gebhart/patrepeval huggingface dataset:
Rapid Oxalate Determination in Blood and Synthetic Urine Using a Newly Developed Oxometer (2012)

Blood and urine oxalate determinations have been limited to the laboratory setting because of complex sample storage and processing methods as well as the need for color spectrophotometry and ion chromatography. We hypothesized that glucometer test strips, impregnated with glucose oxidase and dyes that measure secondary hydrogen peroxide production, could be infused with oxalate oxidase and produce enhanced color changes in the presence of oxalate. By increasing the amount of sodium oxalate in fresh blood, we found that glucometer-measured oxalate increased on a linear scale. In addition, oxalate levels in synthetic urine could be measured using a visual scale, suggesting that strip dwell time or oxalate/oxalate oxidase concentrations could be manipulated to enhance optimal sensitivity. Although further testing is necessary, this simple, first-generation oxometer may eventually allow point of care testing in the home or office, empowering patients with oxalate-based medical conditions and giving healthcare providers real-time oxalate feedback.
Applications of Modeling and Process Analysis to Furnace Operations and Redesign (2008)

This paper will present a brief overview of the mathematical and modeling tools, most of which have been detailed in previous papers1 at the Glass Problems Conference. Several specific examples of the use of this analysis will then be given which refer to operational and design questions with television and lead glass furnaces. Actual results and experiences from the analyses will be related. The key benefit to the author's mind has been the marriage of science with the art of glass manufacture, the synergy of operational knowledge and theoretical studies. This has had a direct impact on the efficient operations of these units.
Quantitative measurement of muscle oxygen saturation without influence from skin and fat using continuous-wave near infrared spectroscopy (2007)

A method to non-invasively and quantitatively measure muscle oxygen saturation (SmO(2)) using broadband continuous-wave diffuse reflectance near infrared (NIR) spectroscopy is presented. The method obtained SmO(2) by first correcting NIR spectra for absorption and scattering of skin pigment and fat, then fitting to a Taylor expansion attenuation model. A non-linear least squares optimization algorithm with set boundary constraints on the fitting parameters was used to fit the model to the acquired spectra. A data preprocessing/optimization scheme for accurately determining the initial values needed for the optimization was also employed. The method was evaluated on simulated muscle spectra with 4 different scattering properties, as well as on in vivo forearm spectra from 5 healthy volunteer subjects during arterial occlusion. Measurement repeatability was assessed on 24 healthy volunteers with 5 repeated measurements, each separated by at least 48 hours.
Synthesis of (−)‐Isofagomine (2006)

Abstract 1,3‐Dipolar cycloaddition of N‐benzyl nitrone 2 to D‐threo δ‐lactone 15 proceeded with excellent stereoselectivity to provide only one adduct 16. Cycloadduct 16 was subsequently subjected to a sequence of reactions involving rearrangement to γ‐lactone, glycolic cleavage/reduction, protection of the terminal hydroxymethyl group, reduction of the lactone, desilylation/mesylation, and hydrogenolysis of the N‐O bond providing (−)‐isofagomine and its N‐substituted derivatives. The biologic activity of N‐substituted (−)‐isofagomines toward commercially available α‐ and β‐glucosidases, α‐D‐mannosidase, α‐L‐fucosidase, β‐D‐glucuronidase, and β‐D‐galactosidase was tested. Keywords: (−)‐IsofagomineIminosugars1,3‐Dipolar cycloadditionNitronesUnsaturated aldonolactones
Supplemental Table 4 from mWTX-330, an IL-12 INDUKINE Molecule, Activates and Reshapes Tumor-Infiltrating CD8<sup><b>+</b></sup> T and NK Cells to Generate Antitumor Immunity (2023)

&lt;p&gt;Z Scores from EMT-6 Tumor Infiltrating CD8+ T cells from Select Pathways&lt;/p&gt;
Model Predictive Control of Combustion Phasing in Compression Ignition Engines by Coordinating Fuel Injection Timing and Ignition Assist (2022)

Internal combustion engines may use ignition assisting heating elements such as glow plugs to facilitate combustion control in automotive or aircraft powertrains that operate with synthetic fuels of varying ignition behavior or at extreme inlet conditions. This work presents a model predictive controller (MPC) that regulates combustion phasing in compression ignition engines on a cycle-to-cycle basis by coordinating fuel start of injection (SOI) with power supplied to a glow plug acting as an ignition assist (IA) device, while enforcing IA actuator range and rate constraints. Simulations were conducted using a nonlinear virtual engine informed by data from a commercial engine operating at a condition that induced high combustion variability. A rate-based MPC formulation leveraging state estimate feedback and integral setpoint tracking was developed. Simulation results show the MPC scheme ensures steady-state tracking of combustion phasing within 70 engine cycles, conserves IA usage whenever possible to reduce thermo-mechanical stress on the actuator, and maintains closed-loop combustion variability at only 4% higher than the open-loop system variability. Furthermore, the controller maintains reference tracking even if combustion sensitivity to the actuators deviates by more than 20% from the controller's internal model, without the need for retuning control parameters.
Dual-layer achromatic metalens design with an effective Abbe number (2020)

Planar achromatic metalenses with a thickness of the order of wavelength have attracted much attention for their potential applications in ultra-compact optical devices. However, realizing single-layer achromatic metalenses across a wide bandwidth requires that the corresponding meta-atoms have complex cross-sections for correct phase profile and dispersion compensation. Herein, we introduce an effective Abbe number and use lens maker equations to design a dual-layer achromatic metalens in which we compensate the dispersion by using a plano-convex liked metalens combined with a plano-concave liked metalens. The stacked metalens are designed based on simple high refractive index dielectric cylindrical meta-atoms with different radii, which simplify the design and fabrication processes. We demonstrate that a dual-layer achromatic metalens has a small focal length difference across the visible wavelength range and an average focusing efficiency above 50%, which proves that the design method is promising for many potential applications in multi-functional flat optical devices.
Chemotherapy Alone Versus Chemotherapy Plus Radiotherapy for Early Stage Hodgkin Lymphoma. (2007)

Abstract Both chemotherapy (CT) alone and combined modality therapy (CMT) are effective modalities for the treatment of early stages of Hodgkin lymphoma (HL). However, the optimal choice of treatment is still being discussed. Different research groups reported that ABVD-like CT followed by radiotherapy is highly effective for early favourable and early unfavourable (intermediate) stage HL. A recently conducted randomized trial aimed at determining whether CMT is superior to CT alone in early stages, showed no significant difference in 5 year overall survival (OS) and event-free survival in patients treated with either 4–6 cycles of ABVD alone or 2 cycles of ABVD plus radiotherapy. Thus, this systematic review and meta-analysis was performed for a more comprehensive comparison. Methods: Only randomized controlled trials (RCT) comparing CT alone with CMT in newly diagnosed adults with early stages of HL (CS IA, IB, IIA, IIB) were included. Medline and Cochrane Library were systematically searched for randomized controlled trials from 1975 to 2007. Patients who received CMT were considered as experimental group and patients who received ABVD-like CT alone were considered as control group. Data were collected from full text publications or abstracts and treatment effects for OS were calculated as hazard ratios (HR). Results: A total of 590 references were screened. Four eligible RCTs were identified, including 1207 patients with early-stage HL (early favourable and early unfavourable stages). Between 1983 and 2004, 765 patients where treated with CMT and 442 patients with CT alone. The OS for the CMT group was significantly better than the OS for the CT-alone group (HR: 0.54; 95% CI [0.35 - 0.84]; p = 0.006), but there was evidence for a substantial heterogeneity between the studies (I2 = 69%, p=0.02). Discussion: First results of this systematic review showed improved OS for patients treated with CMT in early-stage HL compared to patients treated with CT alone. The substantial heterogeneity between the trials should be clarified. Further comprehensive analyses are ongoing and will provide more detailed information.
Nystatin—dextran conjugates: Synthesis and characterization (1996)

The coupling of nystatin (Nys), a water-insoluble antifungal agent, to dextran via an imine or amine bond was systematically investigated. Dextran was first oxidized to dialdehyde dextran using potassium periodate, purified from the oxidizing agent, and reacted with Nys to form the Schiff base. The Schiff base was reduced to the amine using borohydride. All reactions took place in water. The purification of the oxidized dextran from the oxidizing agent was essential to prevent oxidative degradation of Nys at the coupling step. The effects on the coupling yield of the following factors: dextran molecular weight, degree of oxidation (aldehyde content), Nys to dextran ratio, temperature, and reaction pH were studied. A 95% coupling yield was obtained at the optimized coupling conditions: pH 8.9 ± 0.1, 50% degree of oxidation, and initial ratio of Nys to dialdehyde dextran 1:2.5. In all experiments, dextran was decreased in molecular weight during the oxidation step. Both imine and amine forms of Nys-dextran conjugates were soluble in water and exhibited improved stability in aqueous solutions as compared to the unbound drug. The conjugates showed comparable minimum inhibitory concentration (MIC) values against Candida albicans and Cryptococcus neoformans. The conjugates were about 25 times less toxic than free Nys after a single injection in mice. © 1996 John Wiley & Sons, Inc.
Early determination and long-term persistence of adult-generated new neurons in the hippocampus of mice (2002)

New neurons are continually generated in the adult hippocampus, but the important question, whether adult neurogenesis is transient or leads to the lasting presence of new neurons, has not yet been answered. Dividing cells were labeled with bromodeoxyuridine (BrdU) and were investigated by means of immunofluorescence and confocal microscopy at several time-points 1 day to 11 months thereafter. BrdU-labeled neurons remained stable in number and in their relative position in the granule cell layer over at least 11 months. This finding implies that the addition of new neurons is not transient and that their final number and localization are determined early. By contrast, expression of immature markers beta-III-tubulin and doublecortin in BrdU-labeled cells, peaked early after division and was not detectable after 4 weeks. In transgenic mice expressing enhanced green fluorescent protein under the nestin promoter none of the BrdU/nestin-positive cells early after division expressed the mature marker NeuN, confirming that no dividing neurons were detected. These new data suggest that new neurons are recruited early from the pool of proliferating progenitor cells and lead to a lasting effect of adult neurogenesis.
Technical Variations of the Bipedicled TRAM Flap in Unilateral Breast Reconstruction: Effects of Conventional versus Microsurgical Techniques of Pedicle Transfer on Complications Rates (2004)

In cases of unilateral breast reconstruction with a transverse rectus abdominis musculocutaneous (TRAM) flap, poorly perfused tissue, which is normally excised to avoid subsequent fat necrosis, must sometimes be used to achieve adequate breast size and projection. In such cases, incorporation of a second vascular pedicle into the flap design improves perfusion. The authors retrospectively examined their experience with bipedicled TRAM flap-based unilateral breast reconstruction to determine whether the use of microsurgical rather than conventional (nonmicrosurgical) techniques for flap transfer resulted in lower incidences of flap-site fat necrosis and donor-site hernia/bulge. The authors retrospectively reviewed the medical records of all patients who underwent unilateral breast reconstruction with a bipedicled TRAM or deep inferior epigastric perforator flap between January of 1991 and March of 2001. Group 1 consisted of patients who had undergone flap transfer using a conventional technique for both pedicles; group 2, patients who had flap transfer using a conventional technique for one pedicle and a microsurgical technique for the other; and group 3, patients who had flap transfer using a microsurgical technique for both pedicles. Of the 863 patients identified, 72 (8.3 percent) had undergone reconstruction using a bipedicled flap. There were 43 patients in group 1, 24 patients in group 2, and five patients in group 3. Only one case of total flap loss had occurred (group 1). Partial flap loss occurred in two patients in group 1 (5 percent) and three patients in group 2 (13 percent). Fat necrosis occurred more frequently in groups 1 (23 percent) and 2 (29 percent) than in group 3 (0 percent) (p = 0.5, Fisher's exact test). Similarly, bulge or hernia was more common in groups 1 (12 percent) and 2 (4 percent) than in group 3 (0 percent) (p = 0.6, Fisher's exact test). In this study, patients who received a bipedicled TRAM flap using microsurgical techniques alone (group 3) appeared to have better flap perfusion and less frequent hernia/bulge than did patients who underwent flap transfer using conventional (group 1) or combined techniques (group 2). However, these differences were not statistically significant, and this trend must be verified in a larger study.
Supplementary Figure Legends 1-7 from Comprehensive Genome Methylation Analysis in Bladder Cancer: Identification and Validation of Novel Methylated Genes and Application of These as Urinary Tumor Markers (2023)

&lt;p&gt;PDF file - 82K&lt;/p&gt;
The use of a retinoid receptor antagonist in a new model to study vitamin A-dependent developmental events (1998)

Multiple fetal anomalies occur in vitamin A deficient animals as well as in retinoic acid receptor gene 'knockout' mice, indicating that retinoic acid (an active metabolite of vitamin A) performs some essential functions in normal development. Additional approaches are needed to probe directly the stages and sites in the embryo where a presence of endogenous retinoic acid is indispensable. We have employed a new strategy for this purpose which involved an intervention in retinoic acid receptor (RAR)-dependent functions at specific developmental stages by means of a highly effective RAR antagonist, AGN 193109. We report that in an in vitro cell differentiation bioassay, AGN 193109 completely reversed the inhibitory action of a potent RAR agonist, AGN 190121. In pregnant mice, a single oral 1 mg/kg dose of the antagonist given on 8 day post coitum (dpc) produced a severe craniofacial anomaly (median cleft face or frontonasal dysplasia) and eye malformations in virtually all exposed fetuses. On the other hand, treatment on 11 dpc, a time in development when RARs are strategically expressed in the limb bud primordium, no limb anomalies could be induced by the antagonist. Even after a high dose of 100 mg/kg, limb development progressed normally in spite of the fact that measurable concentrations of the antagonist were present. Because retinoids are long known to influence skin morphology, we next monitored the effects of the antagonist on skin development. When given late in gestation, on 14 dpc, we found that the antagonist delayed differentiation and maturation of the fetal skin and hair follicles. We conclude that this model provides a convenient and pertinent system which enables us to seek and clarify true functions of retinoic acid and its cognate receptors in embryogenesis and in adult animals.
A new role for microRNAs, as ligands of Toll-like receptors (2013)

Tumor microenvironment plays a central role in the development and dissemination of cancer cells. In addition to study each specific cellular component of the microenvironment, it has become clear that it is the type and amount of information that cells exchange that ultimately affects cancer phenotype. Recently, it has been discovered that intercellular communication occurs through the release of microvesicles and exosomes, whose cargo represents the information released by one cell to a recipient cell. A key component of this cargo is represented by microRNAs (miRNAs), small non-coding RNAs with gene regulatory functions. We discovered that miRNAs released by cancer cells within microvesicles can reach and bind to Toll-like receptors (TLRs) in surrounding immune cells, and activate them in a paracrine loop. As a result, immune cells produce cytokines that increase cell proliferation and metastatic potential. This discovery provides the rationale for the development of new drugs that might be used in the treatment of cancer as well as other inflammation-related diseases.
Abstract 4200: Targeting cancer stem cells in serous ovarian carcinoma using RP6530, a dual PI3k δ/γ inhibitor (2017)

Abstract Ovarian cancer is one of the most lethal gynecological malignancies as most patients are diagnosed at an advanced stage and have a poor prognosis. Several studies have prospectively isolated cancer stem cells (CSCs) from samples of tumor from patients with serous adenocarcinoma of the ovary (SOC). This has been achieved by using cell surface antigens or functional assays. Targeting this subpopulation could be critical to overcome drug resistance, recurrence, and hence improve the survival of patients. The PI3K pathway is deregulated in 37% of SOC with PI3Kδ and γ amplified in 16% of tumors (TCGA data). We have used a novel and selective PI3K γ/δ inhibitor (RP6530) with high potency against PI3Kγ (IC50=25 nM) and δ (IC50=33 nM) enzymes and selectivity over α (&amp;gt;300-fold) and β (&amp;gt;100-fold) isoforms. RP6530, an orally active and sensitive small molecule inhibitor, is currently being tested in Phase-1 trials in US and Europe to evaluate its safety and efficacy in patients with hematological malignancies. The objective of this study was to test the efficacy of RP6530 against CSCs of EOC. Spheroids, enriched for CSCs were employed as an approach to evaluate the specific potency of the drug. In the experiments, Salinomycin was used as a control drug that targets CSCs. Initially, we have analyzed 3 cell lines (PEO4, OVCAR-5 and CAOV-2) with and without addition of 5µM RP6530. RP6530 significantly inhibited spheroid formation in PEO4 (0.001) and OVCAR-5 (p&amp;lt;0.05) and CAOV-2 (p&amp;lt;0.01) (mean of ≥3 experiments in triplicate). In cell viability assay, RP6530 had no cytotoxic effect as compared to Cisplatin in any of the cell lines. To evaluate the effect of the compound on CSC, we performed analysis of side population (SP) with Hoechst 33342 at 355 nm by flow cytometry. RP6530 either caused a significant reduction (&amp;gt;50%) in the fraction of SP cells (PEO4 and CAOV-2) or was neutral (OVCAR-5) indicating that the compound preferentially targets CSC in ovarian cancer cell lines. Colony assay revealed significantly lesser number of colonies in RP6530 treated cells. Phosphorylation of Akt that is downstream of PI3 kinase was inhibited in a dose dependent manner in all three cell lines. Evaluation of drugs that are intended to target CSCs is different from that of conventional cytotoxic drugs. Taken together, the results indicate that RP6530 shows potent inhibitory effect on CSCs in ovarian cancer cell lines. Citation Format: Sneha S, Nivetha R, R P. Nagare, Srikant Viswanadha, Swaroop Vakkalanka, T S. Ganesan. Targeting cancer stem cells in serous ovarian carcinoma using RP6530, a dual PI3k δ/γ inhibitor [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4200. doi:10.1158/1538-7445.AM2017-4200
O7.01 * RESPONSE ASSESSMENT IN NEURO-ONCOLOGY (RANO) CRITERIA FOR BRAIN METASTASES (2014)

Currently, there are no standard criteria for evaluating response to therapy in patients with brain metastases. An international multidisciplinary group, The Response Assessment in Neuro-Oncology (RANO) Metastatic Working Group has proposed a RANO-Brain Metastases (RANO-BM) Criteria is based on a modification of RECIST 1.1 criteria and uses unidimensional measurements. Since the CNS is considered as a separate compartment. CNS response will be scored independent of extracranial response. Measurable Overall survival
P-Chirogenic Binaphthyl-Substituted Monophosphines:  Synthesis and Use in Enolate Vinylation/Arylation Reactions (2002)

[reaction: see text] New phosphine ligands possessing both axial chirality and a chirogenic phosphorus center were prepared from (R)-2-bromo-2'-N,N-(dimethylamino)-1,1'-binaphthyl (1) via a simple Li-halogen exchange protocol. The asymmetric vinylation of a ketone enolate with (R,R(P))-2-(tert-butylphenylphosphino)-2'-N,N-(dimethylamino)-1,1'-binaphthyl (2a) afforded the coupling product with good enantiomeric excess.
Hepatotoxicity in Children Receiving Isoniazid Therapy for Latent Tuberculosis Infection (2014)

In children who have latent tuberculosis infection, isoniazid hepatotoxicity has low frequency and typically is reversible when isoniazid is stopped. Evidence of late drug-induced liver injury indicates the importance of monitoring symptoms and serum transaminases throughout isoniazid therapy.
Final System Architecture. Document Number D2.4 (2011)

Deliverable D2.4 del projecte Europeu FARAMIR (ICT-2009-257385)
Bone Marrow Origin of Hepatic Macrophages (Kupffer Cells) in Humans (1978)

Hepatic macrophages (Kupffer cells) from two male recipients of bone marrow transplants from females were studied for fluorescent Y body staining and sex chromatin (Barr body). After the transplant, macrophages had the sex karyotype of the donor, indicating that human hepatic macrophages originate in bone marrow.
Catalytic Antibodies: A New Class of Transition‐State Analogues Used to Elicit Hydrolytic Antibodies (1990)

Abstract The design and generation of selective catalysts is an important aim of chemists and biologists. A number of successful strategies have emerged, including the synthesis and derivatization of synthetic hosts, the chemical modification and site‐directed mutagenesis of enzymes, and the attenuation of natural enzyme activities in organic solvents. Since 1986 several laboratories have exploited the immune system to generate selective catalysts capable of catalyzing a wide range of chemical transformations. These include acyl transfer, β‐elimination, carbon—carbon bond‐forming, carbon—carbon bond‐cleaving, porphyrin metalation, peroxidation, and redox reactions. The variety and number of transformations catalyzed by antibodies in this short period of time is testament to the versatility and power of the method in generating selective catalysts for applications in chemistry, biology, and medicine. Here we report the use of a new class of uncharged transition‐state analogues for generating antibodies capable of catalyzing ester and carbonate hydrolysis. These antibodies are compared to those raised against tetrahedral phosphate and phosphonate transition‐state analogues.