gebhart/patrepeval huggingface dataset:
Ultrawide tuning of photonic microcavities via evanescent field perturbation (2006)

Evanescent field perturbation of an integrated microring resonator is examined as a means of achieving high-fidelity reversible tuning of photonic microcavities over large wavelength ranges. A 1.7% wavelength tuning is achieved through the use of a novel silica fiber probe that provides access to the evanescent field of an air-clad high-index-contrast ring resonator. As the microring is perturbed, the probe-ring distance is found through simultaneous nanometric distance calibration and force measurements. Experimental results agree well with theoretical tuning. Possible microelectromechanical systems implementation of this effect is discussed, as well as avenues for improvement of the tuning range.
RFID sensor networks with the Intel WISP (2008)

We demonstrate a simple RFID sensor network comprised of an Intel WISP and a commodity UHF RFID reader. WISPs are devices that gather their operating energy from RFID reader transmissions, in the manner of passive RFID tags, and further include sensors, e.g., accelerometers, and provide a very small-scale computing platform. We believe that the small form factor and lack of battery makes the WISP an attractive alternative to motes for many of the original smart dust applications that require very small or long-lived sensors. The Intel WISP that we demonstrate has an ultra-low-power microcontroller, 32K of program space, 8K of flash, and accelerometer and temperature sensors. It harvests power from and communicates sensor data to standard (EPC Class 1 Gen 2) UHF RFID readers with a range of roughly 10 feet. This combination of RFID technology and sensor networks raises many research challenges, such as how to function with intermittent power and how to modify RFID protocols to support sensor queries.
Improving data-flow analysis with path profiles (1998)

Data-flow analysis computes its solutions over the paths in a control-flow graph. These paths---whether feasible or infeasible, heavily or rarely executed---contribute equally to a solution. However, programs execute only a small fraction of their potential paths and, moreover, programs' execution time and cost is concentrated in a far smaller subset of hot paths .This paper describes a new approach to analyzing and optimizing programs, which improves the precision of data flow analysis along hot paths. Our technique identifies and duplicates hot paths, creating a hot path graph in which these paths are isolated. After flow analysis, the graph is reduced to eliminate unnecessary duplicates of unprofitable paths. In experiments on SPEC95 benchmarks, path qualification identified 2--112 times more non-local constants (weighted dynamically) than the Wegman-Zadek conditional constant algorithm, which translated into 1--7% more dynamic instructions with constant results.
Expression of non-classical islet hormone-like peptides during the embryonic development of the pancreas (1998)

Understanding of islet embryogenesis may prove to be key in the design of future therapies for diabetes directed at re-initiating islet growth, with the goal to replace and/or replenish the impaired beta-cell mass in the disease. In this context, studies of islet neurohormonal peptides, known to play a role in the local regulation of islet function, and their expression during islet embryogenesis are important. Here we review our studies on the embryonic islet expression of islet amyloid polypeptide (IAPP) and the PP-fold peptides pancreatic polypeptide (PP), peptide YY (PYY) and neuropeptide Y (NPY). IAPP, which is constitutively expressed in beta- and delta-cells in the adult rat, was found to occur in the assumed pluripotent islet progenitor cell, together with PYY, glucagon, and to a lesser extent with insulin. As development proceeds, the insulin/IAPP phenotype is segregated from that of PYY/glucagon; with the formation of islet-like structures, insulin/IAPP-expressing cells primarily occupy their central portions, while PYY/glucagon-expressing cells are found in their periphery. At the time of formation of islet-like structures, expression of NPY is induced in the insulin/IAPP-containing cells. Whereas NPY-expression ceases at birth, PYY is constitutively expressed in non-beta-cells in the mature rat. Expression of PP is induced just prior to birth in a separate population of islet cells, occasionally co-expressed with PYY. Although a clear role for these peptides during embryogenesis has not been identified, they conceivably could play a role in the control of insulin secretion, islet growth and islet blood flow.
Induction of apoptosis in HL60 leukemic cells by anticancer drugs in combination with anti-Fas monoclonal antibody. (1997)

Some anticancer drugs kill tumor cells through the mechanism of apoptosis. Fas antigen has been generally noticed as an apoptosis-signalling receptor molecule on the surface of different cells. Recently, it has become clear that some tumor cells express Fas antigen on their surface, and apoptosis is induced in those cells by IgM-anti-Fas monoclonal antibody (IgM-anti-Fas MoAb). If it is possible to induce apoptosis in tumor cells effectively by anticancer drugs in combination with IgM-anti-Fas MoAb, then we may be able to develop a new strategy for cancer chemotherapy. HL60 human leukemic cell line was incubated with anticancer drugs adriamycin (ADM) or cytosine arabinoside (Ara-C) at different doses alone and in combination with IgM-anti-Fas MoAb. We then observed the morphologic changes of tumor cells, the DNA fragmentation by agarose gel electrophoresis, and the changes in the amount of Fas antigen expression in their cell surface by using flow cytometry. In ADM- or Ara-C-treated tumor cells, apoptotic cells increased in number time- and dose-dependently. By the combination of ADM or Ara-C with IgM-anti-Fas MoAb, the induction of apoptosis in HL60 cells was enhanced significantly. The DNA electrophoresis supported those results. The amount of Fas antigen expression was slightly increased only in cells treated with a low dose of Ara-C, not in others. Our results suggest that apoptosis is a major process of leukemic cell death induced by anticancer drugs. Furthermore, it has become clear that the combination of anticancer drugs with IgM-anti-Fas MoAb enhances leukemic cell death through apoptosis in vitro, though the mechanism remains to be resolved.
Monocyte-chemotactic activity of defensins from human neutrophils. (1989)

We investigated the monocyte-chemotactic activity of fractionated extracts of human neutrophil granules. Monocyte-chemotactic activity was found predominantly in the defensin-containing fraction of the neutrophil granules. Purified preparations of each of the three human defensins (HNP-1, HNP-2, HNP-3) were then tested. HNP-1 demonstrated significant chemotactic activity for monocytes: Peak activity was seen at HNP-1 concentrations of 5 X 10(-9) M and was 49 +/- 20% (mean +/- SE, n = 9) of that elicited by 10(-8) M FMLP. HNP-2 (peak activity at 5 X 10(-9) M) was somewhat less active, yielding 19 +/- 10% (n = 11). HNP-3 failed to demonstrate chemotactic activity. Checkerboard analysis of monocyte response to HNP-1 and HNP-2 confirmed that their activity was chemotactic rather than chemokinetic. Neutrophils demonstrated a low level of response to defensins but this reaction was primarily chemokinetic. Defensins may play a role in the recruitment of monocytes by neutrophils into inflammatory sites.
Handbook of Plant Biotechnology (2004)

This important reference is the first work on Plant Biotechnology. Written by an international team of experienced researchers and professionals from both academia and industry, it will bring together the principles and practice of contemporary plant biotechnology to include: * the techniques of plant genetic modification - applications of plant biotechnology, crop improvement in agriculture and a production system for pharmaceutical proteins * ethics and safety issues - public perception, public relations, scale-up and testing, and legislation within the business of plant biotechnology.
Enclosed outdoor photobioreactors: Light regime, photosynthetic efficiency, scale‐up, and future prospects (2002)

Enclosed outdoor photobioreactors need to be developed and designed for large-scale production of phototrophic microorganisms. Both light regime and photosynthetic efficiency were analyzed in characteristic examples of state-of-the-art pilot-scale photobioreactors. In this study it is shown that productivity of photobioreactors is determined by the light regime inside the bioreactors. In addition to light regime, oxygen accumulation and shear stress limit productivity in certain designs. In short light-path systems, high efficiencies, 10% to 20% based on photosynthetic active radiation (PAR 400 to 700 nm), can be reached at high biomass concentrations (>5 kg [dry weight] m(-3)). It is demonstrated, however, that these and other photobioreactor designs are poorly scalable (maximal unit size 0.1 to 10 m(3)), and/or not applicable for cultivation of monocultures. This is why a new photobioreactor design is proposed in which light capture is physically separated from photoautotrophic cultivation. This system can possibly be scaled to larger unit sizes, 10 to >100 m(3), and the reactor liquid as a whole is mixed and aerated. It is deduced that high photosynthetic efficiencies, 15% on a PAR-basis, can be achieved. Future designs from optical engineers should be used to collect, concentrate, and transport sunlight, followed by redistribution in a large-scale photobioreactor.
Murine monoclonal antibodies against carcinoembryonic antigen: immunological, pharmacokinetic, and targeting properties in humans. (1990)

We have examined three 131I-labeled murine monoclonal antibodies (MAbs) against carcinoembryonic antigen (CEA), NP-2, NP-3, and NP-4, after i.v. injection in patients with diverse cancers. Although the MAbs had a similar tumor-targeting ability, several important features were discovered that have led us to the selection of one of these MAbs for further clinical evaluation. We found that it is important to evaluate MAbs with a high immunoreactivity. For example, the MAb NP-2 was used initially in patients with an immunoreactivity between 35 and 50%. Although the tumor-imaging properties of this MAb compared favorably with the affinity-purified, goat anti-CEA antibody that we used previously, further purification of NP-2 to an immunoreactivity greater than 70% uncovered a previously unknown cross-reactivity with human granulocytes. It was also discovered that the MAbs differed in their ability to complex with CEA in the blood. Plasma samples were analyzed by gel filtration at 1 or 24 h after injection. The formation of complexes with circulating CEA was dependent on the CEA:MAb ratio in the blood. NP-3 complexed to a greater degree with CEA than NP-4, but NP-2 did not complex with CEA even at CEA:NP-2 ratios of 55 to 1. NP-3 commonly showed enhanced uptake in the colon by external scintigraphy, and examination of the radioactivity in the stool showed that most of the radioactivity was associated with whole IgG and large-sized fragments of NP-3. We also compared the rate of elimination of radioactivity from the blood for all of the MAbs and compared the clearance of NP-3 to NP-4 at three different ranges of MAb protein doses (less than 1.0 mg, 1 to 5 mg, and 5 to 20 mg). The blood clearance rate for NP-3 was fastest among the other MAbs at protein doses exceeding 1.0 mg. Patients given less than 1.0 mg of NP-4 had a significantly (P less than 0.005) shorter elimination half-life than patients given more than 1.0 mg of NP-4. By virtue of NP-4's good targeting properties in patients and its limited complexation with circulating CEA, it was selected as the MAb of choice for CEA tumor imaging.
Silencing of the Novel p53 Target Gene Snk/Plk2 Leads to Mitotic Catastrophe in Paclitaxel (Taxol)-Exposed Cells (2003)

Loss of p53 sensitizes to antimicrotubule agents in human tumor cells, but little is known about its role during mitosis. We have identified the Polo-like kinase family member serum inducible kinase (Snk/Plk2) as a novel p53 target gene. Snk/Plk2 mutagenesis demonstrated that its kinase activity is negatively regulated by its C terminus. Small interfering RNA (siRNA)-mediated Snk/Plk2 silencing in the presence of the mitotic poisons paclitaxel (Taxol) or nocodazole significantly increased apoptosis, similar to p53 mutations, which confer paclitaxel sensitivity. Furthermore, we have demonstrated that the apoptosis due to silencing of Snk/Plk2 in the face of spindle damage occurs in mitotic cells and not in cells that have progressed to a G(1)-like state without dividing. Since siRNA directed against Snk/Plk2 promoted death of paclitaxel-treated cells in mitosis, we envision a mitotic checkpoint wherein p53-dependent activation of Snk/Plk2 prevents mitotic catastrophe following spindle damage. Finally, these studies suggest that disruption of Snk/Plk2 may be of therapeutic value in sensitizing paclitaxel-resistant tumors.
One-step selective hydroxylation of benzene to phenol with hydrogen peroxide catalysed by copper complexes incorporated into mesoporous silica–alumina (2016)

Benzene was hydroxylated with hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>) in the presence of catalytic amounts of copper complexes in acetone to yield phenol at 298 K. At higher temperature, phenol was further hydroxylated with H<sub>2</sub>O<sub>2</sub> by catalysis of copper complexes to yield <i>p</i>-benzoquinone. The kinetic study revealed that the rate was proportional to concentrations of benzene and H<sub>2</sub>O<sub>2</sub>, but to the square root of concentration of a copper(II) complex ([Cu(tmpa)]<sup>2+</sup>: tmpa = tris(2-pyridylmethyl)amine). The addition of a spin trapping reagent resulted in formation of a spin adduct of hydroperoxyl radical (HO<sub>2</sub><sup>•</sup>), as observed by EPR spectroscopy, inhibiting phenol formation. HO<sub>2</sub><sup>•</sup> produced by the reaction of [Cu(tmpa)]<sup>2+</sup> with H<sub>2</sub>O<sub>2</sub> acts as a chain carrier for the radical chain reactions for formation of phenol. When [Cu(tmpa)]<sup>2+</sup> was incorporated into mesoporous silica-alumina (Al-MCM-41) by a cation exchange reaction, the selectivity to production of phenol was much enhanced by prevention of hydroxylation of phenol, which was not adsorbed to Al-MCM-41. The high durability with turnover number of 4320 for the hydroxylation of benzene to phenol with H<sub>2</sub>O<sub>2</sub> was achieved using [Cu(tmpa)]<sup>2+</sup> incorporated into Al-MCM-41 as an efficient and selective catalyst.
A two-ball mouse affords three degrees of freedom (1997)

We describe a prototype two-ball mouse containing the electronics and mechanics of two mice in a single chassis. Unlike a conventional mouse, which senses x-axis and y-axis displacement only, our mouse also senses z-axis angular motion. This is accomplished through simple calculations on the two sets of x-y displacement data. Our mouse looks and feels like a standard mouse, however certain primitive operations are performed with much greater ease. The rotate tool -- common in most drawing programs -- becomes redundant as objects are easily moved with three degrees of freedom. Mechanisms to engage the added degree of freedom and different interaction techniques are discussed.
TT virus. A review of the literature. (2002)

In 1997, a new DNA virus was cloned by a Japanese team and designated TT virus (TTV). This virus seemed to be associated with non-A, non-G post-transfusion hepatitis. It was isolated by polymerase chain reaction (PCR) and was presumed to be human Circoviridae. The virus is heterogenous; 16 different genotypes are currently registered, and it can be classified as a "swarm" of at least 5 different viruses. Depending on the PCR technique used, the prevalence of infection ranges from 1.9 to 36% among blood donors, from 11.5 to 71% in hemodialysis patients, from 47 to 82% among patients with non-A, non-B or non-C fulminant hepatic failure, and the most elevated percentage is found in hemophiliacs. Epidemiological studies have established that the routes of TTV infection might be parenteral, oral-fecal, and possibly salivary. Mother-to-infant transmission is controversial. TTV may play a role in the pathogenesis of non-A, non-B or non-C fulminant hepatic failure. Patients co-infected with hepatitis C virus (HCV) and TTV have a significantly higher histological grade score than patients with isolated HCV infection. Treatment with interferon seems to decrease TT viremia, according to results obtained outside the context of clinical trials. TTV seems to be a light pathogenic virus. Its widespread presence in the blood of infected subjects contrasts with the apparent absence of pathological symptoms. PCR standardization is needed to clearly establish its real prevalence worldwide.
Reverse Transcription-Competitive Multiplex PCR Improves Quantification of mRNA in Clinical Samples—Application to the Low Abundance CFTR mRNA (1999)

This method is precise and reproducible and advantageous for use with limited amounts of tissue, such as from biopsies or from nasal or bronchial brushings.
Different miRNA expression profiles between human breast cancer tumors and serum (2014)

A bunch of microRNAs (miRNAs) have been demonstrated to be aberrantly expressed in cancer tumor tissue and serum. The miRNA signatures identified from the serum samples could serve as potential noninvasive diagnostic markers for breast cancer. The role of the miRNAs in cancerigenesis is unclear. In this study, we generated the expression profiles of miRNAs from the paired breast cancer tumors, normal, tissue, and serum samples from eight patients using small RNA-sequencing. Serum samples from eight healthy individuals were used as normal controls. We identified total 174 significantly differentially expressed miRNAs between tumors and the normal tissues, and 109 miRNAs between serum from patients and serum from healthy individuals. There are only 10 common miRNAs. This suggests that only a small portion of tumor miRNAs are released into serum selectively. Interestingly, the expression change pattern of 28 miRNAs is opposite between breast cancer tumors and serum. Functional analysis shows that the differentially expressed miRNAs and their target genes form a complex interaction network affecting many biological processes and involving in many types of cancer such as prostate cancer, basal cell carcinoma, acute myeloid leukemia, and more.
Simple and rapid process for single cell micro-patterning (2009)

We present a simple and environmentally friendly process for cell patterning on glass covered with an ultrathin layer of poly-l-lysine-grafted-polyethylene glycol (PLL-g-PEG) by exposure to deep UV light. The patterned substrates are stable for months in the lab atmosphere before incubation with proteins. Incubation with proteins resulted in well defined patterns, with high feature resolution. RPE-1 cells seeded on fibronectin/fibrinogen-Alexa 488 patterns were constrained for days on the deep UV exposed regions. Finally, large glass plates were patterned with high homogeneity enabling the assembly of micro-patterned microplates in 96-well format.
PAMELA - a model for an FFAG based hadron therapy machine (2007)

Approximately one third of the world's 15000 accelerators are used for tumour therapy and other medical applications [1]. The characteristics of FFAGs make them ideally suited to such applications, as the much smaller magnet size and greater compactness offers considerable cost and operational benefits. In the first stage the work on PAMELA will focus on the optimization of the FFAG design to deliver the specific machine parameters demanded by therapy applications. In this phase of the PAMELA project the effort will concentrate on the design of a semi-scaling type FFAGs to deliver a 450 MeV/u carbon ion beam, including detailed lattice and tracking studies. The second stage will use the existing expertise in the BASROC consortium [2] to undertake a design of the magnets and RF system for PAMELA. An outline of the overall concept of PAMELA will be discussed and the actual status of the work will be presented.
Targeting CD39 in Cancer Reveals an Extracellular ATP- and Inflammasome-Driven Tumor Immunity (2019)

We explored the mechanism of action of CD39 antibodies that inhibit ectoenzyme CD39 conversion of extracellular ATP (eATP) to AMP and thus potentially augment eATP-P2-mediated proinflammatory responses. Using syngeneic and humanized tumor models, we contrast the potency and mechanism of anti-CD39 mAbs with other agents targeting the adenosinergic pathway. We demonstrate the critical importance of an eATP-P2X7-ASC-NALP3-inflammasome-IL18 pathway in the antitumor activity mediated by CD39 enzyme blockade, rather than simply reducing adenosine as mechanism of action. Efficacy of anti-CD39 activity was underpinned by CD39 and P2X7 coexpression on intratumor myeloid subsets, an early signature of macrophage depletion, and active IL18 release that facilitated the significant expansion of intratumor effector T cells. More importantly, anti-CD39 facilitated infiltration into T cell-poor tumors and rescued anti-PD-1 resistance. Anti-human CD39 enhanced human T-cell proliferation and Th1 cytokine production and suppressed human B-cell lymphoma in the context of autologous Epstein-Barr virus-specific T-cell transfer. SIGNIFICANCE: Overall, these data describe a potent and novel mechanism of action of antibodies that block mouse or human CD39, triggering an eATP-P2X7-inflammasome-IL18 axis that reduces intratumor macrophage number, enhances intratumor T-cell effector function, overcomes anti-PD-1 resistance, and potentially enhances the efficacy of adoptive T-cell transfer.<i>This article is highlighted in the In This Issue feature, p. 1631</i>.