gebhart/patrepeval huggingface dataset:
Automating a Magnetic 3D Spheroid Model Technology for High-Throughput Screening (2019)

Affordable and physiologically relevant three-dimensional (3D) cell-based assays used in high-throughput screening (HTS) are on the rise in early drug discovery. These technologies have been aided by the recent adaptation of novel microplate treatments and spheroid culturing techniques. One such technology involves the use of nanoparticle (NanoShuttle-PL) labeled cells and custom magnetic drives to assist in cell aggregation to ensure rapid 3D structure formation after the cells have been dispensed into microtiter plates. Transitioning this technology from a low-throughput manual benchtop application, as previously published by our lab, into a robotically enabled format achieves orders of magnitude greater throughput but required the development of specialized support hardware. This effort included in-house development, fabrication, and testing of ancillary devices that assist robotic handing and high-precision placement of microtiter plates into an incubator embedded with magnetic drives. Utilizing a "rapid prototyping" approach facilitated by cloud-based computer-aided design software, we built the necessary components using hobby-grade 3D printers with turnaround times that rival those of traditional manufacturing/development practices at a substantially reduced cost. This approach culminated in a first-in-class HTS-compatible 3D system in which we have coupled 3D bioprinting to a fully automated HTS robotic platform utilizing our novel magnetic incubator shelf assemblies.
Fatigue Data for Reliability‐Based Offshore Platform Inspection and Repair (1991)

Fatigue of welded fixed offshore platforms is a primary design and operational concern. Environmental, fatigue data, and method uncertainties, as well as inspection and repair activities, are major parameters that influence the welded joint reliability. This paper investigates and establishes the relation between welded tubular joint fatigue life computed from a deterministic design process and the probability of occurrence of: (1) First detectable crack; (2) first through‐thickness cracking; and (3) total joint failure stages. Several experimental fatigue data bases were used to derive the appropriate probabilistic distributions and relations between different joint failure stages. The effect of repair methods, such as repair welding and grinding, on the fatigue life is studied, and parameters that modify the probability of joint failure states are introduced. The data examined show that time to first discernible surface cracking for welded tubular joints is about 10‐65% of the time to through‐thickness cracking, with a mean value of 35%. The total joint failure will occur at about 150% of the time to through‐thickness crack. Simplified relations between crack size and remaining fatigue life are derived based on recent experimental results. Data presented in this paper provide the basic tools for performing a reliability‐based inspection and repair assessment.
Effect of Nickel on Corrosion Resistance Of Al-Zn-Mg-Cu PM Alloy Produced by Mechanical Alloying (2014)

In this research, comparative study of corrosion resistance of PM Al-Zn-Mg-Cu alloy (A) and PM Al-Zn-Mg-Cu-1%Ni alloy (B) produced using mechanical alloying process has been investigated. PM milled alloy (A) and alloy (B) specimens were sintered after compaction then homogenized, aged then retrogressed and reaged. PM Al-alloys were subjected to corrosive media (acidic: 1.0M HCl) and using weight loss method to evaluate their corrosion resistance. The findings of this study indicated that the precipitation hardening is obtained for PM milled Al- alloy A samples after heat treatment led to enhance their resistance of corrosion. Furthermore, the gain of corrosion resistance for PM Al- Zn-Mg-Cu-Ni alloy B specimens more than what PM Al-Zn-Mg-Cu alloy A caused by having in compounds of Al-Ni as well as precipitates of alloying elements, under the same operation conditions. Scanning electron microscopy (SEM) and energy dispersive X-ray spectroscopy (EDS) were used to show the corroded surfaces.
Immunological Consequences of Epithelial–Mesenchymal Transition in Tumor Progression (2016)

Microenvironments that tumor cells encounter are different during the stages of cancer progression-primary tumor, metastasis, and at the metastatic site. This suggests potential differences in immune surveillance of primary tumor and metastasis. Epithelial-mesenchymal transition (EMT) is a key reversible process in which cancer cells transition into highly motile and invasive cells for dissemination. Only a tiny proportion successfully metastasize, supporting the notion of metastasis-specific immune surveillance. EMT involves extensive molecular reprogramming of cells conferring many clinically relevant features to cancer cells and affects tumor cell interactions within the tumor microenvironment. We review the impact of tumor immune infiltrates on tumor cell EMT and the consequences of EMT in shaping the immune microenvironment of tumors. The usefulness of EMT as a model to investigate metastasis-specific immune surveillance mechanisms are also explored. Finally, we discuss potential implications of EMT for tumor immunogenicity, as well as current immunotherapies and future strategies.
Mesenchymal and Non‐Epithelial Tumors of the Pelvis (2021)

Tumors arising from tissue of the primitive mesenchymal mesenchyme comprise a heterogeneous group of benign and malignant neoplasms. Peripheral neurogenic tumors which are of ectodermal origin are also included since their behavior is similar; they are treated like soft tissue tumors. Soft tissue sarcomas are more common than primary malignant bone tumors. Chondrosarcoma and Ewing's sarcoma frequently involve the bony pelvis. In addition, prior radiation therapy is associated with development of bone and soft tissue sarcomas, and some chronic inflammatory states such as Paget's disease and chronic osteomyelitis can result in the development of bone sarcomas. Liposarcoma is one of the most common pelvic sarcomas. Epithelioid sarcomas are a rare malignant mesenchymal neoplasm where the cell of origin is unknown. Formally known as malignant fibrous histiocytomas, undifferentiated pleomorphic sarcomas consist of tumor cells with diffuse pleomor-phism and no identifiable line of differentiation.
Method to Quantify Modal Interactions Between Converter Interfaced Generators and Synchronous Generators (2022)

The aim of this paper is to quantify the interactions between the oscillation modes of Converter Interfaced Generators (CIG) and electromechanical oscillation modes of Synchronous Generators (SGs) within the realm of small-signal stability. It is difficult to quantify the modal interactions using the existing analysis such as mode sensitivity, mode loci and participation factors. This paper proposes an extension to the eigenvalue sensitivity analysis in order to determine the interactions between modes and the impacts of the interactions on the system stability. Interaction coefficients are proposed to quantify the interactions between the modes. A modified IEEE 39-bus system with CIGs is considered to carry out the analysis using proposed interaction coefficients. In this paper, results are presented considering CIG based renewable energy penetration levels of 50-70%. It is observed that the interactions between the oscillation modes of CIGs and electromechanical modes of SGs result in increased participation of SGs' states in CIG modes. This increased participation of SG states in the CIG modes results in reduced damping of oscillations in SG states. Possible applications of the proposed interaction coefficients are also identified. The impacts of PLL parameters on the interactions among the oscillation modes are investigated using proposed interaction coefficients. Results demonstrate that the impact of PLL on interactions increases with increasing CIG penetration.
Abstract 2540: Mitotic Golgi vesiculation enables human papillomavirus to evade cGAS/STING (2019)

Abstract Oncogenic human papillomaviruses (HPVs) infect and replicate in differentiating mucosal epithelium, causing 5% of cancers worldwide and essentially all cervical cancers. During infection, HPV must traffic viral genome (vDNA) to the nuclei of basal keratinocytes. Minor capsid protein L2 facilitates intracellular transport of vDNA to the Golgi; upon mitosis, the L2-vDNA complex penetrates limiting membranes and localizes to mitotic chromosomes, ensuring infection of both daughter cells. Cytosolic DNA sensor cGAS recognizes cytosolic dsDNA and produces second messenger cGAMP; cGAMP causes activation and relocalization of ER-resident STING to the Golgi, where it recruits TBK1 to phosphorylate and activate IRF3, initiating a type-I IFN response. The cGAS/STING pathway is assumed, though never demonstrated, to be inactive during mitosis to avoid detecting self-DNA. Since the Golgi is a platform for STING/TBK1/IRF3 recruitment and activation, we hypothesize natural Golgi dispersal deactivates cGAS/STING during mitosis. Further, we hypothesize HPV has evolved to traffic to and translocate from the mitotic Golgi as an immunoevasive tactic to avoid detection by cGAS/STING during mitosis. HaCaTs, a human keratinocyte line, were transfected with DNA or infected with HPV pseudovirions and analyzed for cGAS/STING activation. DNA transfection resulted in IRF3 phosphorylation and nuclear translocation, and STING translocation to the Golgi, indicating cGAS/STING activity. Strikingly, chemical disruption of the Golgi ribbon potently blocked IRF3 activation in response to foreign DNA, suggesting Golgi morphology might modulate cGAS/STING activity during mitosis. In accordance, DNA-dependent IRF3 phosphorylation was transiently reduced in synchronized mitotic cells, but chemical impairment of mitotic Golgi vesiculation enabled cGAS/STING activation, even without foreign DNA transfection. Further, HPV infection resulted in minimal IRF3 phosphorylation, indicating HPV can efficiently evade detection during initial infection. To determine if HPV’s unique trafficking enables evasion, we used cationic liposomes to permit premature virion translocation across limiting membranes. Such treatment renders a non-infectious, translocation-defective mutant HPV infectious, yet susceptible to cGAS/STING sensing. Overall, the cGAS/STING pathway may be inactivated by mitotic Golgi dispersal, allowing HPV to evade detection during mitosis. Citation Format: Brittany L. Forte, Shauna M. Bratton, Samuel K. Campos. Mitotic Golgi vesiculation enables human papillomavirus to evade cGAS/STING [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2540.
Full-spectrum interrogation of fiber Bragg grating sensors for dynamic measurements in composite laminates (2009)

This paper presents a new means for collecting fiber Bragg grating (FBG) data during drop-tower measurements used to assess damage to composite structures. The high repetition-rate collection process reveals transient features that cannot be resolved in quasi-static measurements. The experiments made at a repetition rate of about 500 Hz show that the detected FBG spectrum broadens for a short period of time and relaxes quickly to a narrower static state. Furthermore, this relaxation time increases dramatically as the strike count increases. The information gained by such measurements will enhance the ability to characterize and distinguish failure modes and predict the remaining lifetime in composite laminate structures.
Zinc Promoted Regioselective Friedel-Crafts Acylation of Electron Rich Arenes (1998)

Abstract A simple and convenoent zinc promoted selective Friedel-Crafts acylation is described. The inexpensive metal grade catalyst and minimum waste effluent are the important features of the procedure.
Charging Techniques in Lithium-Ion Battery Charger: Review and New Solution (2018)

In this paper, a new hybrid charging algorithm suitable for Li-ion battery is proposed with the aim of reducing refilling time and improving battery life cycle. The hybrid algorithm combines constant current constant voltage (CCCV) and pulsed charge (PC) techniques to obtain the suitable way for fast charging and ensure a long lifetime. A step by step execution of the new algorithm is presented. Moreover, the algorithm is implemented using bidirectional DC to DC power converter with Simulink. The charger is able to detect initial battery state of charge (SoC) and take the suitable way to charge it. The included results show the obtained performance of the proposed technique in terms of battery refilling time reduction to return to top of-charge and improving its cycle life.
CHAPTER 15: Bemisia tabaci-Mediated Transmission of Begomoviruses: History and Anatomical, Biological, and Cellular Interactions (2016)

All members of the now-deprecated order Homoptera have been moved to Hemiptera because of recent reanalyses of their morphological relationships in conjunction with the use of molecular phylogenetic tools. However, subordinal rank is still in controversy. Both the collective suborder Sternorrhyncha (whiteflies, aphids, psyllids, and scales) and the individual suborders Aleyrodoidea, Aphididoidea, Psylloidea, and Coccoidea are retained by various authors. The common names “aphid,” “psyllid,” and “scale” were originally coined to represent one family each. Presently, they are used for several distinct families, but whiteflies are still the exclusive members of Aleyrodoidea. Even though Aleyrodidae is exclusive, its genera present many unsolved taxonomic problems. Furthermore, Bemisia, the most exhaustively studied genus, is recognized as a species complex so intractable that species demarcations are mostly vague and controversial. Whiteflies have only four nymphal instars, while psyllids have five. However, both have an ambulatory first-instar nymph, called a “crawler,” with proportionally longer legs than the sessile instars that follow. For this reason, first-instar whiteflies and psyllids are correctly termed “hypermetamorphic.” “Hypermetamorphosis” is a classical term referring to development that involves two or more nymphal instars with different morphologies. Original examples were taken from Holometabola, such as the famous “triungulin” of blister beetles, and thereafter the term has undergone considerable alteration and distortion over the decades. Its core intention is certainly applicable to any insect, including whiteflies and psyllids. Key concepts included in this chapter: Background Begomoviruses Whitefly Anatomy and Plant Virus Transmission Future Directions
Biochemical Characterization of Hypothetical Proteins from Helicobacter pylori (2013)

The functional characterization of Open Reading Frames (ORFs) from sequenced genomes remains a bottleneck in our effort to understand microbial biology. In particular, the functional characterization of proteins with only remote sequence homology to known proteins can be challenging, as there may be few clues to guide initial experiments. Affinity enrichment of proteins from cell lysates, and a global perspective of protein function as provided by COMBREX, affords an approach to this problem. We present here the biochemical analysis of six proteins from Helicobacter pylori ATCC 26695, a focus organism in COMBREX. Initial hypotheses were based upon affinity capture of proteins from total cellular lysate using derivatized nano-particles, and subsequent identification by mass spectrometry. Candidate genes encoding these proteins were cloned and expressed in Escherichia coli, and the recombinant proteins were purified and characterized biochemically and their biochemical parameters compared with the native ones. These proteins include a guanosine triphosphate (GTP) cyclohydrolase (HP0959), an ATPase (HP1079), an adenosine deaminase (HP0267), a phosphodiesterase (HP1042), an aminopeptidase (HP1037), and new substrates were characterized for a peptidoglycan deacetylase (HP0310). Generally, characterized enzymes were active at acidic to neutral pH (4.0-7.5) with temperature optima ranging from 35 to 55°C, although some exhibited outstanding characteristics.
New Fluorinated Rhodamines for Optical Microscopy and Nanoscopy (2010)

New photostable rhodamine dyes represented by the compounds 1 a-r and 3-5 are proposed as efficient fluorescent markers with unique combination of structural features. Unlike rhodamines with monoalkylated nitrogen atoms, N',N-bis(2,2,2-trifluoroethyl) derivatives 1 e, 1 i, 1 j, 3-H and 5 were found to undergo sulfonation of the xanthene fragment at the positions 4' and 5'. Two fluorine atoms were introduced into the positions 2' and 7' of the 3',6'-diaminoxanthene fragment in compounds 1 a-d, 1 i-l and 1 m-r. The new rhodamine dyes may be excited with λ=488 or 514 nm light; most of them emit light at λ=512-554 nm (compounds 1 q and 1r at λ=576 and 589 nm in methanol, respectively) and have high fluorescence quantum yields in solution (up to 98 %), relatively long excited-state lifetimes (>3 ns) and are resistant against photobleaching, especially at high laser intensities, as is usually applied in confocal microscopy. Sulfonation of the xanthene fragment with 30 % SO3 in H2SO4 is compatible with the secondary amide bond (rhodamine-CON(Me)CH2CH2COOH) formed with MeNHCH2CH2COOCH3 to providing the sterically unhindered carboxylic group required for further (bio)conjugation reactions. After creating the amino reactive sites, the modified derivatives may be used as fluorescent markers and labels for (bio)molecules in optical microscopy and nanoscopy with very-high light intensities. Further, the new rhodamine dyes are able to pass the plasma membrane of living cells, introducing them as potential labels for recent live-cell-tag approaches. We exemplify the excellent performance of the fluorinated rhodamines in optical microscopy by fluorescence correlation spectroscopy (FCS) and stimulated emission depletion (STED) nanoscopy experiments.
Analytic Methods for Optimizing Realtime Crowdsourcing (2012)

Realtime crowdsourcing research has demonstrated that it is possible to recruit paid crowds within seconds by managing a small, fast-reacting worker pool. Realtime crowds enable crowd-powered systems that respond at interactive speeds: for example, cameras, robots and instant opinion polls. So far, these techniques have mainly been proof-of-concept prototypes: research has not yet attempted to understand how they might work at large scale or optimize their cost/performance trade-os. In this paper, we use queueing theory to analyze the retainer model for realtime crowdsourcing, in particular its expected wait time and cost to requesters. We provide an algorithm that allows requesters to minimize their cost subject to performance requirements. We then propose and analyze three techniques to improve performance: push notications, shared retainer pools, and precruitment, which involves recalling retainer workers before a task actually arrives. An experimental validation nds that precruited workers begin a task 500 milliseconds after it is posted, delivering results below the one-second cognitive threshold for an end-user to stay in ow.
Molecular regulation of IL-6 activation by asbestos in lung epithelial cells: role of reactive oxygen species (1997)

IL-6 has been characterized as a pleiotropic cytokine with multiple biologic activities, but its induction and role in asbestos diseases have not been studied. Asbestos fibers were found to stimulate IL-6 expression and secretion in pulmonary type II-like epithelial A549 cells as well as in normal human bronchial epithelial cells. IL-6 induction was dependent on the intracellular redox-oxidative state, since intracellular hydroxyl scavengers and N-acetylcysteine, a precursor of glutathione, abrogated IL-6 secretion by asbestos or H2O2. IL-6 induction paralleled increased DNA binding activity to the nuclear factor-kappa B (NF-kappa B)- and NF-IL-6-recognized sites in the IL-6 promoter. The NF-kappa B and NF-IL-6 DNA binding proteins were immunochemically characterized as a heterodimer p65/p50 and a homodimer C/EBP beta, respectively. Stimulation of DNA binding activity to the NF-kappa B and NF-IL-6 binding sites of the IL-6 promoter by asbestos or H2O2 were inhibited by tetramethylthiourea, a hydroxyl radical scavenger. The role of local IL-6 production in the pathophysiologic processes of fiber-induced lung disorders was examined. Although less active than fibroblast growth factor, human rIL-6 also stimulated lung fibroblast growth, as evidenced by increased [3H]thymidine incorporation. Furthermore, elevated IL-6 levels were found in bronchoalveolar lavage fluids from patients diagnosed with lung fibrosis and work-related histories of long term asbestos exposure. Taken together, the results suggest that asbestos-induced oxidative stress is involved in the activation of NF-kappa B and NF-IL-6 transcription factors, which recognize the IL-6 promoter. The resulting increase in IL-6 expression may be involved in both inflammatory and fibrotic processes in the lung.
Distribution of Catheter-injected Local Anesthetic in a Model of the Subarachnoid Space (1991)

Maldistribution of local anesthetic administered through a subarachnoid catheter recently has been implicated as a possible cause of sacral root injury. To examine subarachnoid distribution of catheter-injected local anesthetic, we constructed a model of the subarachnoid space and administered solutions containing lidocaine and methylene blue through sacrally directed catheters. We studied three catheters: a 28-G endport, a 20-G endport, and a 20-G multiple sideport. To determine the injection rates to be used, ten clinicians were observed while they performed mock subarachnoid injections: the mean (+/- standard deviation) "normal" injection times for the 28-G and 20-G catheters were 52.6 +/- 17.2 and 11.9 +/- 7.2 s, respectively. The correlation coefficient for lidocaine concentration estimated by methylene blue spectrophotometric absorbance and measured by immunoassay was 0.977. Administration of hyperbaric local anesthetic through a sacrally directed catheter resulted in restricted distribution of anesthetic with a relatively high peak concentration. Rate of injection was a critical factor affecting distribution; faster injections tended to distribute solution more uniformly and to a higher segmental level, resulting in substantially lower peak concentrations. When catheters were injected at clinically relevant rates, the 28-G catheter produced the greatest degree of maldistribution; this difference appeared to be primarily a function of flow rate. Differences in peak lidocaine concentration between the two 20-G catheters were neither large nor consistent. However, despite sacral placement, the multiple-sideport catheter distributed anesthetic toward "higher" spinal segments more consistently. Distribution was more favorable when the injected solution was less dense (closer to isobaric).(ABSTRACT TRUNCATED AT 250 WORDS)
TfOH-Catalyzed One-Pot Domino Reaction for Diastereoselective Synthesis of Polysubstituted Tetrahydrospiro[carbazole-1,3′-indoline]s (2017)

TfOH-catalyzed one-pot sequential reaction of indoles, acetophenones (cyclic ketones), and various 3-methyleneoxindolines in toluene afforded polysubstituted tetrahydrospiro[carbazole-1,3'-indoline]s in satisfactory yields. <sup>1</sup>H NMR spectra and single-crystal structures indicated that the obtained tetrahydrospiro[carbazole-1,3'-indoline]s existing in an unusual trans-configuration. The reaction mechanism was believed to proceed with domino acid-catalyzed 3-alkenylation of indoles with acetophenones, Diels-Alder reaction of 3-alkyenylindoles with 3-methyleneoxindolines, and an acid-catalyzed diastereoisomerization process.
Metabolic Design (2001)

The prelims comprise: Introduction Measurement of Intracellular Metabolites Expansion of the Substrate Spectrum Enhancement of Product Yield and Spectrum Concluding Remarks and Future Aspects References