. The 8-ps output pulses are nearly transform-limited and the timing jitter is dominated, by the radio-frequency driving source. We experimentally demonstrate the dependence of the modulation efficiency and the chirp characteristic on the external injection power level.
Left ventricular sensing in cardiac resynchronization devices—opportunities and pitfalls for device programming (2019)

CRT devices with LV sensing may suffer from impaired resynchronization due to programming pitfalls. If LV sensing is active (nominal setting in Biotronik and Boston Scientific devices), careful lookout for related problems and resynchronization percentage is required. Optimization is mandatory and even deactivation of LV sensing may have to be considered.
Towards chronic deep brain stimulation in freely moving hemiparkinsonian rats: applicability and functionality of a fully implantable stimulation system (2021)

<i>Objective.</i>This study aimed at investigating a novel fully implantable deep brain stimulation (DBS) system and its ability to modulate brain metabolism and behavior through subthalamic nucleus (STN) stimulation in a hemiparkinsonian rat model.<i>Approach.</i>Twelve male rats were unilaterally lesioned with 6-hydroxydopamine in the medial forebrain bundle and received a fully implantable DBS system aiming at the ipsilesional STN. Each rat underwent three cylinder tests to analyze front paw use: a PRE test before any surgical intervention, an OFF test after surgery but before stimulation onset and an ON test under DBS. To visualize brain glucose metabolism in the awake animal, two [<sup>18</sup>F]FDG scans were conducted in the OFF and ON condition. At least 4 weeks after surgery, an [<sup>18</sup>F]FDOPA scan was used to check for dopaminergic integrity.<i>Main results.</i>In general, STN DBS increased [<sup>18</sup>F]FDG uptake ipsilesionally and decreased it contralesionally. More specifically, bilateral orbitofrontal cortex, ipsilateral caudate putamen, sensorimotor cortex and nucleus accumbens showed significantly higher tracer uptake in ON compared to OFF condition. Contralateral cingulate and secondary motor cortex, caudate putamen, amygdala, hippocampus, retrosplenial granular cortex, superior colliculus, and parts of the cerebellum exhibited significantly higher [<sup>18</sup>F]FDG uptake in the OFF condition. On the behavioral level, stimulation was able improve use of the contralesional affected front paw suggesting an effective stimulation produced by the implanted system.<i>Significance.</i>The fully implantable stimulation system developed by us and presented here offers the output of arbitrary user-defined waveforms, patterns and stimulation settings and allows tracer accumulation in freely moving animals. It is therefore a suitable device for implementing behavioral PET studies. It contributes immensely to the possibilities to characterize and unveil the effects and mechanisms of DBS offering valuable clues for future improvements of this therapy.