gebhart/patrepeval huggingface dataset:
Modeling approach for full-system design and rapid hardware prototyping of microelectromechanical systems (2010)

We present a modeling approach for the efficient full system design of MEMS. Our methodology is based on a hierarchical approach, which allows the derivation of predictive system-level models. This procedure starts with high-fidelity continuous-field simulations to determine all model parameters and their dependencies on external impacts followed by a proper experimental calibration of the models in order to adjust the deviations caused by manufacturing-induced fluctuations. In a second step, the physically-based high-level transducer model is connected to a FPGA board, on which the corresponding control algorithms are implemented. The advantage of these hardware/software co-simulations compared to "pure" simulations is a more realistic estimation of the overall performance of the control circuitry and its interplay with the transducer, even before it is realized in hardware. This allows for modifications and optimization of both, the control circuit and the transducer design, in a very early stage of the design process.
The role of TNF-alpha in T-cell-mediated inflammation depends on the Th1/Th2 cytokine balance. (1994)

The role of tumour necrosis factor-alpha (TNF-alpha) in tuberculosis is paradoxical because although there is much evidence for a protective role, there is also evidence that it plays a part in the tissue damage that characterizes human disease. We have shown previously that TNF-alpha frequently induces necrosis when injected into sites undergoing delayed-type hypersensitivity (DTH) responses to mycobacterial antigen. This is dependent on CD4(+) T cells. However the presence of this sensitivity to TNF-alpha-induced necrosis depended on the immunization protocol. We have tested the hypothesis that sensitivity to TNF-alpha depends on the cytokine profile of the induced T-cell response. All subcutaneous doses of mycobacterial immunogen used (10(7) to 10(9) organisms) primed spleen cells so that they secreted interferon-gamma (IFN-gamma) and interleukin-2 (IL-2) when cultured in vitro with soluble antigen. However priming for production of IL-4 was dose dependent as in other systems, and was produced at all times from 7 to 30 days after immunization with 10(9) organisms. Time-course studies over 30 days showed that sensitivity to TNF-alpha was found in DTH sites of animals primed for IL-4 and IFN-gamma production, but not in animals primed only for the Th1 cytokines, We suggest therefore that the paradoxical role of TNF-alpha can be resolved. In 'pure' Th1 responses it may act as an additional macrophage-activating factor. In mixed Th1 + Th2 or Th0 responses it may cause tissue damage. This mixed pattern is characteristic of tuberculosis, and of the late stage of many chronic infections where elimination of the infecting organism is failing, and chronic tissue damage is seen.
Real Time In Vivo Quantitation of Tumor Angiogenesis (2003)

Animal models are crucial to further our understanding of tumor biology. For many years, observation chambers, implanted in various animal species, have been used for intravital microscopy of tumor microcirculation. As far back as 1943, Algire described the adaptation of the transparent chamber technique to the mouse (1). From the introduction of a subsequent paper by Algire et al. (2), the following paragraph is quoted: “Recently, in vivo techniques have been developed which make it possible to make microscopic observations of the development of the blood supply of tumor transplants in the mouse. It has also been possible to obtain a quantitative expression of the morphological changes as they occur over a prolonged periodï The results presented indicate (i) that the rapid growth of tumor transplants is dependent upon the development of a rich vascular supply, and (ii) that an outstanding characteristics of the tumor cell is its capacity to elicit continuously the growth of new capillaries.”
The duodenal microbiome is altered in small intestinal bacterial overgrowth (2020)

Small intestinal bacterial overgrowth (SIBO) is highly prevalent and is associated with numerous gastrointestinal disorders, but the microbes involved remain poorly defined. Moreover, existing studies of microbiome alterations in SIBO have utilized stool samples, which are not representative of the entire gastrointestinal tract. Therefore, we aimed to determine and compare the duodenal microbiome composition in SIBO and non-SIBO subjects, using duodenal aspirates from subjects undergoing standard-of-care esophagogastroduodenoscopy without colon preparation. Using the recently-redefined cutoff for SIBO of >103 colony forming units per milliliter (CFU/mL), 42 SIBO and 98 non-SIBO subjects were identified. Duodenal samples from SIBO subjects had 4x103-fold higher counts than non-SIBO subjects when plated on MacConkey agar (P<0.0001), and 3.8-fold higher counts when plated on blood agar (P<0.0001). Twenty subjects had also undergone lactulose hydrogen breath tests (LHBTs), of whom 7/20 had SIBO. At the 90-minute timepoint, 4/7 SIBO subjects had positive LHBTs (rise in hydrogen (H2) ≥ 20 ppm above baseline), as compared to 2/13 non-SIBO subjects. 16S ribosomal RNA (rRNA) sequencing revealed that SIBO subjects had 4.31-fold higher relative abundance of Proteobacteria (FDR P<0.0001) and 1.64-fold lower Firmicutes (P<0.0003) than non-SIBO subjects. This increased relative abundance of Proteobacteria correlated with decreased α-diversity in SIBO subjects (Spearman R = 0.4866, P<0.0001) Specific increases in class Gammaproteobacteria correlated with the area-under-the-curve for H2 for 0-90 mins during LHBT (R = 0.630, P = 0.002). Increases in Gammaproteobacteria resulted primarily from higher relative abundances of the family Enterobacteriaceae (FDR P<0.0001), which correlated with the symptom of bloating (Spearman R = 0.185, 2-tailed P = 0.028). Increases in family Aeromonadaceae correlated with urgency with bowel movement (Spearman R = 0.186, 2-tailed P = 0.028). These results validate the >103 CFU/mL cutoff for the definition of SIBO, and also reveal specific overgrowth of Proteobacteria in SIBO vs. non-SIBO subjects, coupled with an altered Proteobacterial profile that correlates with symptom severity. Future research may elucidate host-microbiome interactions underlying these symptoms in SIBO patients.
Cognitive Outcomes and Long-term Follow-up Results after Enhanced Chemotherapy Delivery for Primary Central Nervous System Lymphoma (2000)

BBBD-enhanced chemotherapy delivery, without subsequent radiotherapy, resulted in favorable survival and cognitive outcomes for patients with primary central nervous system lymphomas who had not previously undergone irradiation. A cooperative multicenter study of intravenous chemotherapy without radiotherapy versus BBBD-enhanced chemotherapy would address the feasibility and necessity of performing a Phase III study for these rare central nervous system malignancies.
Generalized Approach to SERS-Active Nanomaterials via Controlled Nanoparticle Linking, Polymer Encapsulation, and Small-Molecule Infusion (2009)

Over the past decade the emphasis on single-molecule sensitivity of surface-enhanced Raman spectroscopy (SERS) has brought to prominence the special role played by so-called SERS hot spots, oftentimes nanometer-scale junctions between nanoparticles (NPs). In this report, molecular linkers are used to mediate the assembly of NPs to dimers and small clusters. When the SERS enhancement is optimized, the aggregation process is quenched by polymer and protein stabilizers that subsequently act as encapsulants resulting in SERS substates with unprecedented enhancement uniformity, reproducibility, and stability. The polymer-stabilized NP junctions were then imprinted with a variety of small molecules that permeated the polymer coat and displaced the linker from the hot spot. The average SERS enhancement of these SERS “nanocapsules” was found to be at least 300× greater than for single NPs, while the Raman/Rayleigh scattering ratio was 104 higher for linked NPs versus nonoptimized aggregates. Single-particle statistics showed that almost every nanocapsule produced intense SERS, suggesting that they are NP dimers and small clusters with the probe molecule resident in a hot spot. Nanocapsules were functionalized and shown to compete successfully with fluorescence imaging in multiplexed identification of cancer cell epitopes at the single-cell and single-nanotag level.
Strain-specific diversity of mucus-binding proteins in the adhesion and aggregation properties of Lactobacillus reuteri (2010)

Mucus-binding proteins (MUBs) have been revealed as one of the effector molecules involved in mechanisms of the adherence of lactobacilli to the host; mub, or mub-like, genes are found in all of the six genomes of Lactobacillus reuteri that are available. We recently reported the crystal structure of a Mub repeat from L. reuteri ATCC 53608 (also designated strain 1063), revealing an unexpected recognition of immunoglobulins. In the current study, we explored the diversity of the ATCC 53608 mub gene, and MUB expression levels in a large collection of L. reuteri strains isolated from a range of vertebrate hosts. This analysis revealed that the MUB was only detectable on the cell surface of two highly related isolates when using antibodies that were raised against the protein. There was considerable variation in quantitative mucus adhesion in vitro among L. reuteri strains, and mucus binding showed excellent correlation with the presence of cell-surface ATCC 53608 MUB. ATCC 53608 MUB presence was further highly associated with the autoaggregation of L. reuteri strains in washed cell suspensions, suggesting a novel role of this surface protein in cell aggregation. We also characterized MUB expression in representative L. reuteri strains. This analysis revealed that one derivative of strain 1063 was a spontaneous mutant that expressed a C-terminally truncated version of MUB. This frameshift mutation was caused by the insertion of a duplicated 13 nt sequence at position 4867 nt in the mub gene, producing a truncated MUB also lacking the C-terminal LPxTG region, and thus unable to anchor to the cell wall. This mutant, designated 1063N (mub-4867(i)), displayed low mucus-binding and aggregation capacities, further providing evidence for the contribution of cell-wall-anchored MUB to such phenotypes. In conclusion, this study provided novel information on the functional attributes of MUB in L. reuteri, and further demonstrated that MUB and MUB-like proteins, although present in many L. reuteri isolates, show a high genetic heterogeneity among strains.
Evasion of Neutrophil Extracellular Traps by Respiratory Pathogens (2017)

The release of neutrophil extracellular traps (NETs) is a major immune mechanism intended to capture pathogens. These histone- and protease-coated DNA structures are released by neutrophils in response to a variety of stimuli, including respiratory pathogens, and have been identified in the airways of patients with respiratory infection, cystic fibrosis, acute lung injury, primary graft dysfunction, and chronic obstructive pulmonary disease. NET production has been demonstrated in the lungs of mice infected with Staphylococcus aureus, Klebsiella pneumoniae, and Aspergillus fumigatus. Since the discovery of NETs over a decade ago, evidence that "NET evasion" might act as an immune protection strategy among respiratory pathogens, including group A Streptococcus, Bordetella pertussis, and Haemophilus influenzae, has been growing, with the majority of these studies being published in the past 2 years. Evasion strategies fall into three main categories: inhibition of NET release by down-regulating host inflammatory responses; degradation of NETs using pathogen-derived DNases; and resistance to the microbicidal components of NETs, which involves a variety of mechanisms, including encapsulation. Hence, the evasion of NETs appears to be a widespread strategy to allow pathogen proliferation and dissemination, and is currently a topic of intense research interest. This article outlines the evidence supporting the three main strategies of NET evasion-inhibition, degradation, and resistance-with particular reference to common respiratory pathogens.
Efficient unstructured search implementation on current ion-trap quantum processors (2020)

So far, only the results on 3 qubit spaces (both on superconducting and ion-trap realisations of quantum processors) have beaten the classical unstructured search in the expected number of oracle calls using optimal protocols in both settings. We present experimental results on running unstructured search in spaces defined by 4, 5 and 6 qubits on ion-trapped quantum processor. Our best circuits obtained respectively 66\%, 26\% and 6\% average probability of measuring the marked element. In the case of 4 and 5 qubit spaces we obtained fewer expected number of oracle calls required to find a marked element than any classical approach. Viability of the theoretical result by Grover at these qubit counts is, to authors' knowledge demonstrated experimentally for the first time. Also at 6 qubits, a circuit using a single oracle call returned a measured probability of success exceeding any possible classical approach. These results were achieved using a variety of unstructured search algorithms in conjunction with recent developments in reducing the number of entangling gates. The latter are currently considered to be a dominating source of errors in quantum computations. Some of these improvements have been made possible by using mid-circuit measurements. To our knowledge the latter feature is currently available only on the H0 quantum processor we run on.
Transmission Time Offsets in RTP Streams (2009)

This document describes a method to inform Real-time Transport
Protocol (RTP) clients when RTP packets are transmitted at a time
other than their 'nominal' transmission time. It also provides a
mechanism to provide improved inter-arrival jitter reports from the
clients, that take into account the reported transmission times.
[STANDARDS-TRACK]
New <inline-formula><roman>Er</roman><sup><roman>3+</roman></sup></inline-formula>-doped phosphate glass for ion-exchanged waveguide amplifiers (1998)

A new Er 31 -doped phosphate glass exhibiting an excellent durability in both boiling water and NaNO3 molten salt is developed. The ion-exchange process of this glass is investigated by treating glass samples in a variety of salt baths with various exposure times. A planar waveguide with one mode at 1.54 mm and three modes at 632.8 nm is demonstrated. The spectral properties of Er 31 in this glass are charac- terized by measuring absorption and emission spectra and fluorescence lifetimes. The emission cross section of Er 31 in this glass is calculated to be 0.76310 20 cm 2 using McCumber theory. © 1998 Society of Photo-Optical Instrumentation Engineers. (S0091-3286(98)02012-1)
Fluorescence Properties of Reduced Flavins and Flavoproteins (1979)

Fluorescence lifetimes and polarized emission properties of reduced flavin were measured using several model compounds and flavoproteins. Depending on the conditions of solvent and temperature or reduction method the lifetimes vary between 1 and 15 ns. The longer lifetime values are found in several forms of reduced lactate oxidase, in which a good correlation exists between fluorescence intensity and lifetime. In practically all flavoproteins the fluorescence is heterogeneous. Several mechanisms are proposed to explain the observed heterogeneity in lifetimes. The reduced models in glycerol at subzero temperature exhibit high degrees of polarization of the fluorescence, whereas distinct depolarization is encountered in several reduced flavoproteins suggesting a certain mobility of the flavin chromophor.
Synthesis and α-glucosidase inhibitory activity evaluation of N-substituted aminomethyl-β-d-glucopyranosides (2013)

A series of N-substituted 1-aminomethyl-β-d-glucopyranoside derivatives was prepared. These novel synthetic compounds were assessed in vitro for inhibitory activity against yeast α-glucosidase and both rat intestinal α-glucosidases maltase and sucrase. Most of the compounds displayed α-glucosidase inhibitory activity, with IC50 values covering the wide range from 2.3μM to 2.0mM. Compounds 19a (IC50=2.3μM) and 19b (IC50=5.6μM) were identified as the most potent inhibitors for yeast α-glucosidase, while compounds 16 (IC50=7.7 and 15.6μM) and 19e (IC50=5.1 and 10.4μM) were the strongest inhibitors of rat intestinal maltase and sucrase. Analysis of the kinetics of enzyme inhibition indicated that 19e inhibited maltase and sucrase in a competitive manner. The results suggest that the aminomethyl-β-d-glucopyranoside moiety can mimic the substrates of α-glucosidase in the enzyme catalytic site, leading to competitive enzyme inhibition. Moreover, the nature of the N-substituent has considerable influence on inhibitory potency.
Crystallization of Cyclosporine in a Multistage Continuous MSMPR Crystallizer (2011)

Crystallization processes can be batch or continuous. Potential advantages such as operating at steady state, small equipment size (relative to batch), and ability to recycle are encouraging the pharmaceutical industry to investigate continuous processes. In this work, a continuous cooling crystallization process for the immunosuppressant drug cyclosporine was developed. A multistage mixed suspension mixed product removal (MSMPR) crystallizer was employed which allowed simple analysis of kinetic parameters employing the population balance. Experimentally, the continuous crystallization system was able to operate without any clogging issues for more than four residence times. The experimental yield and purity of the crystals was determined as 71% and 96%, respectively (without recycle) and 87% and 94%, respectively (with recycle). In a batch cooling crystallization experiment, carried out under conditions similar to those of the continuous experiment without recycle, the experimental yield and purity of the crystals were 74% and 95%, respectively. The equilibrium distribution coefficients of cyclosporine impurities were measured experimentally as a function of impurity % of the starting solution. The distribution coefficients increase with a decrease in the purity of the starting solution, indicating a decrease in purification. The MSMPR model was used to estimate the nucleation and crystal growth rate kinetic parameters for cyclosporine crystallization and to evaluate the effect of process conditions on the purity of the crystals and the process yield. Results showed that the temperature of the third stage has a large impact on the final purity of the crystals. As the temperature of the third stage increases, the purity of the crystals also increases while the yield of the process decreases. The effect of recycle ratio on both crystal purity and process yield was also evaluated. A 93% process yield was obtained with a recycle ratio of 0.9. The yield of the process can be significantly improved by increasing the recycle ratio while the crystal purity decreases.
A Cost-Effective Single-Stage Inverter With Maximum Power Point Tracking (2004)

Renewable energy, such as solar energy, is desirable for power generation due to their unlimited existence and environmental friendly nature. However, the high initial investment impedes its wide commercialization. This paper proposes a cost-effective single-stage inverter with maximum power point tracking (MPPT) in combination with one-cycle control (OCC) for photovoltaic power generation. This control scheme is based on the output current-adjusting feature of OCC. The output current of the inverter can be adjusted according to the voltage of the photovoltaic (PV) array so as to extract the maximum power from it. In the mean time, OCC guarantees that the output current is proportional and in phase with the grid voltage. All these are accomplished in one power stage and a simple control circuit. No detection and calculation of power are needed. Compared with previously proposed approaches, this method is much more efficient and cost-effective and yet exhibits excellent performance. The principle is explained qualitatively and extensive experiments have been carried out to verify the proposed method.
Demonstration of Planar Type-II Superlattice-Based Photodetectors Using Silicon Ion-Implantation (2020)

In this letter, we report the demonstration of a pBn planar mid-wavelength infrared photodetectors based on type-II InAs/InAs1−xSbx superlattices, using silicon ion-implantation to isolate the devices. At 77 K the photodetectors exhibited peak responsivity of 0.76 A/W at 3.8 µm, corresponding to a quantum efficiency, without anti-reflection coating, of 21.5% under an applied bias of +40 mV with a 100% cut-off wavelength of 4.6 µm. With a dark current density of 5.21 × 10−6 A/cm2, under +40 mV applied bias and at 77 K, the photodetector exhibited a specific detectivity of 4.95 × 1011 cm·Hz1/2/W.
Surface Plasmon Resonance-Laser Desorption/Ionization-Time-of-Flight Mass Spectrometry (1998)

The laser desorption/ionization (LDI) process is investigated under surface plasmon resonance (SPR) conditions using time-of-flight mass spectrometry (TOFMS). We demonstrate that LDI-TOFMS at the SPR angle requires a lower minimum laser fluence for the production of silver monomer and cluster cations from ablation of a thin silver film substrate. In the LDI of gramicidin S deposited on a thin silver film substrate, the largest intensity for the molecular cation peak occurs when the laser light is incident on the substrate at a specific SPR angle. These results fully confirm SPR enhancement of the LDI process. The capability to perform SPR-LDI on a larger molecular weight analyte (1141 amu for gramicidin S) represents a new milestone beyond the previous achievement with rhodamine B (479 amu). A better understanding of the SPR mechanism is gained with respect to the substrate metals (silver vs aluminum), desorption (microscopic vs mesoscopic), and ionization (chemical vs multiphoton). These findings may be useful in the future design of SPR-LDI techniques for better TOFMS analysis of higher mass biomolecules.
<i>Agrobacterium tumefaciens</i> -mediated transformation of an elite Australian barley cultivar with virus resistance and reporter genes (2001)

Efficient transformation of barley cv. Schooner was achieved using Agrobacterium delivery, hygromycin or bialaphos selection and embryogenic callus. Using this system, transgenic plants were generated that contained either the green fluorescent protein gene, or transgenes derived from barley yellow dwarf (BYDV) and cereal yellow dwarf (CYDV) viruses. Many of these plants contained 1–3 transgene copies that were inherited in a simple Mendelian manner. Some plants containing BYDV and/or CYDV derived transgenes showed reduced virus symptoms and rates of viral replication when challenged with the appropriate virus. The ability to transform Schooner is a significant advance for the Australian barley industry, as this elite malting variety is, and has for the last 15 years been, the most widely grown barley variety in eastern Australia.
A simple and bandwidth efficient staggered broadcasting protocol for hot videos in VoD service (2007)

In providing video-on-demand (VoD) service to a number of clients through networks, two major technical issues are focused on both to reduce the viewer’s waiting time maintaining a given bandwidth allocation and the client’s buffer requirements. In this paper, we propose a pagoda staggered broadcasting (PSB) method which has a simple structure and substantially improves VoD efficiency. The proposed method performs significantly better than the existing VoD methods in the viewer’s waiting time and the buffer requirement with simplicity. The numerical results demonstrate that the viewer’s waiting time of the PSB method is nearly equal to the existing pagoda broadcasting methods. However the complexity of this method decreases up to 60% if dividing coefficient h is 1 by adjusting the short front part of a video.