gebhart/patrepeval huggingface dataset:
Use of photopatterned porous polymer monoliths as passive micromixers to enhance mixing efficiency for on-chip labeling reactions (2009)

We introduce a passive micromixer with novel architecture using photopatterned porous polymer monoliths (PPM) and demonstrate an improvement in mixing efficiency by monitoring the fluorescence of an on-chip labeling reaction. UV light was used to photopattern a periodic arrangement of PPM structures directly within the channel of a plastic microfluidic chip. By optimizing the composition of the polymerization solution and irradiation time we demonstrate the ability to photopattern PPM in regularly repeating 100 microm segments at the tee-junction of the disposable device. To evaluate the efficiency of this dual functional mixer-reactor fluorescamine and lysine were introduced in separate channels upstream of the tee-junction and the intensity of laser-induced fluorescence resulting from the fluorogenic labeling reaction was monitored. The fluorescence level after the photopatterned periodic monolith configuration was 22% greater than both an equivalent 1 cm continuous segment of PPM and an open channel. Results indicate that this periodic arrangement of PPM, with regularly spaced open areas between 100 microm plugs of PPM, is directly responsible for enhancing the mixing and overall rate of chemical reaction in the system. In addition to facilitating preparation of a dual functional mixer-reactor, the ability to accurately photopattern PPM is an enabling technology for seamlessly integrating multiple monoliths into a single device. This technology will be particularly important to proteomic applications requiring preconcentration, enzymatic digestion and two-dimensional separations.
Oil-in-Water Emulsion MF59 Increases Germinal Center B Cell Differentiation and Persistence in Response to Vaccination (2015)

Induction of persistent protective immune responses is a key attribute of a successful vaccine formulation. MF59 adjuvant, an oil-in-water emulsion used in human vaccines, is known to induce persistent high-affinity functional Ab titers and memory B cells, but how it really shapes the Ag-specific B cell compartment is poorly documented. In this study, we characterized the Ab- and Ag-specific B cell compartment in wild-type mice immunized with HlaH35L, a Staphylococcus aureus Ag known to induce measurable functional Ab responses, formulated with MF59 or aluminum salts, focusing on germinal centers (GC) in secondary lymphoid organs. Taking advantage of single-cell flow cytometry analyses, HlaH35L-specific B cells were characterized for the expression of CD38 and GL-7, markers of memory and GC, respectively, and for CD80 and CD73 activation markers. We demonstrated that immunization with MF59-, but not aluminum salt-adjuvanted HlaH35L, induced expanded Ag-specific CD73(+)CD80(-) GC B cells in proximal- and distal-draining lymph nodes, and promoted the persistence of GC B cells, detected up to 4 mo after immunization. In addition to increasing GC B cells, MF59-adjuvanted HlaH35L also increased the frequency of T follicular helper cells. This work extends previous knowledge regarding adaptive immune responses to MF59-adjuvanted vaccines, and, to our knowledge, for the first time an adjuvant used in human licensed products is shown to promote strong and persistent Ag-specific GC responses that might benefit the rational design of new vaccination strategies.
Epigenetic Targeting of Waldenström Macroglobulinemia Cells with Bet Inhibitors Synergizes with BCl2 or Histone Deacetylase Inhibition (2020)

AIM: Waldenström macroglobulinemia (WM) is a low-grade B-cell lymphoma characterized by overproduction of monoclonal IgM. To date, there are no therapies that provide a cure for WM patients, and therefore, it is important to explore new therapies. Little is known about the efficiency of epigenetic targeting in WM. MATERIALS & METHODS: WM cells were treated with BET inhibitors (JQ1 and I-BET-762) and venetoclax, panobinostat or ibrutinib. RESULTS: BET inhibition reduces growth of WM cells, with little effect on survival. This finding was enhanced by combination therapy, with panobinostat (LBH589) showing the highest synergy. CONCLUSION: Our studies identify BET inhibitors as effective therapy for WM, and these inhibitors can be enhanced in combination with BCL2 or histone deacetylase inhibition.
Mode conversion losses in SOI photonic wire based racetrack resonators (2006)

We found that in low loss SOI sub-micron photonic wire racetrack resonators, when the air gap between the resonator and access waveguide is ≪120nm, the mode conversion losses in the coupling region dominate bending and propagation losses.
Recovery of the soliton self-frequency shift by optical phase conjugation (1994)

The recovery of the self-frequency shift effect on a soliton by optical phase conjugation is investigated. It is proved that, without third-order dispersion and fiber loss, the soliton self-frequency shift can be completely recovered. The recoveries for a fundamental soliton and a second-order soliton in the presence of third-order dispersion and of fiber loss, which is compensated by the distributed erbium-doped fiber amplifiers, are numerically studied.
Hyaluronic acid conjugates for topical treatment of skin cancer lesions (2021)

Skin cancer is one of the most common types of cancer in the United States and worldwide. Topical products are effective for treating cancerous skin lesions when surgery is not feasible. However, current topical products induce severe irritation, light-sensitivity, burning, scaling, and inflammation. Using hyaluronic acid (HA), we engineered clinically translatable polymer-drug conjugates of doxorubicin and camptothecin termed, DOxorubicin and Camptothecin Tailored at Optimal Ratios (DOCTOR) for topical treatment of skin cancers. When compared to the clinical standard, Efudex, DOCTOR exhibited high cancer-cell killing specificity with superior safety to healthy skin cells. In vivo studies confirmed its efficacy in treating cancerous lesions without irritation or systemic absorption. When tested on patient-derived primary cells and live-skin explants, DOCTOR killed the cancer with a selectivity as high as 21-fold over healthy skin tissue from the same donor. Collectively, DOCTOR provides a safe and potent option for treating skin cancer in the clinic.
The Emerging Role of Stereotactic Ablative Radiotherapy for Primary Renal Cell Carcinoma: A Systematic Review and Meta-Analysis (2019)

Stereotactic ablative radiotherapy is a high-precision, noninvasive radiation treatment requiring few outpatient visits, and represents a safe and effective management option for primary renal cell carcinoma.
Statistical approaches to temporal and spatial autocorrelation in resting-state functional connectivity in mice measured with optical intrinsic signal imaging (2022)

<b>Significance:</b> Resting-state functional connectivity imaging in mice with optical intrinsic signal (OIS) imaging could provide a powerful translational tool for developing imaging biomarkers in preclinical disease models. However, statistical interpretation of correlation coefficients is hampered by autocorrelations in the data. <b>Aim:</b> We sought to better understand temporal and spatial autocorrelations in optical resting-state data. We then adapted statistical methods from functional magnetic resonance imaging to improve statistical inference. <b>Approach:</b> Resting-state data were obtained from mice using a custom-built OSI system. The autocorrelation time was calculated at each pixel, and <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mi>z</mml:mi></mml:mrow> </mml:math> scores for correlation coefficients were calculated using Fisher transforms and variance derived from either Bartlett's method or xDF. The significance of each correlation coefficient was determined through control of the false discovery rate (FDR). <b>Results:</b> Autocorrelation was generally even across the cortex and parcellation reduced variance. Correcting variance with Bartlett's method resulted in a uniform reduction in <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mi>z</mml:mi></mml:mrow> </mml:math> scores, with xDF preserving high <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mi>z</mml:mi></mml:mrow> </mml:math> scores for highly correlated data. Control of the FDR resulted in reasonable thresholding of the correlation coefficient matrices. The use of Bartlett's method compared with xDF results in more conservative thresholding and fewer false positives under null hypothesis conditions. <b>Conclusions:</b> We developed streamlined methods for control of autocorrelation in OIS functional connectivity data in mice, and Bartlett's method is a reasonable compromise and simplification that allows for accurate autocorrelation correction. These results improve the rigor and reproducibility of functional neuroimaging in mice.
ChemInform Abstract: Discovery of a Novel Series of Selective MMP Inhibitors: Identification of the γ‐Sulfone‐thiols. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Radial tracking in high-speed DVD players (an application of notch filtering and multirate control) (2003)

The problem considered is the radial tracking of the optical pick-up in a DVD-ROM. For low-speed players, it is known that this problem can be solved by means of simple lead-lag regulators. For high-speed players, the servo design is much more tricky, and a more sophisticated control scheme is required. The control scheme proposed is constituted by a lead-lag filter, two notch filters and a low-pass filter. This set of filters is implemented in a parallel structure. This architecture is adequate to provide a good radial tracking. The performance of the controller are tested on a real plant, and experimental results are reported.
Development of Plasmid DNA‐Based Gene Transfer (2007)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Metabolism of Flavone-8-acetic Acid in Mice. (2016)

Flavone-8-acetic acid (FAA) is a potent antivascular agent in mice but not in humans. Assuming that FAA was bioactivated in mice, we previously demonstrated that 6-OH-FAA was formed from FAA by mouse microsomes but not by human microsomes; its antivascular activity was 2.1- to 15.9-fold stronger than that of FAA, and its antivascular activity was mediated through the Ras homolog gene family (Rho) protein kinase A (RhoA) pathway. The present work aimed to study FAA metabolism in order to verify if 6-OH-FAA is formed in mice. Using synthesized standards and high-performance liquid chromatography (HPLC) coupled with ultraviolet (UV) detection and mass spectrometry (MS) analysis, we herein demonstrated, for the first time, that in vitro FAA and its monohydroxylated derivatives could directly undergo phase II metabolism forming glucuronides, and two FAA epoxides were mostly scavenged by NAC and GSH forming corresponding adducts. FAA was metabolized in mice. Several metabolites were formed, in particular 6-OHFAA. The antitumor activity of 6-OH-FAA in vivo is worthy of investigation.
Interaction of 5-S RNA, 5.8-S RNA and tRNA with Rat-Liver Ribosomal Proteins (1978)

In order to ascertain 5-S RNA, 5.8-S RNA and tRNA binding proteins from eukaryotic ribosomes, affinity chromatography of the rat liver ribosomal 40-S and 60-S subunit proteins on immobilized RNAs was used. Rat liver 5-S RNA, 5.8-S RNA and tRNA were immobilized via 3′-end ribose to adipic-acid-hydrazide-epoxy-activated Sepharose 6B. Using two-dimensional polyacrylamide gel electrophoresis in a urea-urea system, the bound proteins were identified as follows: a) 5-S RNA was found to form a complex containing mainly proteins L6 and L18 of the large ribosomal subunit, whereas proteins L7, L8 and L35 were present in the complex to a lesser degree. b) 5.8-S RNA bound proteins L5, L6, L7 and L18 from the 60-S subunit. c) tRNA formed a complex containing proteins S3′, S6, S8, S9, S11, S14, S18 and S23/24 from the 40-S subunit and proteins L5, L6, L7, L8, L13, L14, L18, L19, L21, L25, L26, L27, L29, L31, L32, L35 and L36 from the 60-S subunit. From this list of proteins S6, S14 and S23/24 of the small and L6, L13, L19, L21, L26, L32, L35 and L36 of the large subunit gave stronger spots than the others. Proteins from the different complexes are overlapping to a certain extent. The results suggest that 5-S RNA and 5.8-S RNA are in a close neighbourhood in the rat liver ribosome. It is supposed that 5-S RNA, 5.8-S RNA and proteins L5, L6, L7, L8, L13, L19, L21, L26, L32, L35, L36 are at or near the eukaryotic peptidyltransferase centre.
Supplementary Figure 3 from DLL4-Notch Signaling Mediates Tumor Resistance to Anti-VEGF Therapy <i>In Vivo</i> (2023)

&lt;p&gt;PDF 584K, Combination therapy by blockade of both Notch signaling and the VEGF pathway displayed a synergistic therapeutic efficacy in HT1080 xenografted tumors. Single therapy with either DBZ or bevacizumab did not affect tumor growth and animal survival but combined DBZ with bevacizuamb synergistically inhibited tumor growth and increased animal survival in HT1080 xenografted tumors. Mean � SE, N=5. *P&lt;0.05, **P&lt;0.01.&lt;/p&gt;
Challenges and opportunities in automotive transmission control (2005)

Automotive transmission is a key element in the powertrain that connects the power source to the wheels of a vehicle. To improve fuel economy, reduce emission and enhance driving performance, many new technologies have been introduced in the transmission area in recent years. This paper first reviews different types of automotive transmissions and explains their unique control characteristics. We then address the challenges facing automotive transmission control from three aspects: calibration, shift scheduling, and sensing, actuation and electronics. Along the way, research opportunities to further improve system performance are discussed.
Optical and Electrical Interfacing Technologies for Living Cell Bio-Chips (2010)

Whole-cell bio-chips for functional sensing integrate living cells on miniaturized platforms made by micro-system-technologies (MST). The cells are integrated, deposited or immersed in a media which is in contact with the chip. The cells behavior is monitored via electrical, electrochemical or optical methods. In this paper we describe such whole-cell biochips where the signal is generated due to the genetic response of the cells. The solid-state platform hosts the biological component, i.e. the living cells, and integrates all the required micro-system technologies, i.e. the micro-electronics, micro-electro optics, micro-electro or magneto mechanics and micro-fluidics. The genetic response of the cells expresses proteins that generate: a. light by photo-luminescence or bioluminescence, b. electrochemical signal by interaction with a substrate, or c. change in the cell impedance. The cell response is detected by a front end unit that converts it to current or voltage amplifies and filters it. The resultant signal is analyzed and stored for further processing. In this paper we describe three examples of whole-cell bio chips, photo-luminescent, bioluminescent and electrochemical, which are based on the genetic response of genetically modified E. coli microbes integrated on a micro-fluidics MEMS platform. We describe the chip outline as well as the basic modeling scheme of such sensors. We discuss the highlights and problems of such system, from the point of view of micro-system-technology.
Enhancing Fullerene‐Based Solar Cell Lifetimes by Addition of a Fullerene Dumbbell (2014)

Cost-effective, solution-processable organic photovoltaics (OPV) present an interesting alternative to inorganic silicon-based solar cells. However, one of the major remaining challenges of OPV devices is their lack of long-term operational stability, especially at elevated temperatures. The synthesis of a fullerene dumbbell and its use as an additive in the active layer of a PCDTBT:PCBM-based OPV device is reported. The addition of only 20 % of this novel fullerene not only leads to improved device efficiencies, but more importantly also to a dramatic increase in morphological stability under simulated operating conditions. Dynamic secondary ion mass spectrometry (DSIMS) and TEM are used, amongst other techniques, to elucidate the origins of the improved morphological stability.
UTGB/medaka: genomic resource database for medaka biology (2007)

Medaka (Oryzias latipes) is a small egg-laying freshwater teleost native to East Asia that has become an excellent model system for developmental genetics and evolutionary biology. The draft medaka genome sequence (700 Mb) was reported in June 2007, and its substantial genomic resources have been opened to the public through the University of Tokyo Genome Browser Medaka (UTGB/medaka) database. This database provides basic genomic information, such as predicted genes, expressed sequence tags (ESTs), guanine/cytosine (GC) content, repeats and comparative genomics, as well as unique data resources including (i) 2473 genetic markers and experimentally confirmed PCR primers that amplify these markers, (ii) 142,414 bacterial artificial chromosome (BAC) and 217,344 fosmid end sequences that amount to 15.0- and 11.1-fold clone coverage of the entire genome, respectively, and were used for draft genome assembly, (iii) 16,519,460 single nucleotide polymorphisms (SNPs), and 2 859 905 insertions/deletions detected between two medaka inbred strain genomes and (iv) 841 235 5'-end serial analyses of gene-expression (SAGE) tags that identified 344 266 transcription start sites on the genome. UTGB/medaka is available at: http://medaka.utgenome.org/.
A model to measure insulin effects on glucose transport and phosphorylation in muscle: a three-tracer study (1996)

We studied five healthy subjects with perfused forearm and euglycemic clamp techniques in combination with a three-tracer (D-[12C]mannitol, not transportable; 3-O-[14C]methyl-D-glucose, transportable but not metabolizable; D-[3-3H]glucose, transportable and metabolizable) intra-arterial pulse injection to assess transmembrane transport and intracellular phosphorylation of glucose in vivo in human muscle. The washout curves of the three tracers were analyzed with a multicompartmental model. A priori identifiability analysis of the tracer model shows that the rate constants of glucose transport into and out of the cells and of glucose phosphorylation are uniquely identifiable. Tracer model parameters were estimated by a nonlinear least-squares parameter estimation technique. We then solved for the tracee model and estimated bidirectional transmembrane transport glucose fluxes, glucose intracellular phosphorylation, extracellular and intracellular volumes of glucose distribution, and extracellular and intracellular glucose concentrations. Physiological hyperinsulinemia (473 +/- 22 pM) caused 2.7-fold (63.1 +/- 7.2 vs. 23.4 +/- 6.1 mumol.min-1.kg-1, P < 0.01) and 5.1-fold (42.5 +/- 5.8 vs. 8.4 +/- 2.2 mumol.min-1.kg-1, P < 0.01) increases in transmembrane influx and intracellular phosphorylation of glucose, respectively. Extracellular distribution volume and concentration of glucose were unchanged, whereas intracellular distribution volume of glucose was increased (approximately 2-fold) and intracellular glucose concentration was almost halved by hyperinsulinemia. In summary, 1) a multicompartment model of three-tracer kinetic data can quantify transmembrane glucose fluxes and intracellular glucose phosphorylation in human muscle; and 2) physiological hyperinsulinemia stimulates both transport and phosphorylation of glucose and, in doing so, amplifies the role of glucose transport as a rate-determining step of muscle glucose uptake.
Notice of Removal: Shear wave attenuation quantification in viscoelastic transverse isotropic soft tissue using shear wave elastography (2017)

Removed.
Negative Correlation between Circulating CD4+FOXP3+CD127− Regulatory T Cells and Subsequent Antibody Responses to Infant Measles Vaccine but Not Diphtheria–Tetanus–Pertussis Vaccine Implies a Regulatory Role (2017)

Regulatory T cells (Tregs) play a key homeostatic role by suppressing immune responses. They have been targeted in mouse and human cancer studies to improve vaccine immunogenicity and tumor clearance. A number of commercially available drugs and experimental vaccine adjuvants have been shown to target Tregs. Infants have high numbers of Tregs and often have poor responses to vaccination, yet the role Tregs play in controlling vaccine immunogenicity has not been explored in this age group. Herein, we explore the role of CD4<sup>+</sup>FOXP3<sup>+</sup>CD127<sup>-</sup> Tregs in controlling immunity in infant males and females to vaccination with diphtheria-tetanus-whole cell pertussis (DTP) and/or measles vaccine (MV). We find correlative evidence that circulating Tregs at the time of vaccination suppress antibody responses to MV but not DTP; and Tregs 4 weeks after DTP vaccination may suppress vaccine-specific cellular immunity. This opens the exciting possibility that Tregs may provide a future target for improved vaccine responses in early life, including reducing the number of doses of vaccine required. Such an approach would need to be safe and the benefits outweigh the risks, thus further research in this area is required.
Polyvalent Oligonucleotide Gold Nanoparticle Conjugates as Delivery Vehicles for Platinum(IV) Warheads* (2020)

Polyvalent oligonucleotide gold nanoparticle conjugates (DNA-AuNPs) have appealing properties for drug delivery applications, including high cellular uptake in a variety of cell types, no demonstrated toxicity inherent to the conjugate, and resistance to enzymatic degradation. In this chapter, the authors have combined the properties of DNA-AuNPs and platinum(IV) prodrugs into a single agent for drug delivery. DNA-AuNPs were synthesized, characterized, and tested in vitro as carriers for Pt(IV) prodrugs. The conjugate was designed to release a cytotoxic dose of cisplatin upon intracellular reduction. An ideal Pt(IV) complex should be sufficiently stable to travel through the bloodstream until it reaches a tumor cell without decomposition. The ability of Pt-DNA-AuNPs to enter cells was investigated by fluorescence microscopy using particles functionalized with a mixed monolayer of platinated oligonucleotide strands and 5' dye (Cy5)-labeled strands.
Time-Frequency Analysis of Spectrally-Notched Random FM Waveforms (2020)

Various classes of random FM waveforms have recently emerged that are amenable for high-power radar transmitters while providing high dimensionality that facilitates a variety of new applications. One prominent example is the generation of transmit spectral notching to contend with dynamic radio frequency interference (RFI) for the purpose of spectrum sharing. While previous design-focused work has used the aggregate power spectrum and autocorrelation properties of these waveforms to facilitate spectrum-shaping optimization, here we examine their time-frequency characteristics to better understand the efficacy of spectral notching at different time scales. In so doing it is observed that there may be a need for different design perspectives depending on the nature of the RFI.