gebhart/patrepeval huggingface dataset:
Reducing PI3Kδ signaling in a dose-dependent manner promotes human T cell stemness (2023)

Abstract Adoptive T Cell Therapy (ACT) is a promising type of highly personalized immunotherapy against cancer. However, during the clinical production of T cell products for ACT, the cells experience cues that lead to early senescence and poor quality. Thus, ways to improve T cell quality for ACT is warranted. Previous mouse data indicate that inhibiting the PI3Kδ pathway in T cells using Idelalisib, an FDA-approved selective inhibitor of the δ subunit of PI3K, produces less differentiated T cells with enhanced efficacy against cancer. We hypothesized that Idelalisib treatment in human T cells would recapitulate a dose-dependent acquisition of stemness features. Mouse T cells, bulk donor human peripheral blood mononuclear cells (PBMCs), and isolated human CD3+ T cells were cultured in vitro for seven days with dose escalation of Idelalisib. We counted the number of T cells to track expansion and assessed the phenotype through flow cytometry. Reducing PI3Kδ signaling produced a less differentiated phenotype in both murine and human CD3+ T cells. Human CD3+ T cells had lower expression of TCF-1 and LEF-1, transcription factors regulating stemness, due to Idelalisib. However, other markers (CD62L and CD45RA) still suggested dose escalation up to 25 μM led to less differentiation. PBMCs and CD3+ T cells treated with dosages of Idelalisib above 10 μM had limited expansion and decreased viability compared to mouse T cells. Altogether, our data demonstrate that blocking PI3Kδ with Idelalisib in human T cells supports acquisition of stemness features.
Tumor and organ uptake of 64Cu labeled MORAb-009, an anti-mesothelin antibody by PET Imaging and biodistribution studies (2015)

118 Objectives To investigate the effect of the antibody dose and tumor size on tumor and organ uptake of 64Cu-MORAb-009 by biodistribution and PET imaging studies. Methods MORAb-009 conjugated with 2-S-(4-isothiocyanatobenzyl)-1,4,7-triazacyclononane-1,4,7-triacetic acid was labeled with 64CuCl2 in 0.25M acetate buffer, pH 4.2. To investigate the dose effect, the biodistribution (BD) was performed in groups of nude mice (n=5) with mesothelin-expressing A431/H9 tumors (0.08-0.3 g) 1 day after iv injection of 64Cu-MORAb-009 (10µCi, radiochemical purity>95%) containing a total MORAb-009 dose of 2, 30, or 60 µg. The BD and PET imaging were also investigated 3, 24 and 48 h after the injection of a total dose of 30 µg (for BD), and 2 or 60 µg (for PET), respectively. Results Comparing the results of the BDs from three different injection doses, the major difference was shown in the uptake (% ID/g) of the radiolabeled antibody in tumor, liver and blood; the tumor uptake and blood retention from 30 and 60 µg injection were greater whereas the liver uptake was smaller than those from 2 µg injection. The BD studies also demonstrated a positive correlation between tumor size and liver uptake and an inverse correlation both between tumor size and tumor uptake and between tumor size and blood retention of 64Cu-MORAb-009. These findings were confirmed by the PET imaging study which clearly visualized the tumor at 24 h postinjection of 64Cu-MORAb-009 plus 60 µg MORAb-009 with a tumor to liver ratio of 2 whereas the injection of 2 µg MORAb-009 produced a tumor to liver ratio of 0.8 at the time point. Conclusions The uptake and retention of the radiolabeled antibody in tumor, liver and blood are strongly influenced by the injection dose and tumor size. PET imaging of 64Cu labeled Amatuximab (MORAb-009) could provide quantitative information on the optimum injected dose to maximize the tumor uptake.
Development of nomogram for prediction of survival after neoadjuvant chemotherapy with or without interval debulking surgery in advanced ovarian cancer (2023)

Objective: We studied human epidermal growth factor receptor-2 (HER2) receptor status and its dynamic change in ovarian cancer patients, a subset of whom underwent nextgeneration sequencing.Methods: Ovarian cancer patients who underwent HER2 testing between January 2015 and May 2021 at Yonsei Cancer Center were identified.Clinical information, including histology, BRCA status, and immunohistochemistry profile were collected.For patients with multiple biopsies, each anatomical location, timing, and HER2 expression were counted.Results: A total of 200 patients with ovarian cancer were identified.HER2 expressions of 2+ and 3+ were found in 28% and 6%, respectively, and 33 patients (16.5%) received targeted therapy including Herceptin in 16 patients.With respect to histology, HER2 3+ rate was 23% in mucinous, 11% in endometrioid, 9% in clear cell, and 5% in high-grade serous type.HER2 3+ was exclusively identified in BRCA wildtype, mismatch repair proficient, or programmed death ligand 1 low patients.Genomic analysis showed that HER2 2+ or 3+ patients showed relatively enriched for ARID1A, KRAS, and PIK3CA mutation, and not TP53 mutation.Copy number variation analysis showed that 4 out of 5 HER2 3+ patients showed ERBB2 amplification.With respect to anatomic distribution, HER2+ and 3+ were frequently identified in ovary and breast biopsy
Optimization of magnetization transfer contrast for EPI FLAIR brain imaging (2022)

Optimized MT-prepared EPI FLAIR provides comparable brain tissue contrast to the multi-slice TSE FLAIR images used in clinical practice.
Stereotactic radiotherapy as a treatment option for renal tumours in the solitary kidney: a multicenter analysis from the International Radiosurgery Oncology Consortium for Kidney (IROCK). (2019)

AbstractPurpose:Stereotactic ablative radiotherapy (SABR) is an emerging treatment for renal cell carcinoma (RCC). Our study objective was to evaluate SABR in patients with a solitary kidney, focusing on oncological and renal function outcomes.Materials and Methods:Individual patient data from nine IROCK institutions in Germany, Australia, USA, Canada and Japan were pooled. Median follow-up was 2.6 years. Baseline characteristics and outcomes were compared between solitary and bilateral kidney cohorts. Predictors of post-SABR renal function were assessed by logistic regression modelling.Results:81 solitary kidney patients underwent SABR. Mean age was 67.3 years and 97.5% had good performance status (ECOG 0-1 or KPS ≥70%). Median tumour diameter was 3.7cm [IQR: 2.5-4.3], with 37% of tumours ≥4cm. Patients in the bilateral cohort (n=138) harbored larger tumours and were older (p<0.001) with lower baseline eGFR (p=0.024). In the solitary cohort, post-SABR eGFR decrease (mean±SD) was -5.8±10.8 mL/min (or -9%)...
Biological Fluid Separation in Microfluidic Channels Using Flow Rate Control (2005)

A microfluidic device for continuous, real time blood plasma separation is introduced. This device is composed of a blood inlet, a purified plasma outlet, and a concentrated blood cell outlet. It is designed to separate blood plasma from an initial blood sample of up to 45 % hematocrit (Hct). The microfluidic device is designed and analyzed using an analogous electrical circuit, analytical and numerical studies. The numerical study results show that 27 % and 25 % of plasma volume can be separated from a total inlet blood volume of 45 % and 39 % hematocrit, respectively. The functionality of this device was demonstrated using defibrinated sheep blood (Hct=36 %). During 2 hrs. of continuous blood infusion through the device, all the blood cells traveled through the device toward the concentrated blood outlet while only the plasma flowed towards the plasma outlet without any clogging or lysis of cells. The experimentally measured plasma skimming volume was about 33 % for a 36 % inlet hematocrit. Due to the device’s simple structure and control mechanism, this microdevice is expected to be used for highly efficient continuous, real time cell-free blood plasma separation device.
Process for conversion of levulinic acid to ketones (2023)

A method for generating desired platform chemicals from feedstocks such as cellulosic biomass feedstocks containing levulinic acid by decarboxylating a feed stock comprising levulinic acid to generate ketones. This is done by passing a feed stock comprising levulinic acid in a gas phase over a non-precious metal catalyst on a neutral support.
Acute Encephalopathy Associated with Influenza A Infection in Adults (2009)

We report acute encephalopathy associated with influenza A infection in 3 adults. We detected high cerebrospinal fluid (CSF) and plasma concentrations of CXCL8/IL-8 and CCL2/MCP-1 (CSF/plasma ratios >3), and interleukin-6, CXCL10/IP-10, but no evidence of viral neuroinvasion. Patients recovered without sequelae. Hyperactivated cytokine response may play a role in pathogenesis.
Selective Toluene Detection with Mo2CTx MXene at Room Temperature (2020)

MXenes are a promising class of two-dimensional materials with several potential applications, including energy storage, catalysis, electromagnetic interference shielding, transparent electronics, and sensors. Here, we report a novel Mo<sub>2</sub>CT<sub><i>x</i></sub> MXene sensor for the successful detection of volatile organic compounds (VOCs). The proposed sensor is a chemiresistive device fabricated on a Si/SiO<sub>2</sub> substrate using photolithography. The impact of various MXene process conditions on the performance of the sensor is evaluated. The VOCs, such as toluene, benzene, ethanol, methanol, and acetone, are studied at room temperature with varying concentrations. Under optimized conditions, the sensor demonstrates a detection limit of 220 ppb and a sensitivity of 0.0366 Ω/ppm at a toluene concentration of 140 ppm. It exhibits an excellent selectivity toward toluene against the other VOCs. Ab initio simulations demonstrate selectivity toward toluene in line with the experimental results.
Antifouling and Fouling-Release Performance of Photo-Embossed Fluorogel Elastomers (2019)

Oil-infused ‘slippery’ polymer surfaces and engineered surface textures have been separately shown to reduce settlement or adhesion strength of marine biofouling organisms. Here, we combine these two approaches in fluorogel surfaces infused with perfluorinated oils, via a facile photo-embossing method that allows the generation of a micro-scale surface relief structure while retaining the properties of lubricant-infused materials. Testing of these surfaces against a range of marine fouling challenges in laboratory assays demonstrated that when the volume percentage of perfluorinated oil was high, adhesion strengths of attached barnacles and biofilms were low. However, diatoms adhered strongly to test surfaces, highlighting the need to explore different combinations of polymer and oil for such surfaces. Furthermore, the tested surface structures increased settlement and adhesion in the assays, demonstrating the need to optimize any surface structure for specific applications. Nevertheless, the results show the feasibility of combining multiple approaches to create future antifouling technologies.
Fundamentals of T Cell Metabolism and Strategies to Enhance Cancer Immunotherapy (2021)

Emerging reports show that metabolic pathways can be targeted to enhance T cell-mediated immunity to tumors. Yet, tumors consume key metabolites in the host to survive, thus robbing T cells of these nutrients to function and thrive. T cells are often deprived of basic building blocks for energy in the tumor, including glucose and amino acids needed to proliferate or produce cytotoxic molecules against tumors. Immunosuppressive molecules in the host further compromise the lytic capacity of T cells. Moreover, checkpoint receptors inhibit T cell responses by impairing their bioenergetic potential within tumors. In this review, we discuss the fundamental metabolic pathways involved in T cell activation, differentiation and response against tumors. We then address ways to target metabolic pathways to improve the next generation of immunotherapies for cancer patients.
Efficient Addition of Aroyl Radicals to Ketene DithioacetalS,S-Dioxides and its Utilization in Organic Synthesis (1999)

(1999). Efficient Addition of Aroyl Radicals to Ketene Dithioacetal S,S-Dioxides and its Utilization in Organic Synthesis. Phosphorus, Sulfur, and Silicon and the Related Elements: Vol. 153, No. 1, pp. 391-392.
Contribution of connexin26 to electrical feedback inhibition in the turtle retina (2003)

The first synaptic integration in the neuronal cascade of vision in vertebrates includes a feedback from horizontal cells to cones by a mechanism yet not fully understood. Recent observations in teleosts suggested an electrical feedback mechanism mediated by connexin26 (Cx26) hemichannels at the terminal dendrites of horizontal cells. By using reverse transcription-polymerase chain reaction and immunoblotting from retinal homogenate, we detected Cx26 mRNA transcripts in the turtle retina and demonstrated that they were translated into protein. Cx26 immunoreactivity was especially prominent in the outer plexiform layer. Subcellularly, immunoreactivity was located mainly between horizontal cell axon terminals and in horizontal cell dendrites forming the lateral elements at the ribbon synaptic complex of the cone pedicle. The label was confined to the horizontal cell membrane flanking the ribbon and was not found on the opposing photoreceptor membrane. No gap junctions at this location are known, so immunosignaling suggested the presence of hemichannels. Their relevance to the feedback mechanism was investigated by intracellular recordings from horizontal cells during application of the hemichannel blocker carbenoxolone. Carbenoxolone hyperpolarized the dark membrane potential by about 25 mV, decreased the amplitudes of responses to full-field light flashes, and suppressed the feedback-induced depolarizing inflexion in the response profile. These physiological findings are compatible with the involvement of hemichannels in the feedback between horizontal cells and cones and support the anatomical findings. Together, these data suggest the presence of an electrical feedback mechanism in the turtle retina, which therefore might be a common mechanism at the first visual synapse in vertebrates.
Noninvasive temperature measurement in Vivo using a temperature‐sensitive lanthanide complex and 1H magnetic resonance spectroscopy (1996)

A new lanthanide complex, praseodymium-2-methoxyethyl-DO3A, was tested as a temperature indicator for 1H magnetic resonance spectroscopy under in vivo conditions, using a 2-T imaging system. The chemical shift of the methoxy group of the compound is strongly temperature dependent. In vitro, a shift change of -0.131 ppm/degree C was found. The signal was shifted by about -24 ppm relative to the water signal, allowing easy water suppression and signal identification in vivo. The body temperatures of eight anesthetized rats were measured in the liver after intravenous administration of 1 mmol/kg of the praseodymium complex under different heating conditions of the animal. The temperatures calculated from the spectra were in good agreement (deviation < +/- 1 degree C) with values obtained simultaneously with a thermocouple placed in the rectum of the animals.
A multi-dimensional packet classifier for NP-based firewalls (2004)

In this paper we present design and implementation of a new multi-dimensional packet classifier engine using network processor technology. Our classification algorithm is fast and is based on hierarchical trie search for multi-dimensional rules. Moreover, we propose a technique to optimize the memory usage of our classifier. We have used the Intel/spl reg/ IXP1200 network processor pipeline architecture for implementation of the classifier. The final system is targeted to be a fast firewall packet filtering engine that uses the filtering policies as its classification rules. Our experimental result shows that the packet classification throughput results for various distribution of packet sizes, is above 800Mbps.
Evaluation of strain coverage of the multicomponent meningococcal serogroup B vaccine (4CMenB) administered in infants according to different immunisation schedules (2018)

The 4-component vaccine 4CMenB, developed against invasive disease caused by meningococcal serogroup B, is approved for use in infants in several countries worldwide. 4CMenB is mostly used as 3 + 1 schedule, except for the UK, where a 2 + 1 schedule is used, and where the vaccine showed an effectiveness of 82.9%. Here we compared the coverage of two 4CMenB vaccination schedules (3 + 1 [2.5, 3.5, 5, 11 months] versus 2 + 1 [3.5, 5, 11 months of age]) against 40 serogroup B strains, representative of epidemiologically-relevant isolates circulating in England and Wales in 2007-2008, using sera from a previous phase 3b clinical trial. The strains were tested using hSBA on pooled sera of infants, collected at one month post-primary and booster vaccination. 4CMenB coverage was defined as the percentage of strains with positive killing (hSBA titres ≥ 4 after immunisation and negative baseline hSBA titres < 2). Coverage of 4CMenB was 40.0% (95% confidence interval [CI]: 24.9-56.7) and 87.5% (95%CI: 73.2-95.8) at one month post-primary and booster vaccination, respectively, regardless of immunisation schedule. Using a more conservative threshold (post-immunisation hSBA titres ≥ 8; baseline ≤ 2), at one month post-booster dose, strain coverages were 80% (3 + 1) and 70% (2 + 1). We used a linear regression model to assess correlation between post-immunisation hSBA data for each strain in the two groups; Pearson's correlation coefficients were 0.93 and 0.99 at one month post-primary and booster vaccination. Overall, there is no evidence for a difference in strain coverage when 4CMenB is administered according to a 3 + 1 or 2 + 1 infant vaccination schedule.
Clinical Evaluation of a Prototype Passive Fixation Dual Chamber Single Pass Lead For Dual Chamber ICD Systems (1999)

In future dual chamber ICDs the signals from a passive fixation single pass lead could be used for atrial sensing and pacing as long as the sensing electrode for the right atrium remains in contact with the atrial wall. This system might lead to a simpler, less invasive implantation of dual chamber ICD systems.
The J2-Immortalized Murine Macrophage Cell Line Displays Phenotypical and Metabolic Features of Primary BMDMs in Their M1 and M2 Polarization State (2021)

Macrophages are immune cells that are important for the development of the defensive front line of the innate immune system. Following signal recognition, macrophages undergo activation toward specific functional states, consisting not only in the acquisition of specific features but also of peculiar metabolic programs associated with each function. For these reasons, macrophages are often isolated from mice to perform cellular assays to study the mechanisms mediating immune cell activation. This requires expensive and time-consuming breeding and housing of mice strains. To overcome this issue, we analyzed an in-house J2-generated immortalized macrophage cell line from BMDMs, both from a functional and metabolic point of view. By assaying the intracellular and extracellular metabolism coupled with the phenotypic features of immortalized versus primary BMDMs, we concluded that classically and alternatively immortalized macrophages display similar phenotypical, metabolic and functional features compared to primary cells polarized in the same way. Our study validates the use of this immortalized cell line as a suitable model with which to evaluate in vitro how perturbations can influence the phenotypical and functional features of murine macrophages.
Transient Analysis for Contained-Cold-Aisle Data Center (2012)

The objective of this paper is to conduct a transient analysis for a contained-cold-aisle data center using Computational Fluid Dynamics (CFD) modeling. Containing the cold aisle reduces the inherent challenges of predictability and energy consumption of data center cooling systems by separating the hot and cold air streams. Transient analysis is crucial to further show the benefits of this methodology and investigate the potential drawbacks. In this work, we investigate the effect of variable power and flow rate in time on a raised-floor data center with specific geometry. First, a base case numerical model is established. Then, we conduct a transient analysis for the uncontained base case and the three containment configurations. The containment configurations under consideration are ceiling-only, doors-only, and fully-contained cold aisle. We hold a comparison between different geometrical configurations of the containment system under certain transient operating conditions. Computer Room Air Conditioning (CRAC) failure and change in IT-demand are chosen to represent conventional transient scenarios in a data center. The transient analysis shows overshoots of cabinet inlet air temperatures beyond the final steady state, which cannot predicted through a simple steady state analysis. In addition, the uniform temperature distribution inside the cold aisle is affected by the change in air supply and level of containment. The temperature distribution in the cold aisle changes with time. Guidelines can be recommended based on the conclusion of this study.
Passive modelocking in solid state lasers (1995)

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Supplementary Data from Cellular-Resolution Imaging of Bystander Payload Tissue Penetration from Antibody-Drug Conjugates (2023)

Supplementary Data&lt;p&gt;Supplementary Fig. S1-S21, Table S1-S5&lt;/p&gt;
Chemists and the school of nature (2002)

The term biomimicry first appeared in 1962 as a generic term including both cybernetics and bionics. It referred to all sorts of imitation of one form of life by another one, while the term “bionics”, defined as “an attempt to understand sufficiently well the tricks that nature actually uses to solve her problems”, is closer to the meaning of “biomimicry” as it has been used by materials scientists since the 1980s. Biomimetism is an umbrella covering a variety of research fields ranging from the chemistry of natural products to nanocomposites, via biomaterials and supramolecular chemistry. It is an informal movement and the concept itself is so loose that one might wonder whether biomimetism is more than a slogan forged by chemists in order to hop on the “green” bandwagon. Or could it bring a revolution into chemistry with a profound transformation of its practices? It is too early to judge, but a historical perspective helps to highlight some trends and tendencies.