gebhart/patrepeval huggingface dataset:
Abstract 4271: Standardized approach for monitoring plasma cell disorders (2020)

Abstract Multi-color flow cytometry using consensus surface markers (CD138, CD38, CD19, CD45, CD27, CD56, CD81, and CD117), intracellular kappa and lambda, as well as other auxiliary markers is routinely being used for the identification and characterization of plasma cells. Here, we describe the development of a modular 10-color plasma cell panel for immunophenotyping of the plasma cell compartment. The panel was developed as an 8-color dried backbone, which can be supplemented with 2 liquid (drop in) reagents. Lyophilized or dried reagent cocktails in a unit test format are known to drive workflow efficiency in clinical settings by eliminating the need for manual cocktailing (of reagents), and frequent batch to batch verification procedures. Longer shelf life and room temperature storage are additional appealing features for lyophilized and dried products. We have developed a dried-down 8-color plasma cell panel, which is manufactured in a single test-per-tube, ready to use format, and can be supplemented with liquid (drop in) reagents. The flexibility of being able to add 2 liquid reagents to the dried backbone provides the option of using intracellular kappa and lambda to examine clonality or using CD38-multi-epitope and/or anti-p63 (VS38c) reagent(s). The single test-per-tube format is ideally suited for MRD applications, where sample size is limited and there is a need for acquiring a large number of events for data analysis. Also, the dried reagent panel is comprised of multiple high performing polymer dyes, which are brighter than conventional dyes, and afford high resolution of the relevant cell populations. Furthermore, the dried reagent tubes have a long shelf life (12 months) and significantly enhance the workflow efficiency. Comparison of the liquid and dried versions of the 10-color plasma cell panel using peripheral blood from healthy donors (as well as control cell lines) showed similar staining patterns, comparable population statistics, and fluorochrome brightness. The dried plasma cell tube(s) were also tested on bone marrow samples from healthy and diseased subjects in conjugation with intracellular staining for kappa and lambda. Our results demonstrate that the 10-color plasma cell panel can be used for identification of the plasma cell compartment (based on CD38 &amp; CD138 expression), assessment of aberrant marker expression (CD19, CD27, CD81, CD117, CD45, CD56) for the identification of normal and abnormal plasma cells, and examining clonality in multiple patient samples. Citation Format: Ulrika Johansson, Na Li, Suraj Saksena, Natalie Golts, Brent Gaylord. Standardized approach for monitoring plasma cell disorders [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4271.
Cationic polymer synergizing with chemotherapeutics and re-purposing antibiotics against cancer cells (2021)

Chemotherapy is one of the most effective treatments for cancer. However, toxicity and the development of drug resistance have become the major hurdles to the commonly used chemotherapeutics such as doxorubicin and paclitaxel. Antibiotics have also been used as anti-cancer drugs due to their anti-proliferative and cytotoxic effects. However, these anti-tumor antibiotics like ciprofloxacin face the similar resistance and toxicity issues. In this study, we used a quaternary ammonium-functionalized cationic polycarbonate to synergize with the existing chemotherapeutics and re-purpose antibiotics to address the resistance and toxicity issues. When used in combination with the drugs, the cationic polymer induced 2-3 fold more damage in the cancer cell membrane within 2 hours, thus enhancing the uptake of chemotherapeutics up to 2.5 fold more into the breast, liver and even chemotherapeutics-resistant cancer cells. On the other hand, the chemotherapeutics increased the cellular uptake of polymer. The combined effects resulted in 3-10 fold reduction in IC<sub>50</sub> of chemotherapy drugs and yielded therapeutic synergy at a clinically-relevant concentration range of drugs when treating multiple types of cancer cells, while the use of guanidinium-functionalized polymer capable of membrane translocation did not lead to a synergistic effect. Thus, the quaternary ammonium-functionalized cationic polymer can increase the therapeutic efficacies of existing drugs, mitigating toxicities by lowering required dosage and circumventing drug resistance via its membrane disruption mechanism. The findings of this study provide insights into designing future anticancer therapy.
PD 81,723, an Allosteric Enhancer of the A1Adenosine Receptor, Lowers the Threshold for Ischemic Preconditioning in Dogs (1996)

PD 81,723 (PD) acts allosterically to increase agonist binding to A1 adenosine receptors and to enhance functional A1 receptor-mediated responses in the heart and other tissues. To determine if PD lowers the threshold for ischemic preconditioning (PC), pentobarbital-anesthetized dogs were subjected to 60 minutes of left anterior descending coronary artery (LAD) occlusion and 3 hours of reperfusion. Ischemic PC was produced by either 2.5 or 5 minutes of LAD occlusion 10 minutes before the 60-minute occlusion. PD (100 micrograms/kg total dose, 5 to 50 mumol/L in coronary arterial blood) or vehicle was infused intracoronarily for 17.5 minutes before the 60-minute occlusion period in non-PC dogs or in dogs preconditioned with 2.5 minutes of ischemia. Myocardial infarct size was determined by triphenyltetrazolium staining and expressed as a percentage of the area at risk. Compared with the control group (26.3 +/- 3.6%, mean +/- SEM), infarct size was not significantly affected by 2.5 minutes of PC alone (23.4 +/- 4.2%) or by PD alone (26.5 +/- 1.7%) but was decreased by PD + PC (14.6 +/- 1.7%, P < .05) or by a longer period (5 minutes) of PC alone (12.5 +/- 3.3%). The intravenous administration of the selective antagonist of A1 adenosine receptors, 8-cyclopentyl-1,3-dipropylxanthine (1 mg/kg), or the ATP-sensitive K+ channel blocker, glibenclamide (0.3 mg/kg), for 15 minutes before PD + PC blocked the protection (23.6 +/- 2.3% or 25.9 +/- 3.3%, respectively). None of the compounds studied affected systemic hemodynamics, collateral blood flow, or AAR. To determine which subtypes of canine adenosine receptors were affected by 10 mumol/L PD, radioligand binding studies were conducted using membranes derived from COS-7 cells expressing recombinant canine receptors and agonist radioligands. PD enhanced the binding of [125I]N6-4-amino-3-iodobenzyladenosine (125I-ABA) to A1 receptors by increasing the t1/2 for dissociation by 2.18-fold, but PD had no effect on the dissociation kinetics of 125I-ABA from A3 receptors or [125I]-[2-(4-amino-3-iodo-phenyl)ethylamino] adenosine from A2A receptors. Glibenclamide at concentrations up to 10 mumol/L had no effect on the binding of radioligands to recombinant canine A1, A2A, or A3 receptors. These data suggest that PD reduces the amount of time required for ischemia to produce preconditioning by enhancing adenosine binding to its A1 receptor. Glibenclamide prevents the protection afforded by A1 receptor activation by a mechanism not involving adenosine receptor blockade.
Effect of feed salinity on the performance of humidification dehumidification desalination (2015)

Humidification dehumidification (HDH) is a thermal desalination technology that imitates the rain cycle in an engineered setting. It can be advantageous is small-scale, decentralized applications. In addition, the components used in HDH systems are fairly robust, and can treat highly saline water. The technology has recently been commercialized in order to treat highly saline produced water from hydraulically fractured oil and gas wells. That plant has proved HDH’s ability to treat water that most current seawater desalination technologies are unable to treat. The major disadvantage of HDH is its low energy efficiency compared to other desalination technologies when treating seawater. Previous studies have shown that the system’s energy efficiency can be improved greatly by varying the water-to-air mass flow rate ratio within the system. This translates into operating two or more adjacent stages at different mass flow rate ratios, which is done by extracting an air stream from an intermediate location in the humidifier and injecting it at an intermediate location in the dehumidifier. Previous models have used fixed effectiveness or fixed pinch approaches to evaluate the benefits of multi-staging, but these do not take account of the size of the system. In physical systems, what remains constant when going from a single-stage to a multi-stage system is the total size of the system and not the effectiveness or the pinch. Therefore, comparing systems with the same total heat exchanger area is the best way to understand the effect of extraction/injection and whether its implementation is beneficial or not. In this paper, a numerical heat and mass transfer model is used to simulate the operation of HDH at various feed salinities. For each case, the performance of the single-stage system is compared to that of a two-stage system of the same size at different values of feed salinity. The ability of HDH to treat feeds with varying salinity is also studied.
Bisphenol-A polycarbonate/polydimethylsiloxane multiblock copolymers. I. Synthesis and characterization (1997)

Aminopropyl-terminated polydimethylsiloxane (PDMS)-bisphenol-A polycarbonate block copolymers were synthesized by interfacial phosgenation reaction of 2,2-bis(4-hydroxyphenyl) propane (BPA) and aminopropyl-terminated PDMS. A new synthetic procedure shows better conversion yield of PDMS oligomer. IR, 1H, 13C, and 29Si nuclear magnetic resonance spectra were used to identify the exact chemical structures of the PDMS-PC block copolymers. The conversions of PDMS of these copolymers were ∼ 90% and independent of the PDMS content. The intrinsic viscosities, IV, [γ] studied were in the range between 0.23 and 2.25 dL/g in dichloromethane at 25°C with different reaction conditions. The intrinsic viscosity and the glass transition temperature decreased with increasing PDMS content at the same reaction temperature, while the melting flow indices increase with increasing PDMS content. Transparent and colorless films, which showed good oxygen-to-nitrogen permselectivity, could be cast from dichloromethane. © 1997 John Wiley & Sons, Inc. J Appl Polym Sci 66: 57–66, 1997
Nanohybrids with Magnetic and Persistent Luminescence Properties for Cell Labeling, Tracking, In Vivo Real‐Time Imaging, and Magnetic Vectorization (2018)

Once injected into a living organism, cells diffuse or migrate around the initial injection point and become impossible to be visualized and tracked in vivo. The present work concerns the development of a new technique for therapeutic cell labeling and subsequent in vivo visualization and magnetic retention. It is hypothesized and subsequently demonstrated that nanohybrids made of persistent luminescence nanoparticles and ultrasmall superparamagnetic iron oxide nanoparticles incorporated into a silica matrix can be used as an effective nanoplatform to label therapeutic cells in a nontoxic way in order to dynamically track them in real-time in vitro and in living mice. As a proof-of-concept, it is shown that once injected, these labeled cells can be visualized and attracted in vivo using a magnet. This first step suggests that these nanohybrids represent efficient multifunctional nanoprobes for further imaging guided cell therapies development.
Mechanisms of microRNA deregulation in human cancer (2008)

microRNAs (miRNAs) are an abundant class of small non-coding RNAs that function as gene regulators. Although deregulation of miRNA expression is involved in the initiation and progression of tumorigenesis, the underlying mechanisms of miRNA deregulation in human cancer are still largely unknown. Increasing evidence indicates that transcriptional deregulations, epigenetic alterations, mutations, DNA copy number abnormalities and defects in the miRNA biogenesis machinery might contribute to miRNA deregulation in human cancer. A clearer understanding of the mechanisms involved in miRNA deregulation in human cancer will contribute greatly to the development of new miRNA-based strategies in cancer diagnosis and treatment.
Delay-sensitive Joint Optimal Control and Resource Management in\n Multi-loop Networked Control Systems (2020)

In the operation of networked control systems, where multiple processes share\na resource-limited and time-varying cost-sensitive network, communication delay\nis inevitable and primarily influenced by, first, the control systems deploying\nintermittent sensor sampling to reduce the communication cost by restricting\nnon-urgent transmissions, and second, the network performing resource\nmanagement to minimize excessive traffic and eventually data loss. In a\nheterogeneous scenario, where control systems may tolerate only specific levels\nof sensor-to-controller latency, delay sensitivities need to be considered in\nthe design of control and network policies to achieve the desired performance\nguarantees. We propose a cross-layer optimal co-design of control, sampling and\nresource management policies for an NCS consisting of multiple stochastic\nlinear time-invariant systems which close their sensor-to-controller loops over\na shared network. Aligned with advanced communication technology, we assume\nthat the network offers a range of latency-varying transmission services for\ngiven prices. Local samplers decide either to pay higher cost to access a\nlow-latency channel, or to delay sending a state sample at a reduced price. A\nresource manager residing in the network data-link layer arbitrates channel\naccess and re-allocates resources if link capacities are exceeded. The\nperformance of the local closed-loop systems is measured by a combination of\nlinear-quadratic Gaussian cost and a suitable communication cost, and the\noverall objective is to minimize a defined social cost by all three policy\nmakers. We derive optimal control, sampling and resource allocation policies\nunder different cross-layer awareness models, including constant and\ntime-varying parameters, and show that higher awareness generally leads to\nperformance enhancement at the expense of higher computational complexity.\n
Distinct Morphological Stages of Dentate Granule Neuron Maturation in the Adult Mouse Hippocampus (2006)

Adult neurogenesis in the dentate gyrus may contribute to hippocampus-dependent functions, yet little is known about when and how newborn neurons are functional because of limited information about the time course of their connectivity. By using retrovirus-mediated gene transduction, we followed the dendritic and axonal growth of adult-born neurons in the mouse dentate gyrus and identified distinct morphological stages that may indicate different levels of connectivity. Axonal projections of newborn neurons reach the CA3 area 10-11 d after viral infection, 5-6 d before the first spines are formed. Quantitative analyses show that the peak of spine growth occurs during the first 3-4 weeks, but further structural modifications of newborn neurons take place for months. Moreover, the morphological maturation is differentially affected by age and experience, as shown by comparisons between adult and postnatal brains and between housing conditions. Our study reveals the key morphological transitions of newborn granule neurons during their course of maturation.
Binding site elucidation and structure guided design of macrocyclic IL-17A antagonists (2016)

Interleukin-17A (IL-17A) is a principal driver of multiple inflammatory and immune disorders. Antibodies that neutralize IL-17A or its receptor (IL-17RA) deliver efficacy in autoimmune diseases, but no small-molecule IL-17A antagonists have yet progressed into clinical trials. Investigation of a series of linear peptide ligands to IL-17A and characterization of their binding site has enabled the design of novel macrocyclic ligands that are themselves potent IL-17A antagonists.
Singling out Ill-fit Items in a Classification. Application to the Taxonomy of Enterobacteriaceae (2000)

We address the problem of evaluating the quality of cluster assignment of in- dividual items in a classification. The problem can also be viewed as outlier detection in classifications. We describe simple methods for this task based on the use of Naive Bayes classification. Applied to two existing classifica- tions of 5313 strains of bacteria the method indicated that one classification is far more robust than the other. The observations that fit badly to their clusters are typically items whose classification is suspect also from other considerations. Removing these elements from the data set, performing clus- tering on the reduced data set, and adding the outliers back one-by-one yielded a clustering that has a higher likelihood than the previous accepted classifications. Investigation of this new clustering lead to suggested changes in the classification of 69 strains in the material.
The Modulating Possibilities of Dicarbollide Clusters:  Optimizing the Kharasch Catalysts (2003)

exo-Cluster dicarbollides substitution has allowed tuning of the E degrees (Ru(II)/Ru(III)) potential to obtain the best-performing Kharasch catalyst. We postulate that this is possible through the to-and-fro electron movement between the boron cluster and the sulfonium moieties.
GaSb-based infrared detectors utilizing InAsPSb absorbers (2013)

InPSb and InAsPSb have been investigated for use as absorber materials in GaSb-based n-type/barrier/n-type (nBn) detectors with cutoff wavelengths shorter than 4.2 μm. The growth temperature window for high-quality InPSb lattice-matched to GaSb by molecular beam epitaxy is approximately 440–460 °C. InPSb films with thicknesses greater than approximately 1 μm or films grown outside this temperature window have high densities of large defects, with films grown at lower temperatures exhibiting evidence of significant phase separation. In contrast, InAsPSb films can be grown with excellent surface morphologies and no apparent phase separation over a wide temperature range. InAsPSb samples with low-temperature photoluminescence between 3.0 and 3.4 μm and lattice mismatch of less than 1 × 10−3 have been grown, although both photoluminescence and x-ray diffraction data exhibit peak splitting indicative of compositional nonuniformity. AlAsSb-barrier nBn detectors with InPSb and InAsPSb absorbers have been fabricated. At 160 K, InPSb-absorber devices have a photocurrent responsivity edge at approximately 2.8 μm and a dark current of approximately 1.4 × 10−7 A/cm2, and InAsPSb devices with responsivity edges of 3.1–3.2 μm have a dark current of 2.3 × 10−8 A/cm2. Both InPSb and InAsPSb devices require significant reverse bias for full photocurrent collection at low temperature, suggesting the existence of an undesirable valence band energy discontinuity. The temperature dependence of dark current indicates that it is dominated by a mechanism other than generation in the undepleted absorber region.
Relativistic description of quark-antiquark bound states. II. spin-dependent treatment (1990)

We present the results of a study of light- and heavy-quark-antiquark bound states in the context of the reduced Bethe-Salpeter equation, including the full spin dependence. We obtain good fits to the observed spin splittings in the $b\overline{b}$ and $c\overline{c}$ systems using a short-distance single-gluon-exchange interaction, and a long-distance scalar confining interaction. However, we cannot obtain satisfactory fits to the centers of gravity of the $b\overline{b}$ and $c\overline{c}$ spin multiplets at the same time, and the splittings calculated for $q\overline{Q}$ mesons containing the lighter quarks are very poor. The difficulty appears to be intrinsic to the reduced Salpeter equation for reasons which we discuss.
Amelioration of endotoxin-induced sepsis in rats by membrane anchored lipid conjugates (2003)

ExPLIs may be considered as potentially effective compounds to prevent the production of inflammatory mediators and to improve mortality rate in septic patients.
Dual PAK4-NAMPT Inhibition Impacts Growth and Survival, and Increases Sensitivity to DNA-Damaging Agents in Waldenström Macroglobulinemia (2018)

These results support the clinical investigation of KPT-9274 in combination with DNA-damaging agent for treatment of WM.
Non-Linear Label Ranking for Large-Scale Prediction of Long-Term User Interests (2014)

We consider the problem of personalization of online services from the viewpoint of ad targeting, where we seek to find the best ad categories to be shown to each user, resulting in improved user experience and increased advertiser's revenue. We propose to address this problem as a task of ranking the ad categories depending on a user's preference, and introduce a novel label ranking approach capable of efficiently learning non-linear, highly accurate models in large-scale settings. Experiments on real-world advertising data set with more than 3.2 million users show that the proposed algorithm outperforms the existing solutions in terms of both rank loss and top-K retrieval performance, strongly suggesting the benefit of using the proposed model on large-scale ranking problems.
Increasing Dietary Vitamin K Intake Stabilizes Anticoagulation Therapy in Warfarin-Treated Patients with a History of Instability: A 24-week Randomized Controlled Trial (OR36-04-19) (2019)

Warfarin (W) is a highly prescribed anticoagulant for the treatment and prevention of thromboembolic diseases. However, anticoagulation stability is often a challenge due to the narrow therapeutic range of the drug. In recent years, dietary vitamin K (VK) has emerged as an important modulator of long-term anticoagulation stability. In trials, patients receiving small doses of supplemental VK (100–150 mg/d) spend significantly more time in the therapeutic range (%TTR) and present fewer bleeding and thrombotic complications. Whether similar beneficial effects can be achieved through diet remains unknown. We determined whether increasing dietary VK intake by ≥150 μg/day improves anticoagulation stability of W-treated patients with a history of INR instability. We conducted a 24-week randomized controlled trial at the Anticoagulation Clinics of the Montreal Heart Institute and the Jewish General Hospital (Montreal). The main inclusion criteria were: 1) be anticoagulated for >6 months with a target international normalized ratio (INR) range of 2.0–3.0 or 2.5–3.5, and 2) present a %TTR <50% in the previous 6 months. Patients randomized to the intervention group (VK) received dietary counsel to increase their VK intake by ≥150 μd/day through specific food choices, recipes and cooking strategies. Patients from the control (C) group received general dietary information of similar intensity. Warfarin therapy was monitored weekly by INR. The primary clinical outcome was anticoagulation stability as defined by %TTR > 70% during weeks 4 through 24. Groups were compared in an intention-to-treat method using the exact Fisher test. In total, 49 patients aged 32–85 years completed the study. Mean (±SEM) %TTR over the assessment period were 67.7 ± 3.4 and 61.4 ± 3.5 for the VK and C groups, respectively (ns). Increasing dietary VK intakes resulted in a greater proportion of patients with %TTR > 70% over the assessment period. Specifically, 14 of the 28 patients (50%) from the VK group met the criteria versus 4 of the 21 patients (19%) from the C group (P = 0.026). Increasing VK intake ≥150 μd/day through diet strategies improves anticoagulation stability of W-treated patients with a history of anticoagulation instability. This study was funded by the CIHR.