gebhart/patrepeval huggingface dataset:
WHOLE‐GENOME SEQUENCING REVEALS IMMUNOTHERAPEUTIC OPTIONS FOR NATURAL‐KILLER/T CELL LYMPHOMA PATIENTS (2019)

Introduction: Natural-killer/T cell lymphoma (NKTL) is an uncommon and aggressive malignancy with a predilection for Asian, Mexican and South American populations. Currently, no published studies have used whole-genome sequencing (WGS) to study NKTL. With the aim of exploring the NKTL tumor genomes for actionable pathways, we used WGS to study the somatic genomic landscape of NKTL. Methods: Study Design: Patients were diagnosed with NKTL according to the 2008 World Health Organization classification with cytotoxic, CD3ε+ and EBER+ phenotypes. All subjects in this study provided written informed consent. Somatic analysis: All analysis was based on the human reference genome hs37d5. Alignment was performed by BWA-MEM. Somatic short-variant calling and annotation were done by Strelka2 and wAnnovar, respectively. Somatic copy number analysis was performed by CNVkit. Somatic structural analysis and annotation were performed by MantaSV and AnnotSV. Somatic mutational signatures analysis were performed with Non-negative factorization package. Results: An average of 39 (range: 1 – 80) somatic non-silent protein-coding variants per sample was identified. Our bioinformatics analysis has also reidentified recurrent non-silent short variants in TP53, DDX3X, STAT3, FAT4 and JAK3. These observations suggest similar pathology between previously studied cohorts and our study cohorts. Non-negative factorization also defined 4 robust mutational signatures, including ‘COSMIC Signature 5’ that has been reported in many cancer types, APOBEC ‘COSMIC Signature 2’, Oxidative Stress ‘COSMIC Signature 18’ and MUTYH-associated ‘COSMIC Signature 17’. A predominant mutational signature to represent each sample and ‘COSMIC Signature 5’ was found to dominate NKTL samples (n = 21) as compared the other mutational signatures. Somatic structural rearrangements analysis found frequent disruptions (n = 8, 25%) to the 3’UTR of PD-L1 and not of the PD-L2gene. PD-L1 was found to be more frequently altered than other known commonly mutated genes such as DDX3X, STAT3, and JAK3 as reported in other studies. This makes PD-L1 the most frequent mutated gene in NKTL. We have previously reported the association of PD-L1 SR with durable response to PD-1 blockade therapy in relapsed/refractory NKTL patients. However, the extent of treatment effect and the mechanisms of response/resistance to PD-1 blockade in the treated patients still remains to be elucidated. To summarize, this study reveals that a large proportion of NKTL patients could very well benefit from PD-1 blockade therapy. Conclusion: We reported the whole-genome mutational profiles of NKTL patients using WGS data, which uncovered a large extent of genomic alterations in immune checkpoint related genes. Keywords: non-Hodgkin lymphoma (NHL); PD-1.
Supplementary Figure 6 from Arrest Defective 1 Autoacetylation Is a Critical Step in Its Ability to Stimulate Cancer Cell Proliferation (2023)

Supplementary Figure 6 from Arrest Defective 1 Autoacetylation Is a Critical Step in Its Ability to Stimulate Cancer Cell Proliferation
Application of human lymphoid cells for the evaluation of antivirals against human adenovirus type 19: Zalcitabine has superior activity compared to cidofovir (2020)

Human adenovirus type 19 (HAdV-19) is a major cause of the epidemic keratoconjunctivitis. Outbreaks of keratoconjunctivitis are problematic to human health, especially for infants, the elderly, and immunocompromised individuals. However, the development of anti-HAdV drugs has been hampered by inconvenient screening systems; therefore, development of a simple screening method is highly desirable. In this study, we identified that HAdV-19 can infect a human lymphoid cell line transformed with human T-cell leukemia virus (MT-2 cells). MT-2 cells supported HAdV-19 replication and showed apparent cytopathic effects within five days post-infection. Using a thiazolyl blue tetrazolium bromide (MTT)-based colorimetric assay on MT-2 cells, we were able to detect the anti-HAdV-19 activities of previously reported nucleoside/tide compounds, including (S)-1-(3-hydroxy-2-phosphonylmethoxypropyl)cytosine (cidofovir), 2',3'-dideoxycytidine (zalcitabine) and 3'-deoxy-3'-fluorothymidine (trifluridine). Compared with previous methods, this system represents a more simple and rapid method to screen anti-HAdV-19 agents.
Carbon Nanotubes in the Coulomb-Blockade regime connected to superconducting leads (2001)

Single-Walled Carbon Nanotubes are connected to superconducting electrodes with a contact resistance considerably higher than the quantum resistance of h/2e2. For the charge transport this excludes proximity effects and/or Andreev reflections but single-charging effects should be observable. The output characteristics of these devices are different from those observed in Single-Walled Carbon Nanotubes contacted by noble metal leads within the Coulomb-Blockade regime.
Combination of DGA and LN Columns: A Versatile Option for Isotope Production and Purification at Oak Ridge National Laboratory (2021)

The chromatographic resins DGA and LN have been used sequentially to separate curium, californium, plutonium, and various fission products (FPs) to obtain products with a pure radioisotope or a radioelement with high isotopic purity. This 2-step combination of resins has found applications in the 252Cf and 238Pu campaigns performed at Oak Ridge National Laboratory. Experiments have been carried out in glove boxes, shielded caves, and hot cells, demonstrating that these resins are adequate and maintain their performance in highly radiolytic environments. Using these resins has led to the recovery of curium highly enriched (>95%) in 248Cm, the clean separation of 251Cf for the superheavy element research, and the recovery of 147Pm from the FP stream obtained during the 238Pu production campaign while demonstrating that the raffinate post DGA is essentially free of transuranic elements.
Phenolic Acid Concentrations in Plasma and Urine from Men Consuming Green or Black Tea and their Chemopreventive Properties for Colon Cancer (2012)

Green (GT) and black tea (BT) polyphenols are metabolized to phenolic acids (PAs) by colonic microflora and may contribute to teas’ chemopreventive activity. The concentration of PAs was quantified in urine and serum from men drinking 6 cups daily of GT, BT or water by high performance liquid chromatography and electrochemical detection. 3,4‐dihydroxyphenyl acetic acid (3,4‐ DHPAA), 4‐hydroxyphenylacetic acid (4‐HPAA), 3‐ hydroxyphenylacetic acid (3‐HPAA), 3‐methoxy‐4‐ hydrozyphenylacetic acid (3M4‐HPAA) and hippuric acid were increased significantly in urine from men drinking GT. The consumption of BT was associated with a significant increase in urine 4‐HPAA and 3‐HPAA only. No significant changes were observed in serum. Fecal water contains a mixture of tea polyphenols such as epigallocatechin gallate (EGCG) and their PA metabolites. We therefore investigated the antiproliferative effect and intracellular concentration of EGCG, 3,4‐DHPAA and their methylated forms in HCT116 and HT‐29 colon cancer cells. Incubation with both EGCG and 3,4‐DHPAA exhibited an additive antiproliferative effect, while methylation of 3,4‐DHPAA was significantly decreased. In summary the consumption of GT was associated with a higher increase in urinary phenolic acids compared to BT. Combining EGCG with 3,4‐DHPAA enhanced the antiproliferative activity in colon cancer cells. Supported by RO1CA116242.
Vacuum Acceleration in a Regime Beyond Brunel Absorption (2009)

We describe a new regime of vacuum acceleration in laser-plasmas driven by ultrafast pulses of relativistic intensity, in which space-charge separation leads to strongly enhanced laser absorption and 20 MeV electrons accelerated outward.
Massless Exploration—Humans as a Solar System Species (2021)

A vision for exploration of the solar system in an Earth independent manner is presented taking into account key drivers, challenges, and future technological advances. This work was in response to requirements set by the NASA Advanced Exploration Systems (AES) office. Planetary targets, key assumptions, and approaches to utilizing non-terrestrial resources are presented. The mission was divided into four sprints. The first sprint aims at a settlement on Earth’s moon. The second sprint aims at establishing a Lagrangian point station near the Moon. The third sprint leads to the colonization of Mars and its moons. The fourth and final sprint investigated the exploration of Callisto, a moon of Jupiter. Bio-inspired approaches to technology and processes were considered to ensure that the in-space habitats are Earth like. The conclusion based on exploring the four sprints is that it is feasible to colonize the solar system without relying on Earth, but this relies on critical technology development and investments in emerging areas.
Image-Guided Surgery Using Invisible Near-Infrared Light: Fundamentals of Clinical Translation (2010)

The field of biomedical optics has matured rapidly over the last decade and is poised to make a significant impact on patient care. In particular, wide-field (typically &gt; 5 cm), planar, near-infrared (NIR) fluorescence imaging has the potential to revolutionize human surgery by providing real-time image guidance to surgeons for tissue that needs to be resected, such as tumors, and tissue that needs to be avoided, such as blood vessels and nerves. However, to become a clinical reality, optimized imaging systems and NIR fluorescent contrast agents will be needed. In this review, we introduce the principles of NIR fluorescence imaging, analyze existing NIR fluorescence imaging systems, and discuss the key parameters that guide contrast agent development. We also introduce the complexities surrounding clinical translation using our experience with the Fluorescence-Assisted Resection and Exploration (FLARE™) imaging system as an example. Finally, we introduce state-of-the-art optical imaging techniques that might someday improve image-guided surgery even further.
Comprehensive histologic assessment helps to differentiate multiple lung primary nonsmall cell carcinomas from metastases (2009)

International audience
Fabrication of GaInAs/InP Heterojunction Bipolar Transistors with a Single Tungsten Wire as Collector Electrode (2003)

GaInAs/InP heterojunction bipolar transistors (HBTs) with a single 0.1-µm-wide tungsten wire were fabricated. The tungsten wire was buried in an undoped InP collector layer and functioned as a collector electrode. In a previous process of fabricating HBTs with buried wires, we could not achieve a device operation with only a single wire. One of the possible reasons for this failure was the insufficient growth of the buried wire, because this wire requires a long growth time. The nonuniformity of facet formation in a previous wet etching process used to fabricate an InP emitter also contributed to the failure. By increasing the growth time of the buried wire and changing the wet etching solution used to enable uniform fabrication of emitter mesas, we observed a transistor operation with a current gain of 20 in the fabricated HBT. The emitter area of the device was 0.1×0.5 µm2.
Sphingosine Kinase Transmits Estrogen Signaling in Human Breast Cancer Cells (2003)

Current understanding of cytoplasmic signaling pathways that mediate estrogen action in human breast cancer is incomplete. Here we report that treatment with 17beta-estradiol (E2) activates a novel signaling pathway via activation of sphingosine kinase (SphK) in MCF-7 breast cancer cells. We found that E2 has dual actions to stimulate SphK activity, i.e. a rapid and transient activation mediated by putative membrane G protein-coupled estrogen receptors (ER) and a delayed but prolonged activation relying on the transcriptional activity of ER. The E2-induced SphK activity consequently activates downstream signal cascades including intracellular Ca2+ mobilization and Erk1/2 activation. Enforced expression of human SphK type 1 gene in MCF-7 cells resulted in increases in SphK activity and cell growth. Moreover, the E2-dependent mitogenesis were highly promoted by SphK overexpression as determined by colony growth in soft agar and solid focus formation. In contrast, expression of SphKG82D, a dominant-negative mutant SphK, profoundly inhibited the E2-mediated Ca2+ mobilization, Erk1/2 activity and neoplastic cell growth. Thus, our data suggest that SphK activation is an important cytoplasmic signaling to transduce estrogen-dependent mitogenic and carcinogenic action in human breast cancer cells.
Nicotine Hydrogen Tartrate: Effect on Essential Fatty Acid Deficiency in Mature Pigs (1969)

Structural studies on a very lysine-rich histone show that the carboxyl-terminal half of the molecule is enriched in lysine (and proline). which suggests that it is a site for binding to DNA. The amino-terminal half. containing most of the acidic residues. resembles small, nonhistone proteins and so might have specificity for factors other than DNA.
Cryogenic absorption spectra of hydroperoxo‐ferric heme oxygenase, the active intermediate of enzymatic heme oxygenation (2002)

Using radiolysis with (32)P enriched phosphate as an internal source of ionizing radiation, the formation of hydroperoxo-ferric complex from oxy-ferrous precursor with a high yield was monitored at 77 K in heme oxygenase (HO) by means of optical absorption spectroscopy. Well-resolved absorption spectra (maxima at 421 nm, 530 nm, 557 nm) of hydroperoxo-ferric intermediate of this heme enzyme were measured in 70% glycerol/buffer frozen glasses. After annealing at 210-215 K this complex converts to the product complex, alpha-meso hydroxyheme-HO. No heme degradation products were formed in control experiments with ferric HO or other heme proteins.
Spectral Imaging for Microbubble Characterization (2019)

Microbubbles stabilized by an outer lipid shell have been studied extensively for both diagnostic and therapeutic applications. The shell composition can significantly influence microbubble behavior, but performing quantitative measurements of shell properties is challenging. The aim of this study is to investigate the use of spectral imaging to characterize the surface properties of a range of microbubble formulations representing both commercial and research agents. A lipophilic dye, C-laurdan, whose fluorescence emission varies according to the properties of the local environment, was used to compare the degree and uniformity of the lipid order in the microbubble shell, and these measurements were compared with the acoustic response and stability of the different formulations. Spectral imaging was found to be suitable for performing rapid and hence relatively high throughput measurements of microbubble surface properties. Interestingly, despite significant differences in lipid molecule size and charge, all of the different formulations exhibited highly ordered lipid shells. Measurements of liposomes with the same composition and the debris generated by destroying lipid microbubbles with ultrasound (US) showed that these exhibited a lower and more varied lipid order than intact microbubbles. This suggests that the high lipid order of microbubbles is due primarily to compression of the shell as a result of surface tension and is only minimally affected by composition. This also explains the similarity in acoustic response observed between the formulations, because microbubble dynamics are determined by the diameter and shell viscoelastic properties that are themselves a function of the lipid order. Within each population, there was considerable variability in the lipid order and response between individual microbubbles, suggesting the need for improved manufacturing techniques. In addition, the difference in the lipid order between the shell and lipid debris may be important for therapeutic applications in which shedding of the shell material is exploited, for example, drug delivery.
Procoagulant Activity of T Lymphoblastoid Cells due to Exposure of Negatively Charged Phospholipid (2002)

We have characterised the Procoagulant activity (PCA) of six well-established cell lines by assays of tissue factor (TF), thrombin and FXa generation, flow cytometry using Annexin V, and by binding studies with Factors VIII and IXa. The monocytic (THP-1 & U937) and promyelocytic (NB4) cells expressed high concentrations of TF antigen and activity, whereas TF in the lymphocytic cells (Molt 4, Jurkat & Nalm 6) was very low or absent. However the T-lymphoblastoid cells (Molt 4 & Jurkat) promoted the generation of large amounts of thrombin despite their low TF content, and these cells were also the most active in supporting Factor Xa generation. Molt 4 cells bound Factors VIII and IXa with high capacity and their activity was inhibited by Annexin V. These results indicate that the PCA of T-lymphoblastoid lines is due to expression of negatively charged phospholipids. Flow cytometry studies showed Annexin V binding to the major population of nonapoptotic Molt 4 cells and the PCA of Molt 4 was not increased when apoptosis was induced by staurosporine, indicating that PCA is independent of apoptotic status.
Top-k Substring Matching for Auto-Completion (2013)

Given the user's input as a query, auto-completion selects the top-k strings with the highest scores from the strings matching the query in a dictionary. A recent study [14] proposed space-efficient data structures for top-k prefix matching for auto-completion. In practical applications, however, top-k substring matching is required for many purposes. In this paper, we present a novel approach to solve the top-k substring matching problem. We combined two trie-based data structures derived from the same dictionary for prefix and key search, and we search them alternately leveraging the implicit tree structure shared by them. Experimental results show that our algorithm can suggest top-k completion sufficiently fast, while taking much less space than a compressed full-text index of the dictionary.
The Nike electron-beam-pumped KrF laser amplifiers (1997)

Nike is a recently completed multikilojoule krypton-fluoride (KrF) laser that has been built to study the physics of direct-drive inertial confinement fusion. The two final amplifiers of the Nike laser are both electron-beam-pumped systems. This paper describes these two amplifiers, with an emphasis on the pulsed power. The smaller of the two has a 20/spl times/20 cm aperture, and produces an output laser beam energy in excess of 100 J. This 20 cm Amplifier uses a single 12 kJ Marx generator to inject two 300 kV, 75 kA, 140 ns flat-top electron beams into opposite sides of the laser cell. The larger amplifier in Nike has a 60/spl times/60 cm aperture, and amplifies the laser beam up to 5 W. This 60 cm amplifier has two independent electron beam systems. Each system has a 170 kT Marx generator that produces a 670 kV, 540 kA, 240 ns Bat-top electron beam. Both amplifiers are complete, fully integrated into the laser, meet the Nike system requirements, and are used routinely for laser-target experiments.
Utilising the Curriculum Committee to Strengthen Teaching-Learning in a Medical School (2018)

The article examines various initiatives undertaken by the curriculum committee at an offshore Caribbean medical school to strengthen teaching-learning. The authors examined various initiatives undertaken by the committee since September 2017. They also searched the scientific literature for brief descriptions of similar initiatives at other medical schools in the Caribbean and other regions. A number of initiatives have been introduced to strengthen the curriculum and teaching-learning. Among the new initiatives were creating a structured outline for course syllabi, initiating online modules on nutrition in medicine and patient safety, introducing a health humanities module, starting a module on integrative medicine, system-wise sequencing of the fourth semester, conducting sessions on critical appraisal of scientific literature, and introducing a day long orientation programme. The impact of these initiatives can be assessed in the future.
Aerophones in flatland (2015)

We present the first real-time technique to synthesize full-bandwidth sounds for 2D virtual wind instruments. A novel interactive wave solver is proposed that synthesizes audio at 128,000Hz on commodity graphics cards. Simulating the wave equation captures the resonant and radiative properties of the instrument body automatically. We show that a variety of existing non-linear excitation mechanisms such as reed or lips can be successfully coupled to the instrument's 2D wave field. Virtual musical performances can be created by mapping user inputs to control geometric features of the instrument body, such as tone holes, and modifying parameters of the excitation model, such as blowing pressure. Field visualizations are also produced. Our technique promotes experimentation by providing instant audio-visual feedback from interactive virtual designs. To allow artifact-free audio despite dynamic geometric modification, we present a novel time-varying Perfectly Matched Layer formulation that yields smooth, natural-sounding transitions between notes. We find that visco-thermal wall losses are crucial for musical sound in 2D simulations and propose a practical approximation. Weak non-linearity at high amplitudes is incorporated to improve the sound quality of brass instruments.
Logic Synthesis for AND-XOR-OR Type Sense-Amplifying PLA (2002)

In this paper, a new logic synthesis method for an AND-XOR-OR type sense-amplifying PLA is proposed. An AND-XOR-OR type sense-amplifying PLA can achieve low-power dissipation and high-speed operation by using latch sense-amplifiers and a charge sharing scheme. In addition, 2-input XOR function is conveniently implemented in place of the conventional AND/OR planes. Therefore it can realize some classes of logic functions in a smaller circuit area. Since the proposed method makes full use of the existing two-level logic minimization algorithms, it can handle large circuits such as 64-input Boolean function. The method has been implemented and the experimental results are presented. The experimental results show that some classes of Boolean functions can become much smaller and hence we can obtain significantly faster circuits than conventional PLAs with a small area penalty.
Umbilical cord mesenchymal stem cell transplantation in severe and refractory systemic lupus erythematosus (2010)

Our findings indicate that UC MSCT results in amelioration of disease activity, serologic changes, and stabilization of proinflammatory cytokines. These data provide a foundation for conducting a randomized controlled trial of this new therapy for severe and treatment-refractory SLE.
Differential evolution for discrete optimization: An experimental study on Combinatorial Auction problems (2008)

Differential evolution (DE) mutates solution vectors by the weighted difference of other vectors using arithmetic operations. As these operations cannot be directly extended to discrete combinatorial space, DE algorithms have been traditionally applied to optimization problems where the search space is continuous. In this paper, we use JADE, a self-adaptive DE algorithm, for winner determination in Combinatorial Auctions (CAs) where users place bids on combina tions of items. To adapt JADE to discrete optimization, we use a rank-based representation schema that produces only feasible solu tions and a regeneration operation that constricts the problem search space. It is shown that JADE compares favorably to a local stochastic search algorithm, Casanova, and a genetic algorithm based approach, SGA.