gebhart/patrepeval huggingface dataset:
Model studies on the active site of cytochrome P-450 : an FeII–porphyrin carrying a strapped thiolate ligand (1982)

An FeII–porphyrin has been synthesised with a strap carrying a thiolate residue covalently bound across one face of the macrocycle; the spectroscopic properties of the carbon monoxide complex of this model system closely match those of the CO-complex of cytochrome P-450.
Method and system for formation and withdrawal of a sample from a surface to be analyzed (2023)

A method and system for formation and withdrawal of a sample from a surface to be analyzed utilizes a collection instrument having a port through which a liquid solution is conducted onto the surface to be analyzed. The port is positioned adjacent the surface to be analyzed, and the liquid solution is conducted onto the surface through the port so that the liquid solution conducted onto the surface interacts with material comprising the surface. An amount of material is thereafter withdrawn from the surface. Pressure control can be utilized to manipulate the solution balance at the surface to thereby control the withdrawal of the amount of material from the surface. Furthermore, such pressure control can be coordinated with the movement of the surface relative to the port of the collection instrument within the X-Y plane.
Accuracy of 18F-Fluorocholine PET for the Detection of Parathyroid Adenomas: Prospective Single-Center Study (2021)

The purpose of this prospective study was to determine the correct localization rate (CLR) of <sup>18</sup>F-fluorocholine PET for the detection of parathyroid adenomas in comparison to <sup>99m</sup>Tc-sestamibi imaging. <b>Methods:</b> This was a single-arm prospective trial. Ninety-eight patients with biochemical evidence of primary hyperparathyroidism were imaged before parathyroidectomy using <sup>18</sup>F-fluorocholine PET/MRI. <sup>99m</sup>Tc-sestamibi imaging performed separately from the study was evaluated for comparison. The primary endpoint of the study was the CLR on a patient level. Each imaging study was interpreted by 3 masked readers on a per-region basis. Lesions were validated by histopathologic analysis of surgical specimens. <b>Results:</b> Of the 98 patients who underwent <sup>18</sup>F-fluorocholine PET, 77 subsequently underwent parathyroidectomy and 60 of those had <sup>99m</sup>Tc-sestamibi imaging. For <sup>18</sup>F-fluorocholine PET in patients who underwent parathyroidectomy, the CLR based on the masked reader consensus was 75% (95% CI, 0.63-0.82). In patients who underwent surgery and had an available <sup>99m</sup>Tc-sestamibi study, the CLR increased from 17% (95% CI, 0.10-0.27) for <sup>99m</sup>Tc-sestamibi imaging to 70% (95% CI, 0.59-0.79) for <sup>18</sup>F-fluorocholine PET. <b>Conclusion:</b> In this prospective study using masked readers, the CLR for <sup>18</sup>F-fluorocholine PET was 75%. In patients with a paired <sup>99m</sup>Tc-sestamibi study, the use of <sup>18</sup>F-fluorocholine PET increased the CLR from 17% to 70%. <sup>18</sup>F-fluorocholine PET is a superior imaging modality for the localization of parathyroid adenomas.
Control topology options for single-phase UPS inverters (1997)

Four control topologies for single-phase uninterruptible power system (UPS) inverters are presented and compared, with the common objective of providing a dynamically stiff, low total harmonic distortion (THD), sinusoidal output voltage. Full-state feedback, full-state command controllers are shown, utilizing both filter inductor current and filter capacitor current feedback to augment output voltage control. All controllers presented include output voltage decoupling in a manner analogous to "back EMF" decoupling in DC motor drives. Disturbance input decoupling of the load current and its derivative is presented. An observer-based controller is additionally considered and is shown to be a technically viable, economically attractive option. The accuracy transfer function of the observer estimate is used to evaluate its measurement performance. Comparative disturbance rejection is evaluated by overlaying the dynamic stiffness (inverse of output impedance) frequency response of each controller on a single plot. Experimental results for one controller are presented.
Utilizing partial channel information in the design of space-time block codes (2003)

The assumption of no channel knowledge at the transmitter is inherent in the design of classical space-time codes for wireless communication. This work, on the other hand, assumes that non-perfect quantized channel information obtained from a feedback link is available at the transmitter and investigates how such channel knowledge can be incorporated into the design of space-time block codes. Efficient codes are found by means of a gradient search over a continuous alphabet. Simulation results for a Rayleigh fading scenario in a system using two transmit antennas and one receive antenna show that significant gains are possible.
A Novel Cationic Microbubble Coated with Stearic Acid-Modified Polyethylenimine to Enhance DNA Loading and Gene Delivery by Ultrasound (2013)

A novel cationic microbubble (MB) for improvement of the DNA loading capacity and the ultrasound-mediated gene delivery efficiency has been developed; it has been prepared with commercial lipids and a stearic acid modified polyethylenimine 600 (Stearic-PEI600) polymer synthesized via acylation reaction of branched PEI600 and stearic acid mediated by N, N'-carbonyldiimidazole (CDI). The MBs' concentration, size distribution, stability and zeta potential (ζ-potential) were measured and the DNA loading capacity was examined as a function of the amount of Stearic-PEI600. The gene transfection efficiency and cytotoxicity were also examined using breast cancer MCF-7 cells via the reporter plasmid pCMV-Luc, encoding the firefly luciferase gene. The results showed that the Stearic-PEI600 polymer caused a significant increase in magnitude of ζ-potential of MBs. The addition of DNA into cationic MBs can shift ζ-potentials from positive to negative values. The DNA loading capacity of the MBs grew linearly from (5±0.2) ×10⁻³ pg/µm² to (20±1.8) ×10⁻³ pg/µm² when Stearic-PEI600 was increased from 5 mol% to 30 mol%. Transfection of MCF-7 cells using 5% PEI600 MBs plus ultrasound exposure yielded 5.76±2.58×10³ p/s/cm²/sr average radiance intensity, was 8.97- and 7.53-fold higher than those treated with plain MBs plus ultrasound (6.41±5.82) ×10² p/s/cm²/sr, (P<0.01) and PEI600 MBs without ultrasound (7.65±6.18) ×10² p/s/cm²/sr, (P<0.01), respectively. However, the PEI600 MBs showed slightly higher cytotoxicity than plain MBs. The cells treated with PEI600-MBs and plain MBs plus ultrasound showed 59.5±6.1% and 71.4±7.1% cell viability, respectively. In conclusion, our study demonstrated that the novel cationic MBs were able to increase DNA loading capacity and gene transfection efficiency and could be potentially applied in targeted gene delivery and therapy.
Abstract A53: Prostate cancer cell capture using immobilized inhibitors of prostate-specific membrane antigen. (2011)

Abstract Prostate circulating tumor cells (PCTCs) in the peripheral blood are shed from either a primary tumor or its metastases. These disseminated PCTCs are directly responsible for the most cancer deaths and the major cause of prostate cancer-related mortality. Therefore, elucidating the quantity of the exfoliated PCTCs in blood circulation can serve as an indicator for the clinical management in prostate cancer diseases by providing information on the success/failure of therapy. And the isolation and removal of PCTCs from circulation could potentially reduce prostate cancer metastasis. Furthermore, culturing and characterizing captured PCTCs from a patient is an attractive strategy for developing personalized treatment options. It has been established that prostate-specific membrane antigen (PSMA) is up-regulated and strongly expressed on prostate cancer cells associated with high grade primary, androgen independent, and metastatic tumors. While it is known that PSMA expression is heterogeneous in primary prostate tumors and metastases, completely PSMA negative prostate carcinomas are rare. The present study has outfitted streptavidin coated magnetic beads with a unique irreversible small-molecule PSMA inhibitor, Biotin-PEG12-CTT-54, and demonstrated that they can selectively capture PSMA + cells. The results demonstrated prostate cancer cells capturing is very specific and highly efficient, and high recovery and high viability were obtained. Subsequent in vitro propagation of these viable captured lymph node-based metastatic prostate LnCaP cells is possible without removal of magnetic beads on the cell surface. The results suggested that PCTCs enrichment by streptavidin coated magnetic beads with biotinated PSMA inhibitor has a high PCTC detection rate with an easy manual protocol, and can serve as an additional research tool and clinical assay in PCTC. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2011 Nov 12-16; San Francisco, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2011;10(11 Suppl):Abstract nr A53.
Time-resolved particle image velocimetry measurements with wall shear\n stress and uncertainty quantification for the FDA benchmark nozzle model (2014)

We present validation of benchmark experimental data for computational fluid\ndynamics (CFD) analyses of medical devices using advanced Particle Image\nVelocimetry (PIV) processing and post-processing techniques. This work is an\nextension of a previous FDA-sponsored multi-laboratory study, which used a\nmedical device mimicking geometry referred to as the FDA benchmark nozzle\nmodel. Time-resolved PIV analysis was performed in five overlapping regions of\nthe model for Reynolds numbers in the nozzle throat of 500, 2,000, 5,000, and\n8,000. Images included a two-fold increase in spatial resolution in comparison\nto the previous study. Data was processed using ensemble correlation, dynamic\nrange enhancement, and phase correlations to increase signal-to-noise ratios\nand measurement accuracy, and to resolve flow regions with large velocity\nranges and gradients, which is typical of many blood-contacting medical\ndevices. Parameters relevant to device safety, including shear stress at the\nwall and in bulk flow, were computed using radial basis functions (RBF) to\nimprove accuracy. In-field spatially resolved pressure distributions, Reynolds\nstresses and energy dissipation rates were computed from PIV measurements.\nVelocity measurement uncertainty was estimated directly from the PIV\ncorrelation plane, and uncertainty analysis for wall shear stress at each\nmeasurement location was performed using a Monte Carlo model. (truncated\nabstract)\n
Nanofabrication by self-assembly (2009)

The self-assembly paradigm in chemistry, physics and biology has matured scientifically over the past two-decades to a point of sophistication that one can begin to exploit its numerous attributes in nanofabrication. In what follows we will take a brief look at current thinking about self-assembly and with some recent examples taken from our own work examine how nanofabrication has benefited from self-assembly.
Invited Review (2011)

ADVERTISEMENT RETURN TO ISSUEPREVEditorialNEXTInvited ReviewStéphane Caron and Chris SenanayakeCite this: Org. Process Res. Dev. 2011, 15, 6, 1235Publication Date (Web):September 9, 2011Publication History Published online9 September 2011Published inissue 18 November 2011https://pubs.acs.org/doi/10.1021/op200218mhttps://doi.org/10.1021/op200218meditorialACS PublicationsCopyright © 2011 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views1596Altmetric-Citations-LEARN 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 PDF (604 KB) Get e-AlertscloseSUBJECTS:Hydrocarbons,Hydrogen,Hydrogenation,Physical and chemical processes,Transition metals Get e-Alerts
Restorer genes for different forms of Brassica cytoplasmic male sterility map to a single nuclear locus that modifies transcripts of several mitochondrial genes (1998)

The oilseed rape plant, Brassica napus, possesses two endogenous male sterile cytoplasms, nap and pol. Previous studies have shown that nuclear restoration of pol cytoplasmic male sterility (CMS) is conditioned by a gene, Rfp, that is also involved in modifying transcripts of the pol CMS-associated orf224/atp6 mtDNA region. We now find that the nap nuclear restorer gene Rfn apparently is identical to Mmt, a gene that conditions the modification of transcripts from several different mtDNA regions, including one that is associated with nap CMS and contains orf222, a chimeric gene related to orf224. Mmt, in turn, is found to be allelic to Rfp, suggesting that restorer genes for the two cytoplasms represent different alleles or haplotypes of a single nuclear locus. This view is supported by restriction fragment length polymorphism mapping studies that indicate that Rfn and Rfp map to the same chromosomal position. Thus, in contrast to CMS in other species, different forms of Brassica CMS are restored by alleles of a single nuclear locus, and the restoration properties of these alleles reflect their involvement in the modification of transcripts of corresponding CMS-associated mtDNA regions. A survey of 51 varieties from 8 Brassica and Sinapis species failed to find evidence of Rfn(Mmt) in other than fertility-restored, nap cytoplasm B. napus. This suggests that Rfn(Mmt) arose in Brassica with nap cytoplasm and that the necessity for fertility restoration may have provided the selective pressure for its origin and maintenance.
Pendrin Function in Airway Epithelia (2011)

The expression and function of the anion exchanger pendrin (SLC26A4) was thought to be limited mainly to the inner ear, kidney and thyroid. Recent data indicates that pendrin is also expressed in the bronchial epithelium following exposure to the T(H)2-type cytokines, interleukin (IL)-4 and IL-13. Expression of the transporter is also upregulated in bronchial asthma and chronic obstructive pulmonary disease. Both diseases involve respiratory inflammation leading to tissue destruction/remodeling and decreased airway function, and data so far indicate that increased pendrin expression and/or activity might contribute to their pathogenesis. In this review, we summarize data that have emerged within the past years aimed at revealing the role for pendrin in the airway epithelia.
Use of polyvalent coagglutination reagents for serotyping of Streptococcus suis (1993)

Polyvalent coagglutination reagents (PRs) have been evaluated for the serotyping of Streptococcus suis. Monovalent antisera produced against 28 S. suis reference strains have been grouped to obtain five different pools. A total of 249 field isolates previously identified and belonging to different serotypes were tested with PRs prepared by two different procedures: (i) monovalent coagglutination reagents were individually prepared and mixed in equal proportions, and (ii) antisera were mixed in equal proportions before the addition of the Staphylococcus aureus suspension. Only antisera tested by a tube agglutination test with 2-mercaptoethanol and presenting titers of 1:32 or higher were used. Results obtained with PRs prepared by both procedures were similar, and there was a very good correlation between the capsular type of the isolate and the reaction obtained with PRs. Thus, from a practical viewpoint, it is suggested that PRs be prepared by the first procedure. To isolates, were tested in parallel with both the PRs and the monovalent coagglutination reagents over a 1-year period. Ninety-nine percent of the typeable and all of the untypeable isolates were correctly identified. Serotyping with PRs is suggested to be a very useful and reliable screening procedure, particularly when a large number of S. suis isolates have to be serotyped. In addition, the choice of antisera to be included in a given pool is facultative and should be oriented to the needs of a region or a country.
B-cell malignancies in microRNA Eμ-miR-17∼92 transgenic mice (2013)

miR-17∼92 is a polycistronic microRNA (miR) cluster (consisting of miR-17, miR-18a, miR-19a, miR-19b, miR-20a, and miR-92a) which frequently is overexpressed in several solid and lymphoid malignancies. Loss- and gain-of-function studies have revealed the role of miR-17∼92 in heart, lung, and B-cell development and in Myc-induced B-cell lymphomas, respectively. Recent studies indicate that overexpression of this locus leads to lymphoproliferation, but no experimental proof that dysregulation of this cluster causes B-cell lymphomas or leukemias is available. To determine whether miR-17∼92- overexpression induces lymphomagenesis/leukemogenesis, we generated a B-cell-specific transgenic mouse model with targeted overexpression of this cluster in B cells. The miR-17∼92 overexpression was driven by the Eµ-enhancer and Ig heavy-chain promoter, and a 3' GFP tag was added to the transgene to track the miR expression. Expression analysis using Northern Blot and quantitative RT-PCR confirmed 2.5- to 25-fold overexpression of all six miRs in the transgenic mice spleens as compared with spleens from wild-type mice. Eµ-miR-17∼92 mice developed B-cell malignancy by the age of 12-18 mo with a penetrance of ∼80% (49% splenic B-cell lymphoproliferative disease, 28% lymphoma). At this stage mice exhibited severe splenomegaly with abnormal B-cell-derived white pulp expansion and enlarged lymph nodes. Interestingly, we found three classes of B-cell lymphomas/leukemias at varying grades of differentiation. These included expansion of CD19(+) and CD5(+) double-positive B cells similar to the aggressive form of human B-cell chronic lymphocytic leukemia, B220(+) CD43(+) B1-cell proliferation, and a CD19(+) aggressive diffuse large B-cell lymphoma-like disease, as assessed by flow cytometry and histopathological analysis.
Casirivimab/Imdevimab for Active COVID-19 Pneumonia Which Persisted for Nine Months in a Patient with Follicular Lymphoma during Anti-CD20 Therapy (2022)

Immunocompromised patients are more likely to develop severe COVID-19, and exhibit high mortality. It is also hypothesized that chronic infection in these patients can be a risk factor for developing new variants. We describe a patient with prolonged active infection of COVID-19 who became infected during treatment with an anti-CD20 antibody (obinutuzumab) for follicular lymphoma. This patient had persistent RT-PCR positivity and live virus isolation for nine months despite treatment with remdesivir and other potential antiviral therapies. The computed tomography image of the chest showed that the viral pneumonia repeatedly appeared and disappeared in different lobes, as if a new infection had occurred continuously. The patient's SARS-CoV-2 antibody titer was negative throughout the illness, even after two doses of the BNT162b2 mRNA vaccine were administered in the seventh month of infection. A combination of monoclonal antibody therapy against COVID-19 (casirivimab and imdevimab) and antivirals resulted in negative RT-PCR results, and the virus was no longer isolated. The patient was clinically cured. During the 9-month active infection period, no fixed mutations in the spike (S) protein were detected, and the in vitro susceptibility to remdesivir was retained. Therapeutic administration of anti-SARS-CoV-2 monoclonal antibodies is essential in immunocompromised patients. Therefore, measures to prevent resistance against these key drugs are urgently needed.
Successes and challenges with retroviral enzymes. (2017)

Collaborations between the Wlodawer and Skalka laboratories have covered a period of almost 30 years. During that time our groups have co-authored 18 publications, including several much cited journal articles, book chapters, and scholarly reviews. It has therefore been most rewarding for us to share enthusiasm, insights, and expertise with our Frederick colleagues over the years, and also to enjoy lasting friendships.
Abstract B191: Preclinical assessment of targeting the PI3K/AKT pathway in combination with other signal transduction pathway inhibitors (2015)

Abstract Inhibitors targeting the phosphoinositide 3-kinase (PI3K)/serine-threonine protein kinase B (AKT) pathway have been developed and have shown efficacy in inhibiting tumor growth both in preclinical models and in the clinic. The effectiveness of PI3K/AKT inhibitors, however, is attenuated by the activation of alternative signaling pathways. Conversely, the PI3K/AKT pathway is considered to be a resistance mechanism for other therapeutic or cytotoxic agents. Therefore, understanding these mechanisms may help to inform the most optimal combinations for advancement into clinical studies. Here, we explored the potential of targeting the JAK/STAT or PIM signaling pathways in combination with a novel, potent and selective AKT inhibitor, INCB047775. Consistent with published data, pharmacological inhibition of AKT by INCB047775 caused the upregulation of PIM kinases. The combined therapies of PIM inhibition and AKT inhibition exhibited significant synergistic anti-tumor effects. Combination of PIM inhibition with AKT inhibition resulted in synergistic induction of apoptosis in cancer cells. Similarly, the combination of JAK tyrosine kinase inhibition with INCB047775 exerted synergistic inhibition of the proliferation of multiple myeloma cell lines. Similar data were observed with an inhibitor of PI3Kδ in combination with both PIM and JAK inhibition, demonstrating significant crosstalk between the PI3K/AKT pathway and other critical signaling pathways. These data provide the rationale for combinatorial therapies with inhibitors targeting JAK or PIM kinases with PI3K/AKT pathway inhibitors in the clinic. Citation Format: Sang Hyun Lee, Holly Koblish, Xiangdong Liu, Haifen Ye, Jun Li, Xuesong Liu, Melody Diamond, Yue Zhang, Leslie Hall, Valerie Dostalik, Margaret Favata, Elham Behshad, Richard Wynn, Yun-long Li, Andrew Combs, Chu-Bio Xue, Wenqing Yao, Gregory Hollis, Reid Huber, Peggy Scherle. Preclinical assessment of targeting the PI3K/AKT pathway in combination with other signal transduction pathway inhibitors. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr B191.