gebhart/patrepeval huggingface dataset:
NS0 cell damage by high gas velocity sparging in protein‐free and cholesterol‐free cultures (2008)

Recent developments in high cell density and high productivity fed-batch animal cell cultures have placed a high demand on oxygenation and carbon dioxide removal in bioreactors. The high oxygen demand is often met by increasing agitation and sparging rates of air/O2 in the bioreactors. However, as we demonstrate in this study, an increase of gas sparging can result in cell damage at the sparger site due to high gas entrance velocities. Previous studies have showed that gas bubble breakup at the culture surface was primarily responsible for cell damage in sparged bioreactors. Such cell damage can be reduced by use of surfactants such as Pluronic F-68 in the culture. In our results, where NS0 cells were grown in a protein-free and cholesterol-free medium containing 0.5 g/L Pluronic F-68, high gas entrance velocity at the sparger site was observed as the second mechanism for cell damage. Experiments were performed in scaled-down spinners to model the effect of hydrodynamic force resulting from high gas velocities on antibody-producing NS0 cells. Cell growth and cell death were described by first-order kinetics. Cell death rate constant increased significantly from 0.04 to 0.18 day(-1) with increasing gas entrance velocity from 2.3 to 82.9 m/s at the sparger site. The critical gas entrance velocity for the NS0 cell line studied was found to be approximately 30 m/s; velocities greater than 30 m/s caused cell damage which resulted in reduced viability and consequently reduced antibody production. Observations from a second cholesterol-independent NS0 cell line confirmed the occurrence of cell damage due to high gas velocities. Increasing the concentration of Pluronic F-68 from 0.5 to 2 g/L had no additional protective effect on cell damage associated with high gas velocity at the sparger. The results of gas velocity analysis for cell damage have been applied in two case studies of large-scale antibody manufacturing. The first is a troubleshooting study for antibody production carried out in a 600 L bioreactor, and the second is the development of a gas sparger design for a large bioreactor scale (e.g., 10,000 L) for antibody manufacturing.
Automatic Chemical Design Using a Data-Driven Continuous Representation of Molecules. (2018)

We report a method to convert discrete representations of molecules to and from a multidimensional continuous representation. This model allows us to generate new molecules for efficient exploration and optimization through open-ended spaces of chemical compounds. A deep neural network was trained on hundreds of thousands of existing chemical structures to construct three coupled functions: an encoder, a decoder, and a predictor. The encoder converts the discrete representation of a molecule into a real-valued continuous vector, and the decoder converts these continuous vectors back to discrete molecular representations. The predictor estimates chemical properties from the latent continuous vector representation of the molecule. Continuous representations of molecules allow us to automatically generate novel chemical structures by performing simple operations in the latent space, such as decoding random vectors, perturbing known chemical structures, or interpolating between molecules. Continuous representations also allow the use of powerful gradient-based optimization to efficiently guide the search for optimized functional compounds. We demonstrate our method in the domain of drug-like molecules and also in a set of molecules with fewer that nine heavy atoms.
Gene Delivery Techniques for Adult Stem Cell-Based Regenerative Therapy (2013)

Over the past decade, stem cells have been considered to be a promising resource to cure and regenerate damaged or diseased tissues with research extending from basic studies to clinical application. Furthermore, genetically modified stem cells have the potential to reduce tumorigenic risks and achieve safe tissue formation. Recent advances in genetic modification of stem cells have rendered these cells more accessible and stable. The successful genetic modification of stem cells relies heavily on designing vector systems, either viral or nonviral vectors, which can efficiently deliver therapeutic genes to the cells with minimum toxicity. Currently, viral vectors showing high transfection efficiencies still raise safety issues, whereas safer nonviral vectors exhibit extremely poor transfection in stem cells. Here, we attempt to review and discuss the main factors raising concern in previous reports, and devise strategies to solve the issues in gene delivery systems for successful stem cell-targeting regenerative therapy.
The case against user interface consistency (1989)

Designers striving for user interface consistency can resemble Supreme Court justices trying to define pornography: each of us feels we know it when we see it, but people often disagree and a precise definition remains elusive. A close examination suggests that consistency is an unreliable guide and that designers would often do better to focus on users' work environments.
Candida albicans sphingolipid C9-methyltransferase is involved in hyphal elongation (2009)

C9-methylated glucosylceramide is a fungus-specific sphingolipid. This lipid is a major membrane component in the cell and is thought to play important roles in the growth and virulence of several fungal species. To investigate the importance of the methyl branch of the long-chain base in glucosylceramides in pathogenic fungi, we identified and characterized a sphingolipid C9-methyltransferase gene (MTS1, C9-MethylTransferase for Sphingolipid 1) in the pathogenic yeast Candida albicans. The mts1 disruptant lacked (E,E)-9-methylsphinga-4,8-dienine in its glucosylceramides and contained (E)-sphing-4-enine and (E,E)-sphinga-4,8-dienine. Reintroducing the MTS1 gene into the mts1 disruptant restored the synthesis of (E,E)-9-methylsphinga-4,8-dienine in the glucosylceramides. We also created a disruptant of the HSX11 gene, encoding glucosylceramide synthase, which catalyses the final step of glucosylceramide synthesis, in C. albicans and compared this mutant with the mts1 disruptant. The C. albicans mts1 and hsx11 disruptants both had a decreased hyphal growth rate compared to the wild-type strain. The hsx11 disruptant showed increased susceptibility to SDS and fluconazole, similar to a previously reported sld1 disruptant that contained only (E)-sphing-4-enine in its glucosylceramides, suggesting that these strains have defects in their cell membrane structures. In contrast, the mts1 disruptant grew similarly to wild-type in medium containing SDS or fluconazole. These results suggest that the C9-methyl group of a long-chain base in glucosylceramides plays an important role in the hyphal elongation of C. albicans independent of lipid membrane disruption.
Chemical RNA Editing for Genetic Restoration: The Relationship between the Structure and Deamination Efficiency of Carboxyvinyldeoxyuridine Oligodeoxynucleotides (2015)

Oligodeoxynucleotides containing 5-carboxyvinyl-2'-deoxyuridine ((CV) U-containing ODNs) for successful site-specific transition of cytosine to uridine by photo-cross-linking have three parts: the complementary sequence, hairpin loop and the 5'-terminal photoresponsive nucleobase (CV) U. Photo-cross-linking with (CV) U-containing ODNs was performed using UV (366 nm) irradiation, followed by heat treatment for deamination. The cross-linked nucleotide was cleaved by photosplitting (UV, 312 nm). The products were analyzed using restriction fragment length polymorphism and fluorescence measurements. In previous studies, we have successfully performed site-directed photochemical base substitution toward a synthetic single-stranded 100-mer ODN target (ss100-nt) and in vitro-synthesized full-length blue fluorescent protein mRNA as targets. Although the efficiency of C-to-U site-specific transition strongly depends on the sequence and structure of (CV) U-containing ODNs, the relationship between (CV) U-containing ODNs and the deamination efficiency of targeted editing remains unclear. Therefore, in this study, we attempted to identify the optimal sequence and primary structure of (CV) U-containing ODNs for site-directed specific transition. To evaluate the structure-deamination efficiency relationship, a series of eight (CV) U-containing ODNs were designed and studied. We showed that the optimal deamination efficiency was achieved with ODNs having a complementary sequence length slightly more than 14 nt and a hairpin length of 9 nt.
Cloth grasp point detection based on multiple-view geometric cues with application to robotic towel folding (2010)

We present a novel vision-based grasp point detection algorithm that can reliably detect the corners of a piece of cloth, using only geometric cues that are robust to variation in texture. Furthermore, we demonstrate the effectiveness of our algorithm in the context of folding a towel using a general-purpose two-armed mobile robotic platform without the use of specialized end-effectors or tools. The robot begins by picking up a randomly dropped towel from a table, goes through a sequence of vision-based re-grasps and manipulations-partially in the air, partially on the table-and finally stacks the folded towel in a target location. The reliability and robustness of our algorithm enables for the first time a robot with general purpose manipulators to reliably and fully-autonomously fold previously unseen towels, demonstrating success on all 50 out of 50 single-towel trials as well as on a pile of 5 towels.
Elimination of distortions of nuclear energy spectra caused by pulse pile-up (1994)

Distortions of nuclear energy spectra at high counting rates have been efficiently reduced by two different signal processing methods: pile-up suppression by pulse shortening and pile-up rejection by detection and rejection of the piled-up pulses. By combining these methods new circuits have been developed increasing the limit for the quality gamma ray spectrometry from available, up to now, 100000 s-1 to the range of up to 500000 s-1.
Preparation and application of porous silk fibroin materials (1994)

Abstract This article deals with the preparation and morphological characterization of porous materials obtained by freezing and lyophilizing silk fibroin solutions. When an aqueous silk solution is frozen at different temperatures (−18, −45, and −80°C), the average pore size decreases with lowering of the freezing temperature. Silk fibroin aggregates obtained in these conditions exhibit a sheetlike structure. By lowering the pH from neutrality to 4.01 and 2.65, the morphology of the solid phase changes from a sheet to a fiber structure. The average pore size is smaller at pH 4.01 than is the former value corresponding to the isoelectric point of silk fibroin. The addition of different amounts of methanol to the silk solution results in a sharp fall of the average pore size and hardens the material, as a consequence of the high packing density of the fibroin molecules. Silk fibroin aggregates prepared in these conditions exhibit a typical fibrous structure. A drug‐delivery system was prepared by incorporating acetylsalicyclic acid into a porous silk fibroin carrier, and the kinetics of the drug release was studied. © 1994 John Wiley &amp; Sons, Inc.
Core–Shell Structure of Polypyrrole Grown on V2O5 Nanoribbon as High Performance Anode Material for Supercapacitors (2012)

A core–shell structure of polypyrrole grown on V2O5 nanoribbons as a high performance anode material for supercapacitors is fabricated using anionic dodecylbenzenesulfonate (DBS−) as surfactant. Benefiting from the nanoribbon morphology of V2O5, the improved charge-transfer and polymeric coating effect of PPy, PPy@V2O5 nanocomposites exhibits high energy density, and excellent cycling and rate capability in K2SO4 aqueous electrolyte.
High Speed Optical TIR Switches Using PLZT Thin-Film Waveguides on Sapphire (1985)

We propose a new structure of the PLZT thin film optical TIR (Total Internal Reflection) switches with strip loaded type waveguides. Using these switches, we have achieved 2 GHz intensity modulation of LD light (0.83 µm) and 1 km optical fiber transmission. Both lumped constant electrode and traveling wave electrode were examined up to 26.5 GHz. From the calculation of velocity mismatch between the modulating wave and the light wave, it is estimated that the modulation bandwidth of these switches will be more than 100 GHz.
Mobility and connection management in a wireless ATM LAN (1997)

This paper proposes algorithms for handoff, location, and connection management in a wireless asynchronous transfer mode (ATM) local-area network (LAN). Fast handoffs while maintaining cell sequence and quality-of-service (QoS) guarantees are achieved by distributing switching functionality to base stations, and using a networking scheme based on provisioned virtual trees. A new distributed location management scheme using a minimal registration procedure and broadcasts on wired links is proposed for this LAN. The detailed signaling procedures that support the algorithms for mobility and connection management are described. Finally, an implementation of these procedures and an analysis of the measured data is presented. Measurements of service times obtained from this implementation indicate that over 100 calls/s. can be handled by each node in 50-node network with a high-percentage of mobiles (75%) relative to fixed endpoints. This is comparable to current wired ATM switch call handling throughputs, in spite of the fact that these nodes perform additional handoff and location management functions. The data also indicates handoff latency times of 1.3 ms. This validates our proposal for maintaining cell sequence while performing handoffs.
Combined ECC/RLL codes (1988)

Two novel combined error-correcting/run-length-limited (ECC/RLL) trellis codes are presented. One is a two-state
Effects of Morphine and Tramadol on Somatic and Visceral Sensory Function and Gastrointestinal Motility after Abdominal Surgery (1999)

Pain control was equally effective with morphine and tramadol infusions. No somatic or visceral sensitization was evident during morphine and tramadol infusions, but pain tolerance thresholds as markers of antinociception were increased more during morphine infusions. The significant sensitization seen only after morphine discontinuation may be due to convergent visceral input. Gut motility was prolonged significantly by visceral surgery itself and also by morphine.
Pitavastatin Suppresses Acute and Chronic Rejection in Murine Cardiac Allografts (2007)

Pitavastatin could be effective in the suppression of acute rejection and GAD development in cardiac transplantation.
Methoxyestrogens exert feedback inhibition on cytochrome P450 1A1 and 1B1. (2003)

Cytochrome P450 1A1 (CYP1A1) and 1B1 (CYP1B1) catalyze the oxidative metabolism of 17 beta-estradiol (E2) to catechol estrogens (2-OHE2 and 4-OHE2) and estrogen quinones, which may lead to DNA damage. Catechol-O-methyltransferase catalyzes the methylation of catechol estrogens to methoxyestrogens (2-MeOE2, 2-OH-3-MeOE2, and 4-MeOE2), which simultaneously lowers the potential for DNA damage and increases the concentration of 2-MeOE2, an antiproliferative metabolite. In this study, we showed that CYP1A1 and CYP1B1 recognized as substrates both the parent hormone E2 and the methoxyestrogens. Using purified recombinant enzymes, we demonstrated that CYP1A1 and CYP1B1 O-demethylated the methoxyestrogens to catechol estrogens according to Michaelis-Menten kinetics. Both CYP1A1 and CYP1B1 demethylated 2-MeOE2 and 2-OH-3-MeOE2 to 2-OHE2, whereas CYP1B1 additionally demethylated 4-MeOE2 to 4-OHE2. Because the P450-mediated oxidation of E2 and the O-demethylation of methoxyestrogens both yielded identical catechol estrogens as products, we used deuterated E2 (E2-d4), unlabeled methoxyestrogens, and gas chromatography/mass spectrometry to examine both reactions simultaneously. Kinetic analysis revealed that methoxyestrogens acted as noncompetitive inhibitors of E2 oxidation with K(i) ranging from 27 to 153 micro M. For both enzymes, the order of inhibition by methoxyestrogens was 2-OH-3-MeOE2 > or = 2-MeOE2 > 4-MeOE2. Thus, methoxyestrogens exert feedback inhibition on CYP1A1- and CYP1B1-mediated oxidative estrogen metabolism, thereby reducing the potential for estrogen-induced DNA damage.
Knowledge production and social work (2011)

Practice research can in itself be regarded as a specifi c form of knowledge production in social work with substantial potentials. Its possibilities as well as its challenges depend on the broader picture of knowledge production in the fi eld. Important phenomena and trends in this broader picture are identifi ed and discussed by using three perspectives on knowledge production: the epistemology, sociology of knowledge, and conceptualization of professions. Challenges can be identifi ed in several of the newer trends and may be most clearly seen in the substantial changes in the dominant societal re- creation of 'professionalism', which at the same time from a traditional point of view must be regarded as deprofessionalization. It is suggested, that practice research in this situation can play an important role in a knowledge production scaffolding a new understanding of professionalism and expertise.
Growth of bacteria on chitin, fungal cell walls and fungal biomass, and the effect of extracellular enzymes produced by these cultures on the antifungal activity of amphotericin B. (1985)

Vibrio alginolyticus, Streptomyces griseus, Arthrobacter G12, Bacillus sp. and Cytophaga sp. were grown on solid and liquid media containing soluble and insoluble carbon sources. Arthrobacter G12, Bacillus sp. and Cytophaga sp. grew well on media which contained fungal cell walls or fungal biomass as the main carbon source. All bacteria produced extracellular proteases and all bacteria except Arthrobacter G12 produced extracellular chitinases. Growth of Cytophaga sp. on colloidal chitin was paralleled by the accumulated chitinase activity in the culture filtrate, and growth of Cytophaga sp. and Arthrobacter G12 on cell walls of Geotrichum candidum and cell walls of Candida pseudotropicalis was paralleled by the accumulation of laminarinase activity in the culture filtrate, but little or no extracellular chitinase activity was observed in these cultures. Mycolases purified from the culture filtrates of Cytophaga sp. grown on colloidal chitin on cell walls of C. pseudotropicalis potentiated the antifungal activity of amphotericin B.
Parameterization and Sensitivity Analysis of a Complex Simulation Model for Mosquito Population Dynamics, Dengue Transmission, and Their Control (2011)

Models can be useful tools for understanding the dynamics and control of mosquito-borne disease. More detailed models may be more realistic and better suited for understanding local disease dynamics; however, evaluating model suitability, accuracy, and performance becomes increasingly difficult with greater model complexity. Sensitivity analysis is a technique that permits exploration of complex models by evaluating the sensitivity of the model to changes in parameters. Here, we present results of sensitivity analyses of two interrelated complex simulation models of mosquito population dynamics and dengue transmission. We found that dengue transmission may be influenced most by survival in each life stage of the mosquito, mosquito biting behavior, and duration of the infectious period in humans. The importance of these biological processes for vector-borne disease models and the overwhelming lack of knowledge about them make acquisition of relevant field data on these biological processes a top research priority.
Lightweight Structure in Text (2002)

Pattern matching is heavily used for searching, filtering, and transforming text, but existing pattern languages offer few opportunities for reuse. Lightweight structure is a new approach that solves the reuse problem. Lightweight structure has three parts: a model of text structure as contiguous segments of text, or regions; an extensible library of structure abstractions (e.g., HTML elements, Java expressions, or English sentences) that can be implemented by any kind of pattern or parser; and a region algebra for composing and reusing structure abstractions. Lightweight structure does for text pattern matching what procedure abstraction does for programming, enabling construction of a reusable library. 
Lightweight structure has been implemented in LAPIS, a web browser/text editor that demonstrates several novel techniques: (1) Text constraints is a new pattern language for composing structure abstractions, based on the region algebra. Text constraint patterns are simple and high-level, and user studies have shown that users can generate and comprehend them. (2)  Simultaneous editing uses multiple selections for repetitive text editing. Multiple selections are inferred from examples given by the user, drawing on the lightweight structure library to make fast, accurate, domain-specific inferences from very few examples. In user studies, simultaneous editing required only 1.26 examples per selection, approaching the 1-example ideal. (3)  Outlier finding draws the user's attention to inconsistent selections or pattern matches—both possible false positives and possible false negatives. When integrated into simultaneous editing and tested in a user study, outlier finding reduced user errors. (4) Unix tools for structured text extend tools like grep and sort with lightweight structure, and the browser shell integrates a Unix command prompt into a web browser, offering new ways to build pipelines and automate web browsing. Theoretical contributions include a formal definition of the region algebra, data structures and algorithms for efficient implementation, and a characterization of the classes of languages recognized by algebra expressions. 
Lightweight structure enables efficient composition and reuse of structure abstractions defined by various kinds of patterns and parsers, bringing improvements to pattern matching, text processing, web automation, repetitive text editing, inference of patterns from examples, and error detection.
Gene Therapy of Human Severe Combined Immunodeficiency (SCID)-X1 Disease (2000)

Severe combined immunodeficiency–X1 (SCID-X1) is an X-linked inherited disorder characterized by an early block in T and natural killer (NK) lymphocyte differentiation. This block is caused by mutations of the gene encoding the γc cytokine receptor subunit of interleukin-2, -4, -7, -9, and -15 receptors, which participates in the delivery of growth, survival, and differentiation signals to early lymphoid progenitors. After preclinical studies, a gene therapy trial for SCID-X1 was initiated, based on the use of complementary DNA containing a defective γc Moloney retrovirus–derived vector and ex vivo infection of CD34 + cells. After a 10-month follow-up period, γc transgene–expressing T and NK cells were detected in two patients. T, B, and NK cell counts and function, including antigen-specific responses, were comparable to those of age-matched controls. Thus, gene therapy was able to provide full correction of disease phenotype and, hence, clinical benefit.