gebhart/patrepeval huggingface dataset:
Optimizing quantitative in vivo fluorescence imaging with near‐infrared quantum dots (2010)

Quantum dots (QDs) are fluorescent nanoparticles with broad excitation and narrow, wavelength-tunable emission spectra. They are used extensively for in vitro fluorescence imaging studies and more recently for in vivo small animal and pre-clinical studies. To date there has been little concern about the selection of QD size (and thus emission wavelength peak) and excitation wavelengths, as they have little relevance to the results of in vitro studies. In vivo imaging, however, poses additional constraints, such as the scattering and absorption by tissue, which may influence the signal intensity at the body surface. Here, we demonstrate that longer-wavelength excitation and emission yield less quantization error in measured relative fluorescence intensity, using three near-infrared QDs (QD655, QD705 and QD800) applied to in vivo lymphatic imaging, and a range of excitation wavelengths from the blue to the red. Statistically significant differences in quantization error were observed between nearly all pairs of excitation wavelengths (445-490, 503-555, 575-605, 615-665 and 671-705 nm). Similarly, quantization error decreased with longer emission wavelengths (655, 705 and 800 nm). Light absorbance and scattering were demonstrated to be more potent factors than absorbance efficiency of QDs in producing quantization error in the measured fluorescence intensity. As a result, while wavelengths can be adjusted for qualitative experiments, the longest possible wavelengths should be used if quantification is desired during QD imaging experiments.
Unusual molecular-dynamical method for vector-wave analysis of optical waveguides (1997)

We propose an efficient numerical method, based on the unusual molecular-dynamical algorithm, for the mode analysis in optical waveguides. This method can properly take into account the vector nature of light waves. The vector-wave analysis is treated as the eigenvalue problem of large-scale nonsymmetric matrices with real eigenvalues. The efficiency of the method is demonstrated by calculating dispersion relations of a rectangular dielectric waveguide and supermodes in a nonsymmetric rib waveguide directional coupler. The advantages lie in its being easily vectorized and parallelized for implementation on array-processing modern supercomputers.
Frequency agile optical parametric oscillator (2023)

The frequency agile OPO device converts a fixed wavelength pump laser beam to arbitrary wavelengths within a specified range with pulse to pulse agility, at a rate limited only by the repetition rate of the pump laser. Uses of this invention include Laser radar, LIDAR, active remote sensing of effluents/pollutants, environmental monitoring, antisensor lasers, and spectroscopy.
A Cooperative Human-Adaptive Traffic Simulation (CHATS) (1999)

NASA is considering the development of a Cooperative Human-Adaptive Traffic Simulation (CHATS), to examine and evaluate performance of the National Airspace System (NAS) as the aviation community moves toward free flight. CHATS will be specifically oriented toward simulating strategic decision-making by airspace users and by the service provider s traffic management personnel, within the context of different airspace and rules assumptions. It will use human teams to represent these interests and make decisions, and will rely on computer modeling and simulation to calculate the impacts of these decisions. The simulation objectives will be to examine: 1. evolution of airspace users and the service provider s strategies, through adaptation to new operational environments; 2. air carriers competitive and cooperative behavior; 3. expected benefits to airspace users and the service provider as compared to the current NAS; 4. operational limitations of free flight concepts due to congestion and safety concerns. This paper describes an operational concept for CHATS, and presents a high-level functional design which would utilize a combination of existing and new models and simulation capabilities.
NOx REDUCTION FROM A 44 MW WALL-FIRED BOILER UTILIZING OXYGEN ENHANCED COMBUSTION (2015)

Praxair has developed a novel method of using oxygen to bring about additional NOx reduction from low NOx combustion systems burning pulverized coal or other nitrogen containing fuels. This paper presents results of field tests in a commercial wall-fired boiler burning pulverized bituminous coal. In pilot- and full-scale burner testing NOx emissions were reduced by as much as 60%, to below 0.15 lb/MMBtu, when a small portion of low-NOx burner combustion air was replaced with locally injected oxygen. Oxygen injection allowed burner operation at lowered stoichiometric ratio, and raised the temperature of the primary combustion zone to favor NOx reduction kinetics. Oxygen addition also reduced carbon in ash. These promising results led to beta testing in a commercial 44 MW wall-fired boiler beginning fourth quarter of 2002. Testing as part of the demonstration project showed greater than 40 % reduction in NOx emissions, reduction in LOI, enhanced flame stability, and unanticipated opacity reductions.
Reconsidering Single Disk Failure Recovery for Erasure Coded Storage Systems: Optimizing Load Balancing in Stack-Level (2015)

The fast growing of data scale encourages the wide employment of data disks with large storage capacity. However, a mass of data disks' equipment will in turn increase the probability of data loss or damage, because of the appearance of various kinds of disk failures. To ensure the intactness of the hosted data, modern storage systems usually adopt erasure codes, which can recover the lost data by pre-storing a small amount of redundant information. As the most common case among all the recovery mechanisms, the single disk failure recovery has been receiving intensive attentions for the past few years. However, most of existing works still take the stripe-level recovery as their only consideration, and a considerable performance improvement on single failure disk reconstruction in the stack-level (i.e., a group of rotated stripes) is missed. To seize this potential improvement, in this paper we systematically study the problem of single failure recovery in the stack-level. We first propose two recovery mechanism based on greedy algorithm to seek for the near-optimal solution (BP-Scheme and STP-Scheme) for any erasure array code in stack level, and further design a rotated recovery algorithm (RR-Algorithm) to eliminate the size of required memory. Through a rigorous statistic analysis and intensive evaluation on a real system, the results show that BP-Scheme gains 3.4 to 38.9 percent (the average is 21.2 percent) higher recovery speed than Khan's Scheme and 3.4 to 34.8 percent (the average is 19.1 percent) higher recovery speed than Luo's U-Scheme, while STP-Scheme owns 3.4 to 46.9 percent (the average is 25.15 percent) and 3.4 to 41.1 percent (the average is 22.3 percent) higher recovery speed than Khan's Scheme and Luo's U-Scheme, respectively.
Joint Topology Learning and Graph Signal Recovery Using Variational Bayes in Non-Gaussian Noise (2021)

This brief proposes a joint graph signal recovery and topology learning algorithm using a Variational Bayes (VB) framework in the case of non-Gaussian measurement noise. It is assumed that the graph signal is Gaussian Markov Random Field (GMRF) and the graph weights are considered statistical with the Gaussian prior. Moreover, the non-Gaussian noise is modeled using two distributions: Mixture of Gaussian (MoG), and Laplace. All the unknowns of the problem which are graph signal, Laplacian matrix, and the (Hyper)parameters are estimated by a VB framework. All the posteriors are calculated in closed forms and the iterative VB algorithm is devised to solve the problem. The efficiency of the proposed algorithm in comparison to some state-of-the-art algorithms in the literature is shown in the simulation results.
Requirement for Phosphatidylinositol 3′-Kinase Activity in Platelet-derived Growth Factor-stimulated Tyrosine Phosphorylation of p125 Focal Adhesion Kinase and Paxillin (1996)

The role of phosphatidylinositol 3'-kinase (PI 3'-kinase) activity in platelet-derived growth factor (PDGF)-stimulated tyrosine phosphorylation of focal adhesion kinase (p125FAK) and paxillin has been examined. The tyrosine phosphorylation of p125FAK and paxillin in response to PDGF was markedly inhibited by wortmannin in a dose-dependent manner. PDGF-stimulated PI 3'-kinase activity, membrane ruffle formation, and tyrosine phosphorylation of p125FAK and paxillin were all inhibited by the same low concentrations of wortmannin (>90% inhibition at 40nM). In contrast, tyrosine phosphorylation of p125FAK and paxillin in response to bombesin, endothelin, and phorbol 12,13-dibutyrate was not inhibited by wortmannin in these cells. Furthermore, LY294002, an inhibitor of PI 3'-kinase structurally unrelated to wortmannin, also inhibited PDGF-stimulated p125FAK tyrosine phosphorylation. PDGF was shown to stimulate the tyrosine phosphorylation of p125FAK in porcine aortic endothelial (PAE) cells transfected with the wild type PDGF-beta receptors, but not in PAE cells transfected with PDGF-beta receptors in which the PI 3'-kinase binding sites (Tyr-740/751) were replaced by phenylalanine. PDGF-stimulated, PI 3'-kinase-dependent tyrosine phosphorylation of p125FAK was not inhibited by rapamycin, and thus it was dissociated from the activation of p70 S6 kinase, previously identified as a molecular downstream target of PI 3'-kinase. Thus, we have identified a PI 3'-kinase-dependent signal transduction pathway in the action of PDGF, which leads to the phosphorylation of p125FAK and paxillin.
Homeobox gene expression in acute myeloid leukemia is linked to typical underlying molecular aberrations (2014)

Our results demonstrate that specific molecular genetic aberrations, rather than differentiation per se, underlie the observed differences in HOX gene expression in AML. Moreover, the observed correlations between epigenetic modifiers and HOX expression that are specific to malignant hematopoiesis, suggest their potential causal relationships.
Effects of genetic selection and voluntary activity on the medial gastrocnemius muscle in house mice (1999)

In a previous study, we found that in house mice both genetic selection (10 generations of artificial selection for high voluntary activity on running wheels) and access to running wheels (7-8 weeks) elicited a modest increase in maximal oxygen consumption. Based on these results, we hypothesized that genetic selection would affect the changes in endurance and oxidative capacity of the medial gastrocnemius (MG) muscle induced by wheel access (training response). Wheel access increased the isotonic endurance of the MG in both genetically selected and random-bred (control) mice. However, this exercise-induced improvement in isotonic endurance of the MG was similar between genetically selected and control mice. Wheel access also increased the succinate dehydrogenase activity of MG muscle fibers in both selected and control lines. However, this exercise-induced increase in succinate dehydrogenase activity was comparable between genetically selected and control animals. Taken together, these results indicate that the modest increase in maximal oxygen consumption associated with genetic selection is not reflected by the training-induced changes in oxidative capacity and endurance of MG muscle fibers.
Nanostructured polyelectrolytes for ion-selective membranes (2023)

Nanostructured polyelectrolyte bilayers deposited by Layer-by-Layer deposition on nanoporous membranes can be selectively crosslinked to modify the polyelectrolyte charge density and control ionic selectivity independent of ionic conductivity. For example, the polyelectrolyte bilayer can comprise a cationic polymer layer, such as poly(ethyleneimine), and an anionic polymer layer, such as poly(acrylic acid). Increasing the number of bilayers increases the cation selectivity when the poly(ethyleneimine) layer is crosslinked with glutaraldehyde. Crosslinking the membranes also increases the chemical and mechanical strength of the polyelectrolyte films. This controllable and inexpensive method can be used to create ion-selective and mechanically robust membranes on porous supports for a wide range of applications.
Effect of Subculture and Elicitation on Instability of Taxol Production in Taxus sp. Suspension Cultures (2004)

The production of secondary metabolites through plant cell suspension cultures is challenging because the level and pattern of production is often unstable and unpredictable. To investigate the factors affecting instability of secondary metabolite production, high Taxol (paclitaxel)-producing Taxus cultures induced by methyl jasmonate elicitation and their low Taxol-producing counterparts were compared with respect to growth and Taxol production kinetics. With Taxus subcultures we observe alternating states of high and low productivity. Parental cultures and their subcultures from five different cell lines were used to test whether a high-producing culture grows more slowly or dies more rapidly than a low-producing one. These cell lines were of three types: (1) Taxol-producing with and without methyl jasmonate, (2) Taxol-producing only upon elicitation, and (3) nonproducing. High-producing cultures show growth inhibition upon subculture, whereas nonproducing elicited cultures show little growth inhibition. Thus, growth inhibition is primarily due to Taxol or taxane accumulation and not a direct result of methyl jasmonate treatment. Through media exchange between high- and low-producing cultures, it appears that culture components generated by cells alter culture properties. To assess variability as a function of culture lineage, two groups of replicate cultures were generated either with a mixing of the parental flasks or segregation of parental flasks at each subculture. Although parental culture mixing did not reduce flask-to-flask variation, the production level of Taxol in subcultures resulting from mixing inocula was sustained at a higher level relative to segregated subcultures. The results are consistent with the possibility of cell signaling within the population that can induce Taxol production.
A Low-Cost and Highly Integrated Fiber Optical Pressure Sensor System (2007)

This paper presents a simple fiber-optic based pressure measurement system, in which both sensor and readout parts are constructed using batch micromachining techniques, supplemented with some straightforward assembly steps. Prototypes of relative and absolute pressure sensors parts and a readout part have been realized. Goal of this research is to enable deployment of such harsh environment sensors in high-volume, low-cost applications.
Human embryos commonly form abnormal nuclei during development: a mechanism of DNA damage, embryonic aneuploidy, and developmental arrest (2015)

The study was supported by Columbia University and the New York Stem Cell Foundation. Authors declare no competing interest.
Optimal control of population transfer in an optically dense medium (1996)

We apply the optimal control technique (OCT) to design an optical pulse pair that controls the population transfer in a medium of three-level atoms. The absorption and reshaping of the controlling pulses by the medium are taken into account. The efficiency of the population transfer is improved significantly compared with designs that do not incorporate pulse absorption and reshaping.
miR145 Targets the SOX9/ADAM17 Axis to Inhibit Tumor-Initiating Cells and IL-6–Mediated Paracrine Effects in Head and Neck Cancer (2013)

ALDH1(+)CD44(+) cells are putative tumor-initiating cells (TIC) in head and neck squamous cell carcinomas (HNC). miR-145 regulates tumorigenicity in various cancers but the breadth of its mechanistic contributions and potential therapeutic applications are not completely known. Here, we report that ALDH1(+)CD44(+)-HNC cells express reduced levels of miR145. SPONGE-mediated inhibition of miR-145 (Spg-miR145) was sufficient to drive tumor-initiating characteristics in non-TICs/ALDH1(-)CD44-negative HNC cells. Mechanistic analyses identified SOX9 and ADAM17 as two novel miR145 targets relevant to this process. miR-145 expression repressed TICs in HNC in a manner associated with SOX9 interaction with the ADAM17 promoter, thereby activating ADAM17 expression. Notably, the SOX9/ADAM17 axis dominated the TIC-inducing activity of miR-145. Either miR-145 suppression or ADAM17 overexpression in non-TICs/ALDH1(-)CD44(-)-HNC cells increased expression and secretion of interleukin (IL)-6 and soluble-IL-6 receptor (sIL-6R). Conversely, conditioned medium from Spg-miR145-transfected non-TICs/ALDH1(-)CD44(-)-HNC cells was sufficient to confer tumor-initiating properties in non-TICs/ALDH1(-)CD44(-)-HNC and this effect could be abrogated by an IL-6-neutralizing antibody. We found that curcumin administration increased miR-145 promoter activity, thereby decreasing SOX9/ADAM17 expression and eliminating TICs in HNC cell populations. Delivery of lentivral-miR145 or orally administered curcumin blocked tumor progression in HNC-TICs in murine xenotransplant assays. Finally, immunohistochemical analyses of patient specimens confirmed that an miR-145(low)/SOX9(high)/ADAM17(high) phenotype correlated with poor survival. Collectively, our results show how miR-145 targets the SOX9/ADAM17 axis to regulate TIC properties in HNC, and how altering this pathway may partly explain the anticancer effects of curcumin. By inhibiting IL-6 and sIL-6R as downstream effector cytokines in this pathway, miR-145 seems to suppress a paracrine signaling pathway in the tumor microenvironment that is vital to maintain TICs in HNC.
Signal processing for wireless ad hoc communication networks [from the guest Editors (2006)

Presents the guest editorial for this issue of the publication.
Titanium Hydrazido and Imido Complexes:  Synthesis, Structure, Reactivity, and Relevance to Alkyne Hydroamination (2004)

Treatment of Ti(NMe(2))(2)(dpma) (1) with aniline results in the protonation of the dimethylamido ligands, which are retained as dimethylamines, and generation of a titanium imido complex Ti(NPh)(NHMe(2))(2)(dpma) (2) in 94% yield. The monomeric imido 2 is converted to the reactive dimeric micro-imido [Ti(NPh)(dpma)](2) (3) on removal of the labile dimethylamine donors. The dimer 3 is converted to monomeric terminal imido complexes in the presence of added donors, e.g., 4,4'-di-tert-butyl-2,2'-bipyridine (Bu(t)-bpy) and DME. Compounds 1-3 exhibit the same rate constant for 1-phenylpropyne hydroamination by aniline and are all kinetically competent to be involved in the catalytic cycle. Attempts to use 1 as a catalyst for hydroaminations involving 1,1-dimethylhydrazine resulted in only a few turnovers under the best conditions. Consequently, the chemistry of 1 with hydrazines to generate hydrazido complexes was scrutinized for comparison with the imido species. Through these studies, titanium hydrazido complexes including Ti(eta(2)-NHNC(5)H(10))(2)(dpma) (5), Ti(eta(2)-NHNMe(2))(2)(dpma) (6), and [Ti(micro:eta(1),eta(2)-NNMe(2))(dpma)](2) (7) were characterized. In addition, a terminal hydrazido(2-) complex was available by addition of Bu(t)-bpy to 1 prior to 1,1-dimethylhydrazine addition, which provided Ti(eta(1)-NNMe(2))(Bu(t)-bpy)(dpma) (8). Compound 8 was structurally characterized and compared to Ti(NPh)(Bu(t)-bpy)(dpma) (4b), an imido derivative with the same ancillary ligand set. Compound 8 has a nucleophilic beta-nitrogen consistent with a hydrazido(2-) formulation, as determined by reaction with MeI to form the ammonium imido complex [Ti(NNMe(3))(Bu(t)-bpy)(dpma)]I (9). Analogous pyridinium imido complexes [Ti(N-1-pyridinium)(Bu(t)-bpy)(dpma)](+) (10) are available by addition of 1-aminopyridinium iodide to 1. From the investigations, some conclusions regarding the activity of titanium pyrrolyl complexes in hydroamination were drawn. The lack of conversion of the bis[micro-hydrazido(2-)] 7 to monomeric species in the presence of donor ligands is put forth as one explanation for the poor hydrazine hydroamination activity of 1. This problem was combated in the synthesis of Ti(NMe(2))(2)(dap)(2), which is an active catalyst for hydrazine hydroamination of alkynes.
A Randomized Trial of Interferon alpha Therapy for HIV Type 1 Infection (2000)

The immunologic and virologic efficacy and safety of interferon a (IFN-alpha) administered in combination with zidovudine (ZDV) and zalcitabine (ddC) was evaluated in HIV-infected subjects with CD4+ cell counts between 300 and 500 cells/ml and no more than 14 weeks of prior antiretroviral therapy. A total of 256 subjects enrolled in an open-label, randomized controlled trial. Subjects were randomized equally into treatment groups. All subjects received ZDV and ddC, while half also receive IFN-alpha (3 MU subcutaneously every 24 hr). At 48 weeks the median average area under the curve minus baseline (AAUCMB) for plasma HIV-1 RNA for the two-drug group was -0.68 versus -0.75 log10 copies/ml for the IFN-alpha group (p = 0.046). Mean HIV-1 RNA changes from baseline to 48 weeks for these groups were -0.65 and -1.12 log10 copies/ml, respectively (p = 0.010). The median AAUCMB for CD4+ cell count for the two-drug group was 28 versus -1 cells/mm3 for the IFN-alpha group (p = 0.011). Neutropenia, anemia, and drug intolerance were more common in the IFN-alpha group. This study demonstrates that IFN-alpha inhibits HIV-1 replication but attenuates the CD4+ cell response to dual therapy with ZDV and ddC.
Partial Resistance of Bell Pepper to Cucumber Mosaic Virus Movement within Plants: Field Evaluation of its Efficiency in Southern France (1993)

Abstract The spread of cucumber mosaic virus (CMV) was followed during three years in field plots of bell pepper varieties Yolo Wonder (susceptible) and Milord and Vania (partially resistant to CMV movement within plants). During the three test years, CMV spread was delayed 4 to 6 weeks in var. Milord and in var. Vania as compared to var. Yolo Wonder. Final CMV incidence and the apparent infection rate, the latter calculated from Van der Plank logistic analyses, were lower in var. Milord and in var. Vania than in var. Yolo Wonder. The resistance of var. Milord and var. Vania, expressed as a delay of spread and a reduced CMV incidence over the past three years, provides practical disease control.
Hospital costs, length of stay and prevalence of hip and knee arthroplasty in patients with inflammatory bowel disease (2017)

Costs and mortality rates for hip and knee arthroplasties are the same in patients with IBD and the general population, while a statistical but non-relevant increase in LOS is seen for hip arthroplasties in patients with IBD. Compared to the general population, arthroplasties of the hip and knee are less prevalent in hospitalized patients with IBD.