gebhart/patrepeval huggingface dataset:
Abstract 1725: Tissue-based biomarker analysis of DLBCL using multiplex immunofluorescence AQUA (Automated Quantitative Analysis) algorithms (2022)

Abstract Purpose: Deeper understanding of immune landscape of DLBCL tumor microenvironment is critical for exploration and development of next generation immunotherapies. Although conventional immunohistochemical (IHC) analysis can provide information on the immune landscape or target expression, it is generally limited to single marker analysis. Advantages of multiplex fluorescence IHC (mFIHC) include the ability to assess different cell types, their spatial relationship as well as variable antigen expression on tumor cells. As such, we developed quantitative mFIHC panels using AQUA® (Automated Quantitative Analysis) technology to evaluate T and B cell populations and their functional status to generate detailed spatial information of immune checkpoint (IC) markers. mFIHC combined with hypothesis driven spatial profiling algorithms (e.g., AQUA Technology) were found to provide the most powerful predictors of immunotherapies in a systematic meta-analyses of over 8000 patients treated with PD1/L1 pathway blockers (Lu et al., JAMA Oncol 2019). Implementation of mFIHC coupled with robust image analysis may provide great insight into DLBCL immune surveillance, mechanism of resistance and patient stratification. Study Design: We designed two novel mFIHC assays to (1) characterize various B cell populations (CD19, CD20, CD22, PAX5, CD3, TIM3), and (2) evaluate T cell functional status (CD8, Granzyme B, PD1, PDL1, TIM3, Tumor). We successfully validated clinical grade mFIHC assays using automated staining (Leica Bond RX), imaging (Vectra Polaris) and analyses (AQUA Technology) workflow. Results: Sensitivity, accuracy and specificity were confirmed for all mFIHC assays on known positive and negative controls. Excellent reproducibility (less than 35% CV) and precision were observed across instruments, operators and independent experiments for all markers. Between these two panels, over 200 unique parameters were evaluated. The prevalence of CD19, CD20, CD22, and PAX5 ranged from 30% to &amp;gt;90% positive for the DLBCL samples tested and were overall highly concordant with each other. Conclusion: The validated mFIHC assays examine B cell antigen expression in DLBCL and their interaction with CD3+ T cells and further characterize CD8+ T cells and immune checkpoint expression. These panels may be used to further understand the complex immune cell and tumor cell spatial biology in the context of clinical trials. Citation Format: James Paul Santos, Jacob Levy, Kristen Ruma, David Yang, Steve Woolfenden, Jimmie Lim, Xun Li, Ariana Valencia, James Deeds, Ramu Thiruvamoor, Xin Li, Emmanuel Pacia, Margaret McLaughlin, Thai Tran, Sarah Choi, Jennifer Bordeaux. Tissue-based biomarker analysis of DLBCL using multiplex immunofluorescence AQUA (Automated Quantitative Analysis) algorithms [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1725.
Challenges and Solutions to Passive Rectification in Multi-MHz Frequency Capacitive Wireless Power Transfer Systems for Electric Vehicle Charging (2020)

This paper presents challenges and solutions to implementing a passive rectifier in a high-frequency capacitive wireless power transfer (WPT) system suitable for electric vehicle (EV) charging. For this study, a prototype 13.56-MHz 12-cm air-gap capacitive WPT system utilizing 22-cm diameter coupling plates is designed, built and tested. The system is first tested in dc-to-high-frequency ac mode with a resistive load. In this mode the prototype system transfers 895 W at an efficiency of 93%. The prototype is then evaluated in dc-to-dc mode with a full-bridge passive rectifier. In this mode the power transfer and efficiency are severely reduced. It is found that this degradation is partly due to detuning of the system's resonant frequency, caused by the parasitic output capacitance of the rectifier diodes. To retune the system, its operating frequency is changed to 13.28 MHz, allowing the performance to be partially recovered, but only up to 533 W at an efficiency of 69%. The remainder of the degradation is found to be due to the rectifier's capacitance unfavorably changing the gain and reactive compensation of the L-section matching network that connects the coupling plates to the rectifier. This paper introduces the use of an appropriate-valued inductor in parallel with the rectifier to nullify the effects of its parasitic capacitance. Incorporating this inductor, the system is able to operate at the original 13.56-MHz frequency and transmits 774 W of power at an efficiency of 81%.
Three-dimensional tracking of plus-tips by lattice light-sheet microscopy permits the quantification of microtubule growth trajectories within the mitotic apparatus (2015)

Mitotic apparatus, which comprises hundreds of microtubules, plays an essential role in cell division, ensuring the correct segregation of chromosomes into each daughter cell. To gain insight into its regulatory mechanisms, it is essential to detect and analyze the behavior of individual microtubule filaments. However, the discrimination of discrete microtubule filaments within the mitotic apparatus is beyond the capabilities of conventional light microscopic technologies. Recently, we detected three-dimensional (3-D) microtubule growth dynamics within the cellular cytoplasmic space using lattice light-sheet microscopy in conjunction with microtubule growth marker protein end-binding 1, a microtubule plus-end-tracking protein, which was fused to green fluorescent protein (EB1-GFP). This technique enables high-resolution 3-D imaging at subsecond intervals. We adapted mathematical computing and geometric representation techniques to analyze spatial variations in microtubule growth dynamics within the mitotic spindle apparatus. Our analytical approach enabled the different dynamic properties of individual microtubules to be determined, including the direction and speed of their growth, and their growth duration within a 3-D spatial map. Our analysis framework provides an important step toward a more comprehensive understanding of the mechanisms driving cellular machinery at the whole-cell level.
Ceftriaxone in the Treatment of Bacterial Meningitis in Adults (1988)

Twenty-six adults with acute bacterial meningitis were enrolled in an open randomized comparative study. The organisms isolated from CSF were Streptococcus pneumoniae, Staphylococcus epidermidis, Haemophilus influenzae, Escherichia coli and Salmonella typhi. 13 patients (group A) were treated once daily with intravenous ceftriaxone (Rocephin). The 13 patients in group B received ampicillin or ampicillin plus chloramphenicol in 4 doses/day. The mean duration of therapy in groups A and B was 9.9 and 12.3 days, respectively. This difference in the duration of therapy was statistically significant. All patients from group A showed clinical improvement and all were bacteriologically cured. In group B only 12 patients were clinically and bacteriologically cured; 1 patient had to be withdrawn from the therapy because CSF culture remained positive after 48 h of therapy. Ceftriaxone was well tolerated in all patients; ampicillin or ampicillin plus chloramphenicol were associated with diarrhea and skin rash in 6 patients.
Solution-processed perovskite light emitting diodes with efficiency exceeding 15% through additive-controlled nanostructure tailoring (2018)

Organometal halide perovskites (OHP) are promising materials for low-cost, high-efficiency light-emitting diodes. In films with a distribution of two-dimensional OHP nanosheets and small three-dimensional nanocrystals, an energy funnel can be realized that concentrates the excitations in highly efficient radiative recombination centers. However, this energy funnel is likely to contain inefficient pathways as the size distribution of nanocrystals, the phase separation between the OHP and the organic phase. Here, we demonstrate that the OHP crystallite distribution and phase separation can be precisely controlled by adding a molecule that suppresses crystallization of the organic phase. We use these improved material properties to achieve OHP light-emitting diodes with an external quantum efficiency of 15.5%. Our results demonstrate that through the addition of judiciously selected molecular additives, sufficient carrier confinement with first-order recombination characteristics, and efficient suppression of non-radiative recombination can be achieved while retaining efficient charge transport characteristics.
PHAROH lncRNA regulates Myc translation in hepatocellular carcinoma via sequestering TIAR (2021)

Hepatocellular carcinoma, the most common type of liver malignancy, is one of the most lethal forms of cancer. We identified a long non-coding RNA, <i>Gm19705</i>, that is overexpressed in hepatocellular carcinoma and mouse embryonic stem cells. We named this RNA <i><u>P</u>luripotency and <u>H</u>epatocyte <u>A</u>ssociated <u>R</u>NA <u>O</u>verexpressed in <u>H</u>CC</i>, or <i>PHAROH</i>. Depletion of <i>PHAROH</i> impacts cell proliferation and migration, which can be rescued by ectopic expression of <i>PHAROH</i>. RNA-seq analysis of <i>PHAROH</i> knockouts revealed that a large number of genes with decreased expression contain a <i>Myc</i> motif in their promoter. MYC is decreased in knockout cells at the protein level, but not the mRNA level. RNA-antisense pulldown identified nucleolysin TIAR, a translational repressor, to bind to a 71-nt hairpin within <i>PHAROH</i>, sequestration of which increases MYC translation. In summary, our data suggest that <i>PHAROH</i> regulates MYC translation by sequestering TIAR and as such represents a potentially exciting diagnostic or therapeutic target in hepatocellular carcinoma.
Search for the production of an excited bottom quark decaying to tW in proton-proton collisions at s = 8 $$ \sqrt{s}=8 $$ TeV (2016)

A search is presented for a singly produced excited bottom quark (b * ) decaying to a top quark and a W boson in the all-hadronic, lepton+jets, and dilepton final states in proton-proton collisions at s = 8 TeV recorded by the CMS experiment at the CERN LHC. Data corresponding to an integrated luminosity of 19.7 fb -1 are used. No significant excess of events is observed with respect to standard model expectations. We set limits at 95% confidence on the product of the b * quark production cross section and its branching fraction to tW. The cross section limits are interpreted for scenarios including left-handed, right-handed, and vector-like couplings of the b * quark and are presented in the twodimensional coupling plane based on the production and decay coupling constants. The masses of the left-handed, right-handed, and vector-like b * quark states are excluded at 95% confidence below 1390, 1430, and 1530 GeV, respectively, for benchmark couplings. This analysis gives the most stringent limits on the mass of the b * quark to date.
Dynamic Magnetic Resonance Imaging as a Means of Validating Finite Element Modeling Assumptions for Abdominal Aortic Aneurysms (2004)

The assessment of patient-specific abdominal aortic aneurysm (AAA) rupture risk using finite element (FE) modeling has been shown to be an improvement over current diameter-based prediction techniques (Fillinger, 2002, 2003). However, certain modeling assumptions are made which may have significant effects on the computed AAA wall stresses. For example, the FE meshes are based on composite computed tomography (CT) images obtained during multiple cardiac cycles. This results in meshes that are averaged representations of pressurized AAAs, yet are assumed to represent AAAs at the zero-stress state. Also, the proximal and distal ends of the AAA FE models are assumed to be fixed in place, which may be satisfactory boundary conditions, but have yet to be validated. Recent developments in dynamic magnetic resonance (dMR) imaging allow AAA cross-sectional images to be obtained at multiple locations and time points throughout a cardiac cycle. These images are used to determine the geometries and positions of AAAs at various times throughout the cardiac cycle.
Chemical synthesis of novel base pairs and their enzymatic incorporation into DNA (1999)

A novel base pair, 2-amino-6-(N,N-dimethylamino)purine (denoted x) and the counter part, pyridin-2-one (denoted y) were designed. The bulky 6-dimethylamino group of x is expected to eliminate base pairing with all natural bases. The phosphoramidite of x for DNA templates and the 2'-deoxyribonucleoside triphosphate of y (dyTP) for a substrate were synthesized, and the selectivity of the enzymatic incorporation of dyTP opposite x in the templates was examined. dyTP was preferentially incorporated opposite x than canonical dNTPs by Klenow fragment of Escherichia coli DNA polymerase I. While dyTP was also incorporated opposite A and G, the misincorporation was suppressed in the presence of dTTP and dCTP, respectively.
ChemInform Abstract: The Oxidation of ReCl5 with Oleum: Synthesis and Crystal Structure of Re2O4Cl4(SO4). (2012)

Abstract Red, needle shaped single crystals of the title compound are prepared by reaction of ReCl 5 with fuming sulfuric acid containing 25% SO 3 at (200 °C, sealed glass tube, 2 d).
Video-rate near-infrared tomography using spectral analysis for hemodynamic imaging (2009)

Using extracted spectral features is proposed to reconstruct video-rate optical-properties images. Compared with reconstruction through time-sequence data, the results through spectral features are exempt from noise affection, and are able to differentiate hemodynamic conditions in a single heart-beat cycle.
An Efficient and Expeditious Synthesis of Di- and Trisubstituted Amino-phenyl and -benzyl Derivatives of Tetrazole and [1,3,4]Oxadiazol-2-one (2008)

A practical protocol for the parallel synthesis and purification of amino tetrazole and [1,3,4]oxadiazol-2-one derivatives as carboxylic acid bioisosteres is described. Phenyl- and benzyl-amines, substituted with tetrazole or [1,3,4]oxadiazol-2-one, were transformed into functionally diverse and novel compounds, with p K a values ranging from 4.9 to 8.4, by two sequential reductive alkylation reactions. These series of di- and trisubstituted amino-phenyl and -benzyl derivatives were produced in solution using solid-supported reagents and were purified by solid-phase extraction (SPE) techniques.
Ni-foam based heterogenous Bi2S3 polyhedrons/multi walled carbon nanotubes (Bi2S3@MWCNTs/NF) as an advanced battery type electrode for enhanced supercapacitor performance (2023)

In current study, we report the hydrothermal synthesis of highly electroactive bismuth trichloride (Bi2S3) polyhedrons, modified with multi walled carbon nanotubes (MWCNTs). The physiochemical characterizations of pure Bi2S3 and Bi2S3@MWCNTs composite were carried out through X-ray diffraction (XRD), Fourier transform infrared (FTIR) spectroscopy, and scanning electron microscopy (SEM). XRD data revealed orthorhombic crystal structure of Bi2S3 having crystallite size of ∼13.23 nm, that got reduced to ∼10.81 for Bi2S3@MWCNTs composite. Polyhedral Bi2S3 showed some tendency to aggregate after fabricating with MWCNTs. Functional group analysis confirmed the formation of Bi–S bonds through multiple metal-sulfide bonding vibrations in the finger print region (880–550 cm−1). For electrochemical tests, Bi2S3/NF and Bi2S3@MWCNTs/NF were applied as electrodes. Due to the synergistic effects from highly conductive MWCNTs and pseudo-active Bi2S3, as prepared Bi2S3@MWCNTs/NF exhibited a significant enhancement in electrochemical response. The specific capacity of Bi2S3@MWCNTs/NF was measured as 625.1 C g−1, that was ∼1.45 times greater than that of non-fabricated Bi2S3 polyhedrons. Additionally, Bi2S3@MWCNTs/NF delivered a better charge/discharge efficiency. The values of RES (2.25 Ω) and RCT (3.54 Ω) prominently decreased for Bi2S3@MWCNTs/NF due to low internal and diffusional resistance.
Movie 3 from Metabolic Screening of Cytotoxic T-cell Effector Function Reveals the Role of CRAC Channels in Regulating Lethal Hit Delivery (2023)

&lt;p&gt;OT-I CTL conjugation with B16F10/OVA cells in the absence (left) or presence (right) of 100 µM H2O2. Morgenstemning LUT, Fura-2 340/380-ratio. Time stamp, min:sec (0 min denoting the timepoint of contact initiation). Scale bar, 10 µm.&lt;/p&gt;
Active Queue Management for MAC Client Implementation of Resilient Packet Rings (2009)

The IEEE 802.17 is a standardized ring topology network architecture, called the resilient packet ring (RPR), to be used mainly in metropolitan and wide area networks. This paper focuses on the RPR MAC client implementation of the IEEE 802.17 RPR MAC in the aggressive mode of operation and introduces a new active queue management scheme for ring networks that achieves higher overall utilization of the ring bandwidth with simpler and less expensive implementation than the generic implementation provided in the standard. The scheme introduced in this paper provides performance comparable to the per destination queuing implementation, the best achievable performance.
Selective factor VIII and V inactivation by iminodiacetate ion exchange resin through metal ion adsorption* (2008)

The procoagulant activity of factors VIII and V depends on the presence of metal ion(s). We examined the effect of cation-exchange resins with different functional groups on both factors, of which only reaction with iminodiacetate resin resulted in the complete loss of their activity levels in plasma. However, the antigen level of factor VIII was preserved by >95%. This resin reduced divalent cations content present in factor VIII preparations, indicating that it inactivated this factor by direct deprivation of predominant Ca(2+) (>Mn(2+)>>Cu(2+)), rather than adsorption of the factor itself. The antigen level of recombinant factor VIII alone was decreased by >95% by reaction with resin, whilst that complexed with von Willebrand factor was preserved by >95%. Iminodiacetate resin-treated plasma was evaluated by measuring factor VIII and V activity in plasma with various levels of either activity. These were significantly correlated to the values obtained using factor VIII- or V-deficient plasma prepared commercially by immunodepletion. We demonstrated that iminodiacetate resin-induced factors VIII and V inactivation is because of direct deprivation of metal ions, predominantly Ca(2+), which is more essential for the functional structure of their molecules. Furthermore, iminodiacetate resin-treated plasma would be useful as a substrate for measuring the activity of these factors.
Red Blood Cell Lifespan, Erythropoiesis and Hemoglobin Control (2008)

Erythropoietin (EPO) and iron deficiency as causes of anemia in patients with limited renal function or end-stage renal disease are well addressed. The concomitant impairment of red blood cell (RBC) survival has been largely neglected. Properties of the uremic environment like inflammation, increased oxidative stress and uremic toxins seem to be responsible for the premature changes in RBC membrane and cytoskeleton. The exposure of antigenic sites and breakdown of the phosphatidylserine asymmetry promote RBC phagocytosis. While the individual response to treatment with EPO-stimulating agents (ESA) depends on both the RBC's lifespan and the production rate, uniform dosing algorithms do not meet that demand. The clinical use of mathematical models predicting ESA-induced changes in hematocrit might be greatly improved once independent estimates of RBC production rate and/or lifespan become available, thus making the concomitant estimation of both parameters unnecessary. Since heme breakdown by the hemoxygenase pathway results in carbon monoxide (CO) which is exhaled, a simple CO breath test has been used to calculate hemoglobin turnover and therefore RBC survival and lifespan. Future research will have to be done to validate and implement this method in patients with kidney failure. This will result in new insights into RBC kinetics in renal patients. Eventually, these findings are expected to improve our understanding of the hemoglobin variability in response to ESA.
High gain, high efficiency vertical-cavity semiconductor optical amplifiers (2003)

Highly efficient long wavelength vertical-cavity semiconductor optical amplifiers (VCSOAs) are presented. A carrier confining structure was introduced by etching mesas in the active region. The carrier confinement resulted in increased efficiency and amplifier gain. The efficiency was increased by a factor of 3 as compared to previous devices made from the same active region material. 17 dB fiber-to-fiber gain was measured and the internal gain was estimated to be 24 dB. This is the highest reported amplifier gain for a long wavelength VCSOA to date.
Elucidating the Role of a Tetrafluoroborate‐Based Ionic Liquid at the n‐Type Oxide/Perovskite Interface (2019)

Abstract Halide perovskites are currently one of the most heavily researched emerging photovoltaic materials. Despite achieving remarkable power conversion efficiencies, perovskite solar cells have not yet achieved their full potential, with the interfaces between the perovskite and the charge‐selective layers being where most recombination losses occur. In this study, a fluorinated ionic liquid (IL) is employed to modify the perovskite/SnO 2 interface. Using Kelvin probe and photoelectron spectroscopy measurements, it is shown that depositing the perovskite onto an IL‐treated substrate results in the crystallization of a perovskite film which has a more n‐type character, evidenced by a decrease of the work function and a shift of the Fermi level toward the conduction band. Photoluminescence spectroscopy and time‐resolved microwave conductivity are used to investigate the optoelectronic properties of the perovskite grown on neat and IL‐modified surfaces and it is found that the modified substrate yields a perovskite film which exhibits an order of magnitude lower trap density than the control. When incorporated into solar cells, this interface modification results in a reduction in the current–voltage hysteresis and an improvement in device performance, with the best performing devices achieving steady‐state PCEs exceeding 20%.
WIPP/SRL in-situ testing program (1986)

The first in situ tests of comparative nuclear waste glass performance in the US are scheduled to begin in early 1986. In these tests, multiple nonradioactive waste glass samples will be emplaced in brine and rock salt in an underground test facility under conditions closely simulating those in a salt repository. This program is a joint effort of the Waste Isolation Pilot Plant (WIPP) and the Savannah River Laboratory (SRL). Part of the WIPP/SRL program is the Materials Interface Interactions Tests or MIIT. This is an international effort which involves the burial of almost 1000 waste glass samples, consisting of 14 different glass or waste glass compositions from 7 countries. In addition to these samples, there are also over 300 potential canister or overpack metal specimens and over 500 backfill and salt geologic samples. Over 1900 relevant interactions will be studied by combining brine leachant analyses with a variety of detailed surface analytical techniques. This program is one of the largest cooperative efforts ever undertaken in the waste management field and will produce a data base that will benefit a variety of disciplines in the waste management community. 8 refs., 5 figs.