gebhart/patrepeval huggingface dataset:
Data from Antigen Experienced T Cells from Peripheral Blood Recognize p53 Neoantigens (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;The purpose of this study was to evaluate antigen experienced T cells in peripheral blood lymphocytes (PBL) for responses to p53 neoantigens.&lt;/p&gt;Experimental Design:&lt;p&gt;PBLs from patients with a mutated &lt;i&gt;TP53&lt;/i&gt; tumor were sorted for antigen-experienced T cells and &lt;i&gt;in vitro&lt;/i&gt; stimulation (IVS) was performed with p53 neoantigens. The IVS cultures were stimulated with antigen-presenting cells expressing p53 neoantigens, enriched for 41BB/OX40 and grown with rapid expansion protocol.&lt;/p&gt;Results:&lt;p&gt;T-cell responses were not observed in the PBLs of 4 patients who did not have tumor-infiltrating lymphocyte (TIL) responses to mutated &lt;i&gt;TP53&lt;/i&gt;. In contrast, 5 patients with TIL responses to mutated &lt;i&gt;TP53&lt;/i&gt; also had similar T-cell responses in their PBLs, indicating that the PBLs and TILs were congruent in p53 neoantigen reactivity. CD4&lt;sup&gt;+&lt;/sup&gt; and CD8&lt;sup&gt;+&lt;/sup&gt; T cells were specific for p53&lt;sup&gt;R175H&lt;/sup&gt;, p53&lt;sup&gt;Y220C&lt;/sup&gt;, or p53&lt;sup&gt;R248W&lt;/sup&gt; neoantigens, including a 78% reactive T-cell culture against p53&lt;sup&gt;R175H&lt;/sup&gt; and HLA-A*02:01. Tracking &lt;i&gt;TCRB&lt;/i&gt; clonotypes (clonality, top ranked, and &lt;i&gt;TP53&lt;/i&gt; mutation-specific) supported the enrichment of p53 neoantigen–reactive T cells from PBLs. The same T-cell receptor (TCR) from the TIL was found in the IVS cultures in three cases and multiple unique TCRs were found in another patient. &lt;i&gt;TP53&lt;/i&gt; mutation–specific T cells also recognized tumor cell lines bearing the appropriate human leukocyte antigen restriction element and &lt;i&gt;TP53&lt;/i&gt; mutation, indicating these T cells could recognize processed and presented p53 neoantigens.&lt;/p&gt;Conclusions:&lt;p&gt;PBL was a noninvasive source of T cells targeting &lt;i&gt;TP53&lt;/i&gt; mutations for cell therapy and can provide a window into intratumoral p53 neoantigen immune responses.&lt;/p&gt;&lt;p&gt;&lt;i&gt;See related commentary by Olivera et al., p. 1203&lt;/i&gt;&lt;/p&gt;&lt;/div&gt;
ChemInform Abstract: A Novel Testosterone 5α‐Reductase Inhibitor, 8′,9′‐ Dehydroascochlorin Produced by Verticillium sp. FO‐2787. (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Three distinct tolerogenic CD14+ myeloid cell types to actively manage autoimmune disease: Opportunities and challenges (2021)

Current treatment for patients with autoimmune disorders including rheumatoid arthritis, multiple sclerosis and type 1 diabetes, often consists of long-term drug regimens that broadly dampen immune responses. These non-specific treatments are frequently associated with severe side effects creating an urgent need for safer and more effective therapy to promote peripheral tolerance in autoimmune diseases. Cell-based immunotherapy may offer an encouraging alternative, where tolerogenic CD14<sup>+</sup> myeloid cells are infused to inhibit autoreactive effector cells. In this review, we compared in depth three promising tolerogenic CD14<sup>+</sup> candidates for the treatment of autoimmune disease: 1) tolerogenic dendritic cells, 2) monocytic myeloid-derived suppressor cells and 3) CD14<sup>+</sup> type 2 conventional dendritic cells. TolDC-based therapy has entered clinical testing whereas evidence from the latter two cell types m-MDSCs and CD14<sup>+</sup> cDC2s is predominantly coming from cancer immunology research. These three cell types have distinct cellular properties and immunosuppressive mechanisms offering unique opportunities to be explored. However, these cells differ in stage of development towards immunotherapy each facing additional hurdles. Therefore, we speculate on the potential benefits and risks of these cell types as novel cell-based immunotherapies to control autoimmune disease in patients.
Integrated overcurrent protection system for class-D audio power amplifiers (2005)

A fully integrated overcurrent protection system is presented suitable for application in integrated class-D audio power amplifiers. Accurate overcurrent detection is used based on parallel measurement of the voltage drop across the DMOS power transistors. A logic circuit enables continuous current limiting during overload situations. Actual short circuits can be distinguished from load impedance minima using a simple short-circuit discrimination method.
Méthodes de nettoyage et de désinfection en endoscopic gastrointestinale (1991)

Every endoscopic procedure provides a potential source for transmitting an infection. If current recommendations regarding cleaning and disinfection are followed, the risk of these infections are extremely low. It is essential to comply with standard cleaning and disinfection procedures. Specific reasons for lack of compliance have not been characterized, but may relate to time restraints, costs, shortage of staff and equipment, as well as a lack of appreciation of the potential to transmit infections via endoscopy. In the future, strict adherence to accepted guidelines for endoscopic cleaning and disinfection is needed byall persons performing these procedures. In addition, carefully designed studies of each aspect of the cleaning and disinfection process should be performed in order to better understand the problems associated with current methods. These studies may lead to improvements in techniques, chemical solutions employed, and endoscope design. Continued attention to proper endoscopic cleaning and disinfection procedures will aid the ongoing expansion of diagnostic and therapeutic gastrointestinal endoscopy.
Proposal of l-diversity algorithm considering distance between sensitive attribute values (2017)

Consideration of privacy is crucial when sharing a database that contains personal information with other organizations. Many organizations have utilized personal information while realizing the importance of personal privacy protection by anonymizing personal information according to existing indicators, such as k-anonymity. A database with personal information is defined as satisfying l-diversity when a specific record group that has the same combination of quasi-identifiers (QIDs) holds at least / kinds of sensitive attribute value. By satisfying l-diversity, the identification probability of the individual's sensitive attribute value becomes less than 1/l, and it can be said that privacy is protected. The l-diversity has been widely studied in the area of privacy-preserving data mining. However, if a database containing certain personal information holds similar sensitive attribute values, there is a possibility that de facto diversity is not satisfied, even if anonymization is performed to satisfy l-diversity. In this research, we propose (l, d)-semantic diversity that is able to consider more actual diversity to solve the problem of not being able to satisfy de facto diversity with the existing indicator. The (l, d)-semantic diversity considers the similarity of sensitive attribute values by adding distances, d, defined using categorization. We also propose an anonymization algorithm and analysis algorithm suitable for the proposal indicator, and we conduct evaluation experiments.
Quantitative phase-contrast tomography of a liquid phantom using a conventional x-ray tube source (2009)

Over the last few years, differential phase-contrast x-ray computed tomography (PC-CT) using a hard x-ray grating interferometer and polychromatic x-ray tube sources has been developed. The method allows for simultaneous determination of the attenuation coefficient and the refractive index decrement distribution inside an object in three dimensions. Here we report experimental results of our investigation on the quantitativeness and accuracy of this method. For this study, a phantom consisting of several tubes filled with chemically well-defined liquids was built and measured in PC-CT. We find, that the measured attenuation coefficients and refractive index decrements closely match calculated, theoretical values. Moreover, the study demonstrates, how substances with similar attenuation coefficient or refractive index decrement, can be uniquely distinguished by the simultaneous, quantitative measurement of both quantities.
From Bytes to Bedside: Data Integration and Computational Biology for Translational Cancer Research (2007)

ajor advances in genome science and molecular technologies provide new opportunities at the interface between basic biological research and medical practice. The unprecedented completeness, accuracy, and volume of genomic and molecular data necessitate a new kind of computational biology for translational research. Key challenges are standardization of data capture and communication, organization of easily accessible repositories, and algorithms for integrated analysis based on heterogeneous sources of information. Also required are new ways of using complementary clinical and biological data, such as computational methods for predicting disease phenotype from molecular and genetic profiling. New combined experimental and computational methods hold the promise of more accurate diagnosis and prognosis as well as more effective prevention and therapy.
Simultaneous high-frequency ultrasound and optoacoustic imaging of in vivo mouse embryos. (2011)

An integrated optoacoustic (OA) and high-frequency ultrasound (HFU) system that provides detailed images of anatomical structure and molecular contrast in small animals and transgenic embryos is presented. Volumetric imaging was achieved by raster scanning a vertically oriented imaging probe. The imaging probe was a five-element, 40-MHz, PVDF-TrFE-based annular array. A PBS-filled Petri-dish with a center hole was placed on the abdomen of an anesthetized mouse, and a laparotomy was performed to expose an intact uterus. A bifurcated beam from a 532-nm pulsed laser illuminated the embryos from opposing directions normal to the image plane. The central element of the array was excited with a high-voltage impulse synchronized with the light pulse. The resulting ultrasound echo and OA signals from each scan location were digitized from all five array channels and postprocessed. The anatomy of the embryonic head (HFU image) was coregistered with the embryonic vasculature (OA image). Delay-and-sum beamforming was performed and the resulting HFU and OA images exhibited a notable improvement in the depth of field and signal-to-noise ratio in comparison to the images constructed using signals acquired from the central array element alone. The feasibility of real-time, spatially coregistered, dual-modality in vivo imaging of mouse embryos was demonstrated.
Experimental Studies of the Air Coolability of TRIGA Reactors Following a Loss-of-Coolant Accident (1987)

To investigate the coolability of a uniformly heated tube by free convection of atmospheric air, heat transfer experiments were conducted using vertical open an-nuli with adiabatic outer walls. To examine the effect of the annulus ratio on the coolability of the heated tube, the experiments employed four annuli (diameter ratios of 1.155, 1.33, 1.63, and 12.0). The operating parameters included heat fluxes up to 1.38 W/cm2 with a corresponding surface temperature of 856 K.The results, extrapolated to 1200 K, were used to provide a qualitative estimate of the coolability of multirod bundles, as a function of the equilibrium surface temperature and the pitch-to-diameter (P/D) ratio. Although the decay heat removal rate for P/D values <1.5 increased rapidly with P/D ratio, for larger P/D values the decay heat removal rate was insensitive to either the P/D value or the rod arrangement in the bundle. These results suggest that in TRIGA-type reactors at a typical P/D ratio of 1.12, the maximum decay heat removal level is ∼1 kW/m. This maximum corresponds to an initial decay power following sustained operation at ∼12.5 kW/m.
Fabrication of High Quality Superconducting Tunnel Junctions (1998)

High quality Nb/AlO x /Nb superconducting tunnel junctions (STJs) are fabricated for the radiation detection. The fabrication process includes a MgO thin film, an underlayer method, a control of critical current, a nitrogen plasma passivation, and a SiO 2 insulating layer. Subgap current characteristics of STJs have been investigated in the temperature range of 0.35K to 4.2K in order to evaluate the junction quality for the radiation detection. The STJs fabricated by present process show extremely high quality junction characteristics with a leakage current density of 0.1 pA/µm 2 , a resistance ratio R d / R n of 6×10 6 for a 200×200–µm 2 STJ with a critical current density of 200A/cm 2 .
Write-optimized dynamic hashing for persistent memory (2019)

Low latency storage media such as byte-addressable persistent memory (PM) requires rethinking of various data structures in terms of optimization. One of the main challenges in implementing hash-based indexing structures on PM is how to achieve efficiency by making effective use of cachelines while guaranteeing failure-atomicity for dynamic hash expansion and shrinkage. In this paper, we present Cacheline-Conscious Extendible Hashing (CCEH) that reduces the overhead of dynamic memory block management while guaranteeing constant hash table lookup time. CCEH guarantees failure-atomicity without making use of\nexplicit logging. Our experiments show that CCEH effectively adapts its size as the demand increases under the finegrained ailure-atomicity constraint and its maximum query latency is an order of magnitude lower compared to the stateof-the-art ashing techniques.
The Role of Membrane Glycoprotein Plasma Cell Antigen 1/Ectonucleotide Pyrophosphatase Phosphodiesterase 1 in the Pathogenesis of Insulin Resistance and Related Abnormalities (2008)

Insulin resistance is a major feature of most patients with type 2 diabetes mellitus (T2D). A number of laboratories have observed that PC-1 (membrane [corrected] glycoprotein plasma cell antigen 1; also termed [corrected] ectonucleotide pyrophosphatase phosphodiesterase 1 or ENPP1) [corrected] is either overexpressed or overactive in muscle, adipose tissue, fibroblasts, and other tissues of insulin-resistant individuals, both nondiabetic and diabetic. Moreover, PC-1 (ENPP1) overexpression [corrected] in cultured cells in vitro and in transgenic mice in vivo, [corrected] impairs insulin stimulation of insulin receptor (IR) activation and downstream signaling. PC-1 binds to the connecting domain of the IR alpha-subunit that is located in residues 485-599. The connecting domain transmits insulin binding in the alpha-subunit to activation of tyrosine kinase activation in the beta-subunit. When PC-1 is overexpressed, it inhibits insulin [corrected]induced IR beta-subunit tyrosine kinase activity. In addition, a polymorphism of PC-1 (K121Q) in various ethnic populations is closely associated with insulin resistance, T2D, and cardio [corrected] and nephrovascular diseases. The product of this polymorphism has a 2- to 3-fold increased binding affinity for the IR and is more potent than the wild-type PC-1 protein (K121K) in inhibiting the IR. These data suggest therefore that PC-1 is a candidate protein that may play a role in human insulin resistance and T2D by its overexpression, its overactivity, or both.
Rituximab for autoimmune haemophilia: a proposed treatment algorithm (2005)

We previously reported durable complete responses following brief courses of rituximab and prednisone with or without cyclophosphamide in four patients with autoimmune haemophilia and inhibitor titres of 5-60 BU. We report here responses to this monoclonal anti-CD20 antibody in four additional patients, including two patients with inhibitor titres >200 BU. Factor VIII levels became normal 2-35weeks after 4 or 8 weekly doses of rituximab, brief courses of prednisone and in one patient immunoglobulin. Complete responses are ongoing at 10 months in two patients. Two patients relapsed: a patient whose initial inhibitor titre was 525 BU relapsed at 3.5 months and a long-term prednisone-dependent patient at 8.5 months. Both responded to second courses of rituximab and prednisone and are in remission. Our experience suggests that rituximab is a safe and effective addition to immunosuppression with prednisone and cyclophosphamide to treat autoimmune haemophilia, and may permit early discontinuation or even avoidance of these potentially toxic agents. High-titre inhibitor patients, however, may require multiple courses of rituximab or the addition of cyclophosphamide. Pending randomized studies, we propose an algorithm based on our experience and other reports for incorporating rituximab in the treatment of this rare disorder.
Bi-SQUID noise simulation (2013)

We present an analysis of noise characteristics of bi-SQUID through its voltage response and compare to characteristics of dc SQUID in the open loop configuration. The additional Josephson junction in bi-SQUID gives an additional source of fluctuations, changes transfer function, nonlinear dynamics and nonlinear noise spectrum transformation. These result in different input noise level versus applied magnetic flux.
Paranoid schizophrenia in adolescence. (1991)

Given the incidence of paranoid schizophrenia in an adolescent population, adolescent psychiatrists are likely to encounter this disorder. DSM-III-R should be used in future studies to further clarify the issue of the prevalence of paranoid schizophrenia in adolescents.
MITHRA: Multiple data independent tasks on a heterogeneous resource architecture (2009)

With the advent of high-performance COTS clusters, there is a need for a simple, scalable and fault-tolerant parallel programming and execution paradigm. In this paper, we show that the popular MapReduce programming model can be utilized to solve many interesting scientific simulation problems with much higher performance than regular cluster computers by leveraging GPGPU accelerators in cluster nodes. We use the Massive Unordered Distributed (MUD) formalism and establish a one-to-one correspondence between it and general Monte Carlo simulation methods. Our architecture, MITHRA, leverages NVIDIA CUDA technology along with Apache Hadoop to produce scalable performance gains using the MapReduce programming model. The evaluation of our proposed architecture using the Black Scholes option pricing model shows that a MITHRA cluster of 4 GPUs can outperform a regular cluster of 62 nodes, achieving a speedup of about 254 times in our testbed, while providing scalable near linear performance with additional nodes.
Novel Visible Light-Driven Photocatalytic Chlorine Activation Process for Carbamazepine Degradation in Drinking Water (2020)

Photolysis of free chlorine (HOCl/ClO<sup>-</sup>) is an advanced oxidation process (AOP) to produce hydroxyl (HO<sup>•</sup>) and other radicals for refractory micropollutant degradation. However, HOCl/ClO<sup>-</sup> is only conducive to activation and production of radicals by ultraviolet (UV) light. For the first time, we show the use of visible light (>400 nm) to produce HO<sup>•</sup> and ClO<sup>•</sup>, through use of graphitic carbon nitride (g-C<sub>3</sub>N<sub>4</sub>) and photogenerated h<sub>vb</sub><sup>+</sup>, e<sub>cb</sub><sup>-</sup>, and O<sub>2</sub><sup>•-</sup> in the presence of HOCl/ClO<sup>-</sup>, which was termed visible light g-C<sub>3</sub>N<sub>4</sub>-enabled chlorine AOP (VgC-AOP). The VgC-AOP increased the pseudo first-order degradation rate constant of a model micropollutant, carbamazepine, by 16 and 7 times higher than that without g-C<sub>3</sub>N<sub>4</sub> and HOCl/ClO<sup>-</sup>, respectively, and remained active over multiple use cycles. Effects of water quality [pH, alkalinity, Cu(II), and natural organic matter (NOM)] and the operational conditions (g-C<sub>3</sub>N<sub>4</sub> and HOCl/ClO<sup>-</sup> concentrations, irradiation wavelength, and dose) were investigated. Of particular significance is its superior performance in the presence of NOM, which absorbs less light at visible light wavelengths and scavenges less surface-bonded reactive species, compared against UV/TiO<sub>2</sub> or UV/chlorine AOPs. The VgC-AOP is practically relevant, feasible, and easily implementable and it expands the potential types of light sources (e.g., LEDs and solar light).
Catalytic nickel nanoparticles embedded in a mesoporous metal–organic framework (2010)

Ni nanoparticles embedded in the pores of a mesoporous MOF (MesMOF-1) act as a catalyst for hydrogenolysis of nitrobenzene or hydrogenation of styrene.
Cholesterol Biosynthesis and Trafficking in Cortisol-Producing Lesions of the Adrenal Cortex (2015)

CPAs displayed characteristics of "cholesterol-starved" tissues when compared to PPNAD and PMAH and appeared to have increased intrinsic cholesterol production and uptake from the periphery, as well as decreased cholesterol efflux. This has implications for a potential new way of treating these tumors.
Conjugated Polymer Donor-Molecular Acceptor Nanohybrids for Photocatalytic Hydrogen Evolution (2019)

A library of 237 organic binary/ternary nanohybrids consisting of conjugated polymers donors and both fullerene and non-fullerene molecular acceptors was prepared and screened for sacrificial photocatalytic hydrogen evolution. These donor-acceptor nanohybrids (DANHs) showed significantly enhanced hydrogen evolution rates compared with the parent donor or acceptor compounds. DANHs of a polycarbazole-based donor combined with a methanofullerene acceptor (PCDTBT/PC60BM) showed a high hydrogen evolution rate of 105.2 mmol g-1 h-1 under visible light (λ > 420 nm). This DANH photocatalyst produced 5.9 times more hydrogen than a sulfone-containing polymer (P10) under the same conditions, which is one of the most efficient organic photocatalysts reported so far. An apparent quantum yield of hydrogen evolution of 3.0 % at 595 nm was measured for this DANH. The photocatalytic activity of the DANHs, which in optimized cases reached 179.0 mmol g-1 h-1, is attributed to efficient charge transfer at the polymer donor/molecular acceptor interface. We also show that ternary donorA-donorB-acceptor nanohybrids can give higher activities than binary donor-acceptor hybrids in some cases.
The PSI structural genomics knowledgebase (2008)

Rv2844 is a conserved hypothetical protein from M. tuberculosis. Among the 4.5 million protein sequences in the non-redundant (NR) sequence database, only 12 proteins share sequence homology with Rv2844, and none of them has a known function. The crystal structure of Rv2844 was determined by Se-SAD experiments and refined at 2.0 resolution. It revealed a fold of a 4-helix bundle closely related to the Ferritin-like iron storage and electron transport proteins. It is quite possible that Rv2844 defines a novel class of 4-helix bundle metal-binding proteins. High-throughput ligand analysis (Roberts and Kim, to be published) suggested that Rv2844 strongly interacts with s-adenosylmethionine (SAM), a coenzyme involved in more than 40 metabolic reactions in cells. Structural study of Rv2844-SAM complex is underway to understand the nature of their interaction. Since Rv2844 has no sequence homologs in higher organisms, and since experimental data strongly indicate Rv2844's relationship to proteins critical to cell's metabolic pathways, we are in the process of evaluating Rv2844's potential as a drug target. Updated results will be presented.