gebhart/patrepeval huggingface dataset:
Tumor‐infiltrating lymphocytes can be activated in situ by using in vivo activants plus F(ab′)2 bispecific antibodies (1996)

In vitro-activated T lymphocytes can be retargeted with anti-CD3 × anti-tumor bispecific antibodies (BsAb) to kill tumor cells in vitro and in vivo. The purpose of the present study was to examine the systemic and intra-tumor effects of in vivo T-cell activation with BsAb, staphylococcal enterotoxin B (SEB), and β-glucan in combination with BsAb as a retargeting agent. CL-62 melanoma cells were injected subcutaneously into C3H/HeN mice. Mice were subsequently treated with BsAb alone or with SEB or β-glucan plus BsAb. Fresh splenocytes, lymph-node cells and tumor-infiltrating lymphocytes (TIL) were tested for their proliferative response using incorporation of 3H-thymidine, and for their ability to lyse CL-62 cells in the presence or absence of BsAb in 4-hr 51Chromium release assays. Toxicity of treatments was assessed in a D-galactosamine model. BsAb, alone or combined with β-glucan, had essentially no effect on systemic T-cell cytotoxicity, and essentially no effect on systemic proliferation, unless exogenous IL-2 was provided. At the tumor site, BsAb alone, BsAb plus β-glucan, and SEB plus BsAb all significantly increased BsAb-mediated TIL cytotoxicity. In contrast to the TIL-limited effects of BsAb and of BsAb plus β-glucan, SEB plus BsAb markedly increased both systemic and intra-tumor T-lymphocyte activation. Toxicity correlated with measures of systemic activation, with limited effects from BsAb alone and from β-glucan plus BsAb, and with marked lethality from SEB plus BsAb. Overall, these results suggest moderate intra-tumor activation of TIL, but no measurable systemic activation after in vivo treatment with BsAb or β-glucan plus BsAb. SEB plus BsAb results in complete T-cell activation in both systemic and intra-tumor compartments, but at the expense of increased systemic toxicity. In conclusion, TIL can be activated in situ with different combinations of in vivo activants. In vivo-activated TIL can be retargeted with bispecific antibodies to lyse tumor cells, and may be an alternative to ex vivo T-cell activation and adoptive transfer therapy. © 1996 Wiley-Liss, Inc.
Method and structure for local emission regulation and arc prevention in field emitter arrays (2004)

We propose an alternative arc-prevention and emission regulation method that allows high current densities and enforces a narrow energy distribution. The method requires a structure incorporating a filter aperture over the usual gate aperture. The top aperture acts as a high-pass energy filter. When the filter is negative with respect to the gate, a potential energy barrier is created in the path of the emitted electrons. Also, the energy distribution often becomes narrower and shifts closer to E/sub F/ after operating the emitters in UHV. The energy shift shows that the potential drop in the emitter is reduced, suggesting that the dielectric surface layer has become more conductive and/or thinner.
A Soil‐free Plant Growth System to Facilitate Analysis of Plant Pathogen Interactions in Roots (2009)

Abstract Analysis of the interaction of pathogens with plant roots is often complicated by the growth of plants in a soil substrate. A soil‐free plant growth system (SPS) was developed that removes the need for a substrate while supporting the growth of seedlings in a nutrient rich, oxygenated environment. The model legume Lupinus angustifolius was used to compare the growth of seedlings within soil and the SPS. Seedlings grown under both conditions were similar in morphology, anatomy and health (measured by leaf chlorophyll abundance) and importantly there was little difference in root growth and development although straighter and fuller root systems were achieved in the SPS. The ease of access to the root system proved efficient for the analysis of root and pathogen interactions with no interference from soil or adhering particulate matter. Following inoculation of L. angustifolius roots with Phytophthora cinnamomi the host/pathogen interaction was easily observed and tissues sampled undamaged.
Effects of treatment on long‐term survivors with malignant astrocytomas (1990)

We reviewed the records of 160 consecutive patients with glioblastoma and anaplastic astrocytoma to evaluate the long-term consequences of radiation therapy and chemotherapy. We defined long-term survivors as those patients with glioblastoma or anaplastic astrocytoma who lived at least 100% longer than median survival of historical controls, for example, 2 years for patients with glioblastoma and 4 years for patients with anaplastic astrocytoma. There were 9 (5.6%) long-term survivors. Three (30%) became demented and died without evidence of tumor recurrence. One, after survival of 10 years, died of tumor recurrence. Of the remaining survivors, 2 (22%) have significantly impaired short-term memory function and other neurological deficits such as gait apraxia. Three (30%) can function independently. It is likely but cannot be proved that it is radiotherapy and not chemotherapy that is the causal factor of this dismal therapeutic outcome. Our study suggests restraint in the use of radiotherapy for patients with brain tumors that have more favorable prognoses than glioblastomas and anaplastic astrocytomas, such as low-grade astrocytomas and oligodendrogliomas.
Systems Biology and Synthetic Biology (2009)

Chapter 1: Introduction (Pengcheng Fu). Chapter 2: Basics of Molecular Biology, Genetic Engineering and Metabolic Engineering (Michael X. Wang and Huidong Shi). Chapter 3: High-Throughput Technologies and Functional Genomics (Henry Wang and Dorothea K. Thompson). Chapter 4: Predicting the Lymph Node Status of Breast Cancer Tumors Using Gene Expression Patterns and Genomic Signal Processing (Gordon Okimoto). Chapter 5: From Recombinant Genes to Recombinant Genomes for Systems Biology (Mitsuhiro Itaya). Chapter 6: In silico Genome-scale Metabolic Models: The Constraint-based Approach and its Applications (Andrew Joyce and Bernhard Palsson). Chapter 7: Mathematical Modeling of Genetic Regulatory Networks: Stress Responses in Escherichia coli (Delphine Ropers, Hidde de Jong, and Johannes Geiselmann). Chapter 8: Systems Approaches in Molecular Diagnostics and Drug Development (Martin Latterich). Chapter 9: Yeast as a Prototype for Systems Biology (Gautham Vemuri and Jens Nielsen). Chapter 10: Construction and Applications of Genome-Scale In Silico Metabolic Models for Strain Improvement (Sang Yup Lee, Jin Sik Kim, Hongseok Yun, Tae Yong Kim, Seung Bum Sohn, Hyun Uk Kim). Chapter 11: Synthetic Biology: Putting Engineering into Bioengineering (Matthias Heinemann and Sven Panke). Chapter 12: Rationals of Gene Design and de novo Gene Construction (Marcus Graf, Thomas Schoedl and Ralf Wagner). Chapter 13: Self-replication in Chemistry and Biology (Phil Holliger and David Loakes). Chapter 14: The Synthetic Approach for Regulatory and Metabolic Circuits (Wilson W. Wong and James C. Liao). Chapter 15: Synthetic Genetic Networks (David Greber and Martin Fussenegger). Chapter 16: The theory of biological robustness and its implication to cancer (Hiroaki Kitano). Chapter 17: Nucleic Acid Engineering (Wenlong Cheng, Liang Ding, Hisakage Funabashi, Nokyoung Park, Soong Ho Um, Jianfeng Xu, and Dan Luo). Chapter 18: Potential Applications of Synthetic Biology in Marine Microbial Functional Ecology and Biotechnology (Guangyi Wang and Juanita Mathews). Chapter 19: On fundamental implications of systems and synthetic biology (Cliff Hooker). Chapter 20: Outstanding Issues in systems and synthetic biology (Pengcheng Fu and Cliff Hooker).
Experimental validation of multiphase flow models and testing of multiphase flow meters: a critical review of flow loops worldwide (2007)

Around the world, research into multiphase flow is performed by scientists with hugely diverse backgrounds: physicists, mathematicians and engineers from mechanical, nuclear, chemical, civil, petroleum, environmental and aerospace disciplines. Multiphase flow models are required to investigate the co-current or counter-current flow of different fluid phases under a wide range of pressure and temperature conditions and in several different configurations. To compliment this theoretical effort, measurements at controlled experimental conditions are required to verify multiphase flow models and assess their range of applicability, which has given rise to a large number of multiphase flow loops around the world. These flow loops are also used intensively to test and validate multiphase flow meters, which are devices for the in-line measurement of multiphase flow streams without separation of the phases. However, there are numerous multiphase flow varieties due to differences in pressure and temperature, fluids, flow regimes, pipe geometry, inclination and diameter, so a flow loop cannot represent all possible situations. Even when experiments in a given flow loop are believed to be sufficiently exhaustive for a specific study area, the real conditions encountered in the field tend to be very different from those recreated in the research facility. This paper presents a critical review of multiphase flow loops around the world, highlighting the pros and cons of each facility with regard to reproducing and monitoring different multiphase flow situations. The authors suggest a way forward for new developments in this area.
Optical diffraction technique for determination of crystal orientations (1981)

An optical technique for determination of crystal orientations is described. This technique uses texture etching to generate pseudoperiodic surface structures whose groove shape is characteristic of the surface orientation. When such a textured surface is illuminated with monochromatic light, a far-field diffraction pattern characteristic of the surface orientation is observed. A procedure for analysis of diffraction patterns to determine crystal orientations is discussed. Results obtained by this technique agree very well with those using the x-ray Laue technique.
Syntheses of p-phenylene- and p-biphenylylene-bridged methylated binuclear ferrocenes (1988)

p-Phenylene and p-biphenylene-bridged methylated cyclopentadienyl rings were prepared. Reaction of the dilithio salts of the ligands with (η5-C5Me5)Fe(acac) provides cleanly ferrocenes bridged by p-phenylene and p-biphenylene groups. The electrochemistry of these compounds shows that a mixed-valence state is stabilized only in the p-C6H4-bridged species; if the bridge is extended to two aromatic rings, the individual ferrocenes do not interact. Methyl substitution on the ring increases the interaction between the metals centers as shown for (η5-C5H5)Fe[(η5-C5Me4)C6H4(η5-C5Me4)]Fe(η5-C5H5), in which the mixed-valence state is less stable as compared with the analogous, fully methylated compound. © 1988, American Chemical Society. All rights reserved.
Distinct stages in stress granule assembly and disassembly (2016)

Stress granules are non-membrane bound RNA-protein (RNP) assemblies that form when translation initiation is limited and contain a biphasic structure with stable core structures surrounded by a less concentrated shell. The order of assembly and disassembly of these two structures remains unknown. Time course analysis of granule assembly suggests that core formation is an early event in granule assembly. Stress granule disassembly is also a stepwise process with shell dissipation followed by core clearance. Perturbations that alter liquid-liquid phase separations (LLPS) driven by intrinsically disordered protein regions (IDR) of RNA binding proteins in vitro have the opposite effect on stress granule assembly in vivo. Taken together, these observations argue that stress granules assemble through a multistep process initiated by stable assembly of untranslated mRNPs into core structures, which could provide sufficient high local concentrations to allow for a localized LLPS driven by IDRs on RNA binding proteins.
High-Level Neuronal Expression of Aβ<sub>1–42</sub>in Wild-Type Human Amyloid Protein Precursor Transgenic Mice: Synaptotoxicity without Plaque Formation (2000)

Amyloid plaques are a neuropathological hallmark of Alzheimer's disease (AD), but their relationship to neurodegeneration and dementia remains controversial. In contrast, there is a good correlation in AD between cognitive decline and loss of synaptophysin-immunoreactive (SYN-IR) presynaptic terminals in specific brain regions. We used expression-matched transgenic mouse lines to compare the effects of different human amyloid protein precursors (hAPP) and their products on plaque formation and SYN-IR presynaptic terminals. Four distinct minigenes were generated encoding wild-type hAPP or hAPP carrying mutations that alter the production of amyloidogenic Abeta peptides. The platelet-derived growth factor beta chain promoter was used to express these constructs in neurons. hAPP mutations associated with familial AD (FAD) increased cerebral Abeta(1-42) levels, whereas an experimental mutation of the beta-secretase cleavage site (671(M-->I)) eliminated production of human Abeta. High levels of Abeta(1-42) resulted in age-dependent formation of amyloid plaques in FAD-mutant hAPP mice but not in expression-matched wild-type hAPP mice. Yet, significant decreases in the density of SYN-IR presynaptic terminals were found in both groups of mice. Across mice from different transgenic lines, the density of SYN-IR presynaptic terminals correlated inversely with Abeta levels but not with hAPP levels or plaque load. We conclude that Abeta is synaptotoxic even in the absence of plaques and that high levels of Abeta(1-42) are insufficient to induce plaque formation in mice expressing wild-type hAPP. Our results support the emerging view that plaque-independent Abeta toxicity plays an important role in the development of synaptic deficits in AD and related conditions.
Proposed Square Lattice Photonic Crystal Fiber for Extremely High Nonlinearity, Birefringence and Ultra-High Negative Dispersion Compensation (2017)

Abstract A photonic crystal fiber in square lattice architecture is numerically investigated and proposed for broadband dispersion compensation in optical transmission system. Simulation results reveal that it is possible to obtain an ultra-high negative dispersion of about −571.7 to −1889.7 (ps/nm.km) in the wavelength range of 1340 nm to 1640 nm. Experimentally it is demonstrated that the design fiber covers a high birefringence of order 4.74×10 ‒3 at the wavelength of 1550 nm. Here, numerical investigation of guiding properties and geometrical properties of the proposed PCF are conducted using the finite element method (FEM) with perfectly match layers. Moreover, it is established more firmly that the proposed fiber successfully compensates the chromatic dispersion of standard single mode in entire band of interest. Our result is attractive due to successfully achieve ultra-high negative dispersion that is more promisor than the prior best results.
Real‐time analysis of ethylene vinyl acetate random copolymers using near infrared spectroscopy during extrusion (1996)

Abstract Poly(ethylene vinyl acetate) (EVA) is a very common polymer used in hot melt adhesives. The rheological and thermal‐mechanical properties of these adhesives are strongly related to the content of vinyl acetate (VA) incorporated into this random copolymer during polymerization. Results of in‐line monitoring of VA content in flowing molten EVA polymers, using fiberoptic near infrared spectroscopy, shall be discussed in detail. In‐line monitoring is not only desired for its numerous advantages (such as high quality products, lower waste, lower developmental cycle time, and lower costs) but also because it eliminates the sample handling concerns associated with molten polymers.
Partial primary structure of the T4 antigens of mouse and sheep: assignment of intrachain disulfide bonds. (1986)

The T4 antigens of mouse and sheep have been purified to homogeneity and partially sequenced using protein and peptide microsequencing techniques. Both mouse and sheep antigens bear distinct homology to human T4, having an amino-terminal segment that is homologous to the K-chain variable region (VK). A surprisingly high degree of sequence divergence was nevertheless evident between the T4 antigens of the three mammalian species, suggesting an unusually rapid rate of evolution that is possibly related to the functional role of T4 in class II major histocompatibility complex antigen recognition. The mouse and sheep T4 antigens contain at least three intrachain disulfide bonds which in all cases connect adjacent cysteine residues. All three intrachain disulfide linkages are situated within the putative extracellular domain, and the amino-terminal disulfide bond probably involves the two cysteine residues homologous to those which form the intrachain bridge within the VK domain of immunoglobulin molecules. The structural relationship of the T4 antigen to other members of the immunoglobulin supergene family is discussed.
A Hybrid Piezoelectric Structure for Wearable Nanogenerators (2012)

A hybrid-fiber nanogenerator comprising a ZnO nanowire array, PVDF polymer and two electrodes is presented. Depending on the bending or spreading action of the human arm, at an angle of ∼90°, the hybrid fiber reaches electrical outputs of ∼0.1 V and ∼10 nA cm(-2) . The unique structure of the hybrid fiber may inspire future research in wearable energy-harvesting technology.
Intraoperative detection of sentinel lymph nodes using Patent Blue V in non-small cell lung cancer. (2008)

Although the use of Patent Blue V for SLN identification is feasible, this technique presents relatively low identification rate. The major difficulty on the detection of SLNs was the black coloration of the lymph node, which interfered with the visualization of the dye.
A richly interactive exploratory data analysis and visualization tool using electronic medical records (2015)

We developed a visual mining system to support exploratory data analysis of multi-dimensional categorical EMR data. By using CKD as a model of disease, it was assembled by automated correlational analysis and human-curated visual evaluation. The visualization methods such as Sankey diagram can reveal useful knowledge about the particular disease cohort and the trajectories of the disease over time.
<title>High peak power Ti:sapphire lasers: temporal contrast and spectral narrowing issues</title> (2006)

Two new schemes of chirped pulse amplification (CPA) lasers are demonstrated, which are specially designed to overcome some of the bottlenecks of the current Ti:sapphire lasers. In particular, the issues of temporal contrast and spectral narrowing of the pulse during amplification are considered. The proposed schemes are double CPA (DCPA) and the negatively- and positively-chirped pulse amplification (NPCPA). Both of them are an extension of the conventional CPA scheme to Ti:sapphire lasers of petawatt and higher power levels. The double DCPA laser includes two CPA stages with intermediate non-linear temporal pulse filtering. The method reduces substantially the background, including amplified spontaneous emission as well as pre- and post-pulses. The former is demonstrated by achieving a temporal contrast of at least 10<sup>10</sup> with pulses of 2O mJ output energy and 50fs pulse duration. The NPCPA laser scheme implements a combination of negatively- and positively-chirped pulse amplification. This method of amplification suppresses gain related spectral narrowing, typical to CPA lasers, thus supporting pulse spectrum much broader than a conventional CPA. With a NPCPA Ti:sapphire laser we have achieved laser pulses of 50 nm spectral width and 150 mJ energy without any additional spectral correction. The scheme appears as an easy and reliable solution to preserve spectral bandwidth in Ti:Sapphire lasers, especially at high power levels up to the Petawatt regime.
Nonlinear pulse switching using long-period fiber gratings (2000)

We show that the intensity required to achieve all-optical switching in long-period fiber gratings can be reduced by orders of magnitude through the use of uniform phase-shifting regions between gratings. Predicted switching intensities are of the order 100 MW/cm/sup 2/ compared to 10 GW/cm/sup 2/ for normal device configuration.
Characterization and Expression of an Antifungal Zeamatin-like Protein (Zlp) Gene from Zea mays (1994)

A cDNA clone encoding a basic thaumatin-like protein of Zea mays was recovered from a mid-development seed cDNA library. The gene, Zlp, encoded a protein that was nearly identical with maize zeamatin and alpha-amylase/trypsin inhibitor. Expression of Zlp mRNA was highest in the endosperm tissue of seed 4 weeks after pollination. Expression of zeamatin-like (ZLP) protein correlated with mRNA; also, a low basal level of ZLP expression in leaf was not appreciably induced by abiotic stresses. ZLP was expressed with its own signal peptide in insect cells and in transgenic Arabidopsis and tomato plants. ZLP was secreted in all three systems, with correct processing of the signal peptide. ZLP expressed in transgenic tomato was found to be partially subjected to a proteolytic cleavage after residue 180, by an unknown mechanism, to give a "nicked" isoform of ZLP. Purified ZLP from all three sources, as well as purified "nicked" ZLP from tomato, demonstrated fungal inhibition against Candida albicans and Trichoderma reesei, with marginal inhibition observed against Alternaria solani and Neurospora crassa.
β,β‐Diacyl‐enamine und ‐enole, 9: Zur Darstellung von Aminomethylenderivaten offenkettiger CH<sub>2</sub>‐acider Verbindungen (1981)

Abstract Die Reaktion primärer und sekundärer aromatischer oder aliphatischer Amine mit Orthocarbonsäureestern und offenkettigen CH 2 ‐aciden Verbindungen liefert N ‐substituierten Aminoalkylidenderivate; die Ausbeuten variieren stark mit der Natur der aktivierenden Gruppen. Die Methode kann für solche CH 2 ‐acide Moleküle empfohlen werden, welche durch eine nichtenolisierbare Gruppe (CN, NO 2 oder PhSO 2 ) aktiviert sind, während niedrige Ausbeute oder keine Umsetzung zu erwarten ist, wenn stark enolisierte methylenaktive Verbindungen eingesetzt werden. CH 2 ‐Acide Carbonsäuren liefern die Salze 10a – g .
Three year prospective, randomized evaluation of intraocular lens implantation through 3.2 and 5.5 mm incisions (1998)

Smaller incision cataract surgery led to early recovery of visual function in the short term and less induced astigmatism in the long term.
The performance of cache-based error recovery in multiprocessors (1994)

Several variations of cache-based checkpointing for rollback error recovery from transient errors in shared-memory multiprocessors have been recently developed. By modifying the cache replacement policy, these techniques use the inherent redundancy in the memory hierarchy to periodically checkpoint the computation state. Three schemes, different in the manner in which they avoid rollback propagation, are evaluated in this paper. By simulation with address traces from parallel applications running on an Encore Multimax shared-memory multiprocessor, we evaluate the performance effect of integrating the recovery schemes in the cache coherence protocol. Our results indicate that the cache-based schemes can provide checkpointing capability with low performance overhead, but with uncontrollable high variability in the checkpoint interval.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>