gebhart/patrepeval huggingface dataset:
Towards SMIL as a foundation for multimodal, multimedia applications (2001)

Rich and interactive multimedia applications, where audio, video, graphics and text are precisely synchronized under timing constraints are becoming ubiquitous. Multimodal applications further extend the concept of user interaction combining different modalities, like speech recognition, speech synthesis and gestures. However, authoring dialog-capable multimodal, multimedia services is a very difficult task. Fortunately, the W3C has sponsored the development of SMIL, an elegant notation for multimedia applications, which has been embraced by both Microsoft and RealNetworks. In this paper, we argue that SMIL is an ideal substrate for extending multimedia applications with multimodal facilities. SMIL as it stands is not a general notation for controlling media and input mode resources. We show that all what is needed are few natural extensions to SMIL along with the addition of a simple reactive programming language that we call ReX. Our language is designed to be maximally compatible with existing W3C recommendations through a generic event system based on DOM and an expression language based on XPATH. It is also designed to be simple so that the fundamental notion of seeking time (e.g. going backwards and forwards in presentations) is preserved.
Neural network based integration of assays to assess pathogenic potential (2023)

Limited data significantly hinders our capability of biothreat assessment of novel bacterial strains. Integration of data from additional sources that can provide context about the strain can address this challenge. Datasets from different sources, however, are generated with a specific objective and which makes integration challenging. Here, we developed a deep learning-based approach called the neural network embedding model (NNEM) that integrates data from conventional assays designed to classify species with new assays that interrogate hallmarks of pathogenicity for biothreat assessment. We used a dataset of metabolic characteristics from a de-identified set of known bacterial strains that the Special Bacteriology Reference Laboratory (SBRL) of the Centers for Disease Control and Prevention (CDC) has curated for use in species identification. The NNEM transformed results from SBRL assays into vectors to supplement unrelated pathogenicity assays from de-identified microbes. The enrichment resulted in a significant improvement in accuracy of 9% for biothreat. Importantly, the dataset used in our analysis is large, but noisy. Therefore, the performance of our system is expected to improve as additional types of pathogenicity assays are developed and deployed. The proposed NNEM strategy thus provides a generalizable framework for enrichment of datasets with previously collected assays indicative of species.
A Gram-negative bacterium, identified asPseudomonas aeruginosaAL98, is a potent degrader of natural rubber and syntheticcis-1,4-polyisoprene (2000)

A Gram-negative bacterium, strain AL98, was isolated from foul water inside of a deteriorated car tire on a farmer's field in Münster, Germany. The strain was able to considerably disintegrate natural rubber (NR), either in the raw state as NR latex concentrate or in the vulcanized state as NR latex glove, as well as raw synthetic cis-1,4-polyisoprene (IR). Determination of carbon dioxide evolution and living cell number during batch cultivation with each of the materials as sole source of carbon, revealed mineralization of the rubber polymer during biomass increase. Surface investigation by scanning electron microscopy gave evidence for an adhesive growth behavior of the strain proceeding by colonizing the rubber surface, merging into the rubber and forming a biofilm prior to disintegration of the material. Schiff's reagent staining performed with NR latex gloves indicated production and accumulation of aldehyde groups during colonization. The solid glove substrate disappeared completely after a prolonged cultivation period as a result of continuous degradation. Taxonomic analyses of the strain, which were also based on similarity examination of the complete 16S rRNA gene, revealed classification of strain AL98 as a strain of Pseudomonas aeruginosa. This is the first report about the isolation of a Gram-negative bacterium exhibiting strong rubber decomposing properties.
Infrared Small Maritime Target Detection Based on Integrated Target Saliency Measure (2021)

Robust and effective detection of a small target in an infrared maritime image is a key technology of maritime target search and tracking applications. Infrared small target detection is a challenging task due to the factors such as dim small targets and various complex backgrounds caused by sun glitters and strong waves. In this article, the integrated target saliency measure (ITSM) based on local and nonlocal spatial information is proposed to improve target detection performance. We combine local heterogeneity property of targets and nonlocal self-correlation property of background with targets' sparsity to separate real targets from background clutters. First, local heterogeneity calculation based on cross-window standard deviation (CSD) is proposed to extract candidate targets preliminarily, which enhances the local intensity difference between small targets and neighboring background. Meanwhile, low-rank representation (LRR) is applied to background prediction and removal, which is followed by adaptive threshold segmentation to enhance target saliency. Finally, we integrate the results obtained from the two steps mentioned above to further enhance targets and suppress background clutters. Then, real targets are extracted by an iterative threshold on the integrated map so as to generate the seed map, in addition, the target expansion strategy is exploited to keep full target areas. Experimental results on six datasets show that the proposed method outperforms the state-of-the-art methods in terms of robustness and target detection accuracy.
Supplementary Figure 3 from VEGFA-VEGFR Pathway Blockade Inhibits Tumor-Induced Regulatory T-cell Proliferation in Colorectal Cancer (2023)

&lt;p&gt;PDF file - 1.3MB, SFigure 3 shows that anti-VEGFA or sunitinib treatments only modulate Treg and not other T cell subsets in spleens of tumor-bearing mice&lt;/p&gt;
Induction of Tubuloreticular Structures in Cultured Human Endothelial Cells by Recombinant Interferon Alfa and Beta (1992)

Tubuloreticular structures were induced in human umbilical vein endothelial cells cultured in media containing recombinant interferon alfa and beta but not in media containing recombinant interferon gamma or other agents that induce interferon, such as 5-bromodeoxyuridine or polyinosinicpolycytidylic acid. Recombinant interferon beta induced tubuloreticular structures in endothelial cells at a lower concentration and in a greater percentage of cell sections than recombinant interferon alfa. This report of tubuloreticular structures being induced in vitro in nonlymphoid cells provides evidence that interferon is the substance that causes the formation of tubuloreticular structures in endothelial cells in vivo.
Hamiltonian formulation for the diffusion equation (1997)

A Hamiltonian formulation is presented for the diffusion equation. Going beyond the conservation of property in diffusive transport, conservation is shown to apply in the sense of classical Hamiltonian dynamics, provided the equation is transformed with Hermitian wavelets. The characteristic equations, obtained previously for the wavelet-transformed diffusion equation, are the canonical equations corresponding to a time-independent Hamiltonian. The configuration variables are defined by the canonical structure and its invariants, while the momenta determine the evolution of the system. Irreversibility results from the finite-time escape of trajectories, initiating from the smallest scales and eroding increasingly larger scales. However, this scale-dependent erosion of initial conditions does not necessarily imply memory loss.
Selective Hydrogenation of 9-Aminoacridine over Supported Noble Metal Catalysts (1990)

Abstract The selective hydrogenation of 9-aminoacridine(1) into 1,2,3,4-tetrahydro-derivative(2) was searched using noble metal catalysts(Pd, Rh, Pt, and Ru) at around 80 °C and 60 °C atm of H2. The Pd/Al2O3 catalyst was found most selective to produce 2 in a higher yield of 60% at a conversion of 97%. The hydrogenation pathway of 1 is discussed in comparison with that of acridine.
Role of STAT5 and epigenetics in lactation-associated upregulation of multidrug transporter ABCG2 in the mammary gland (2014)

The multidrug resistance efflux transporter ATP-binding cassette subfamily G member 2 (ABCG2) is not only overexpressed in certain drug-resistant cancers but is also highly expressed in the mammary gland during lactation, carrying xenobiotics and nutrients into milk. We sought to investigate the molecular mechanisms involved in the upregulation of ABCG2 during lactation. Expression profiling of different mouse Abcg2 mRNA isoforms (E1a, E1b, and E1c) revealed that E1b is predominantly expressed and induced in the lactating mouse mammary gland. Despite this induction, analyses of CpG methylation status and published ChIP-seq datasets reveal that E1b promoter sequences in the virgin gland are already hypomethylated and marked with the open chromatin histone mark H3K4me2. Using a forced-weaning model to shut down lactation, we found that within 24 h there was a significant reduction in Abcg2 mRNA expression and a loss of signal transducer and activator of transcription-5 (STAT5) occupancy at the mouse Abcg2 gene. Luciferase reporter assays further showed that some of these STAT5-binding regions that contained interferon-γ-activated sequence (GAS) motifs function as an enhancer after prolactin treatment. We conclude that Abcg2 is already poised for expression in the virgin mammary gland and that STAT5 plays an important role in Abcg2 expression during lactation.
NK cell activation through the NKG2D ligand mult-1 is selectively prevented by the glycoprotein encoded by mouse cytomegalovirus gene M145 (2004)

The NK cell-activating receptor NKG2D interacts with three different cellular ligands, all of which are regulated by mouse cytomegalovirus (MCMV). We set out to define the viral gene product regulating murine UL16-binding protein-like transcript (MULT)-1, a newly described NKG2D ligand. We show that MCMV infection strongly induces MULT-1 gene expression, but surface expression of this glycoprotein is nevertheless completely abolished by the virus. Screening a panel of MCMV deletion mutants defined the gene m145 as the viral regulator of MULT-1. The MCMV m145-encoded glycoprotein turned out to be necessary and sufficient to regulate MULT-1 by preventing plasma membrane residence of MULT-1. The importance of MULT-1 in NK cell regulation in vivo was confirmed by the attenuating effect of the m145 deletion that was lifted after NK cell depletion. Our findings underline the significance of escaping MULT-1/NKG2D signaling for viral survival and maintenance.
Blow-up of solutions to a parabolic system with nonlocal source (2017)

This paper deals with a parabolic system with different diffusion coefficients and coupled nonlocal sources, subject to homogeneous Dirichlet boundary conditions. The conditions on global existence, simultaneous or non-simultaneous blow-up, blow-up set, uniform blow-up profiles and boundary layer are got using comparison principle and asymptotic analysis methods.
An Autophagy-Independent Role for ATG41 in Sulfur Metabolism During Zinc Deficiency (2018)

The Zap1 transcription factor of <i>Saccharomyces cerevisiae</i> is a key regulator in the genomic responses to zinc deficiency. Among the genes regulated by Zap1 during zinc deficiency is the autophagy-related gene <i>ATG41</i> Here, we report that Atg41 is required for growth in zinc-deficient conditions, but not when zinc is abundant or when other metals are limiting. Consistent with a role for Atg41 in macroautophagy, we show that nutritional zinc deficiency induces autophagy and that mutation of <i>ATG41</i> diminishes that response. Several experiments indicated that the importance of <i>ATG41</i> function to growth during zinc deficiency is not because of its role in macroautophagy, but rather is due to one or more autophagy-independent functions. For example, rapamycin treatment fully induced autophagy in zinc-deficient <i>atg41</i>Δ mutants but failed to improve growth. In addition, <i>atg41</i>Δ mutants showed a far more severe growth defect than any of several other autophagy mutants tested, and <i>atg41</i>Δ mutants showed increased Heat Shock Factor 1 activity, an indicator of protein homeostasis stress, while other autophagy mutants did not. An autophagy-independent function for <i>ATG41</i> in sulfur metabolism during zinc deficiency was suggested by analyzing the transcriptome of <i>atg41</i>Δ mutants during the transition from zinc-replete to -deficient conditions. Analysis of sulfur metabolites confirmed that Atg41 is needed for the normal accumulation of methionine, homocysteine, and cysteine in zinc-deficient cells. Therefore, we conclude that Atg41 plays roles in both macroautophagy and sulfur metabolism during zinc deficiency.
Response of mouse brain perfusion to hypo‐ and hyperventilation measured by arterial spin labeling (2011)

We aimed to setup a noninvasive and well-controlled methodology for evaluation of the cerebrovascular response in mice (C57BL/6J; 12 weeks). Therefore we applied a normo-, hypo-, and hyperventilation paradigm combined with arterial spin labeling and monitoring of the expired CO(2) (expCO(2)) (n=7) or arterial pCO(2) (apCO(2)) (n=12). Reducing the tidal volume by 25% and the respiratory rate by 20% resulted in hypercapnia (apCO(2) from 33 ± 6 mmHg to 64 ± 16 mmHg). Increasing the respiratory rate by 25% and the tidal volume by 20% decreased apCO(2) to 22 ± 5 mmHg. Cerebral blood flow (CBF) was 82 ± 21, 163 ± 41 and 64 ± 18 mL/100 g/min during normo, hypo-, and hyperventilation, respectively (midbrain). The correlation of apCO(2) and CBF levels resulted in a cerebrovascular response of 2.7 ± 0.3, 2.1 ± 0.3, 2.1 ± 0.3, and 3.7 ± 0.5 mL/100 g/min/mmHg for midbrain, cortex, hippocampus and thalamus, respectively. As expCO(2) levels were correlated with apCO(2) (r(2)=0.86; n=4) and CBF (r(2)=0.67) a cerebrovascular response based on simultaneously recorded CBF and expCO(2) levels could be derived (3.3 ± 0.5, 2.5 ± 0.4, 3.0 ± 0.4, and 4.5 ± 0.6 mL/100 g/min/mmHg; order as above). A cross-over experiment resulted in similar responses. In conclusion, this protocol allows evaluating basal CBF and cerebrovascular response in mice under well-controlled conditions by simply changing ventilator settings and correlating CBF with apCO(2) and/or simultaneously obtained expCO(2).
Atmospheric NO2:  In Situ Laser-Induced Fluorescence Detection at Parts per Trillion Mixing Ratios (1999)

We describe a time-gated laser-induced fluorescence instrument designed for accurate (+/- 5%, 1 sigma), continuous, autonomous, in situ observations of NO2 with the sensitivity (15 ppt/10 s at S/N = 2) and portability necessary to study NO2 anywhere in the troposphere. The technique is advantageous because it is spectroscopically specific and direct in that it does not require conversion of NO2 into another species (e.g., NO) prior to detection, eliminating a class of potential interferences. Performance of the instrument is illustrated with 15 weeks (July-Oct 1998) of observations at the University of California, Blodgett Forest field station located in the foothills of the Sierra Nevada and 4 weeks (June 15-July 15, 1999) in Nashville, TN during the Southern Oxidants Study. Ambient concentrations of NO2 at Blodgett Forest varied from below 50 ppt to 4000 ppt and NO2 ranged from 5 to 50% of the total reactive nitrogen; while in Nashville, TN, concentrations ranged from 1 to 75 ppb.
Responses to GABA, glycine and β-alanine induced in Xenopus oocytes by messenger RNA from chick and rat brain (1988)

Poly (A)+ messenger RNA (mRNA) was extracted from rat and chick brains, and injected into oocytes of Xenopus laevis. This led to the expression of receptors that evoked membrane currents in response to gamma-aminobutyric acid (GABA), glycine and beta-alanine. These currents all inverted at about the chloride equilibrium potential in the oocyte, and showed a marked rectification at negative potentials. Oocytes injected with mRNA from chick optic lobe gave large responses to GABA and beta-alanine, but small responses to glycine. In contrast, one fraction of mRNA from rat cerebral cortex (obtained by sucrose density gradient centrifugation) caused oocytes to develop sensitivity to GABA, glycine and beta-alanine, but very little to GABA. The pharmacological properties of the three amino acid responses also differed. Barbiturate and benzodiazepines potentiated the responses to GABA and beta-alanine, but not to glycine. Strychnine reduced the responses to glycine and beta-alanine, but not to GABA, whereas bicuculline reduced the responses to GABA and beta-alanine, but not to glycine. We conclude that different species of mRNA code for receptors to GABA and glycine, and possibly also for separate beta-alanine receptors.
Fibrinogen depletion after plasma-dilution: impairment of proteolytic resistance and reversal via clotting factor concentrates (2013)

In trauma patients, resuscitation treatment of intravascular volume may cause haemodilution including blood cell- and plasma-dilution. After plasma-dilution, fibrinogen is the first factor that decreases to critically low concentrations. Fibrin formed in lowered levels is susceptible to fibrinolysis, a natural forerunner for bleeding. To assess whether a fibrinogen concentrate or a factor XIII (FXIII) concentrate can reverse the impairment of fibrin properties after plasma dilution, different laboratory methods were used to determine thrombin generation and fibrin quantity/quality in a normal plasma sample diluted in vitro. Coagulation and clot lysis by plasmin were triggered with tissue factor and rt-PA, respectively.We found that while the endogenous thrombin potential (ETP) was unaffected after plasma-dilution due to postponement of thrombin decay, levels of fibrinogen and hence fibrin were decreased in dilution degree-dependency. The imbalance between influence of the dilution on thrombin activity and fibrin formation brought unexpected outcomes of fibrin properties: the formed clots favoured the degradation by plasminbut the fibrin networks remained tighter/less permeable. This proteolytic tendency was partly overturned by the fibrinogen concentrate added (total fibrinogen ≥ 2 g/l), and much more affected if used in combination with tranexamic acid (a fibrinolysis inhibitor) at small doses. No reversal effect resulted from the FXIII concentrate added. We conclude that plasma-dilution did reduce the proteolytic resistance of formed clots. The fibrinogen concentrate, better together with small doses of tranexamic acid, may reverse the impairment of fibrin property.The FXIII concentrate is not effective in this regard in our in vitro model using platelet-poor plasma.
Optimisation of AlGaN/GaN Heterostructures for Field Effect Transistors Grown by Metalorganic Vapour Phase Epitaxy (2001)

The influence of both the AlGaN barrier and GaN underlayer in single heterostructures has been examined. The results show that room temperature Hall measurements can lead to an overestimate of the sheet carrier concentration due to bulk contributions. Orders of magnitude increase of in the GaN resistivity can be achieved by reducing the growth temperature. The luminescence properties of the structure have been examined by cathodoluminescence showing strong features attributable to the two-dimensional electron gas.
A realistic camera model for computer graphics (1995)

Most recent rendering research has concentrated on two subproblems: modeling the reflection of light from materials, and calculating the direct and indirect illumination from light sources and other surfaces. Another key component of a rendering system is the camera model. Unfortunately, current camera models are not geometrically or radiometrically correct and thus are not sufficient for synthesizing images from physically-based rendering programs. In this paper we describe a physically-based camera model for computer graphics. More precisely, a physically-based camera model accurately computes the irradiance on the film given the incoming radiance from the scene. In our model a camera is described as a lens system and film backplane. The lens system consists of a sequence of simple lens elements, stops and apertures. The camera simulation module computes the irradiance on the backplane from the scene radiances using distributed ray tracing. This is accomplished by a detailed simulation of the geometry of ray paths through the lens system, and by sampling the lens system such that the radiometry is computed accurately and efficiently. Because even the most complicated lenses have a relatively small number of elements, the simulation only increases the total rendering time slightly. CR
Synthesis and Structure Elucidation of Novel Spirooxindole Linked to Ferrocene and Triazole Systems via [3 + 2] Cycloaddition Reaction (2022)

In the present work, a novel heterocyclic hybrid of a spirooxindole system was synthesized <i>via</i> the attachment of ferrocene and triazole motifs into an azomethine ylide by [3 + 2] cycloaddition reaction protocol. The X-ray structure of the heterocyclic hybrid (1″<i>R</i>,2″<i>S</i>,3<i>R</i>)-2″-(1-(3-chloro-4-fluorophenyl)-5-methyl-1<i>H</i>-1,2,3-triazole-4-carbonyl)-5-methyl-1″-(ferrocin-2-yl)-1″,2″,5″,6″,7″,7a″-hexahydrospiro[indoline-3,3″-pyrrolizin]-2-one revealed very well the expected structure, by using different analytical tools (FTIR and NMR spectroscopy). It crystallized in the triclinic-crystal system and the <i>P</i>-<i>1</i>-space group. The unit cell parameters are <i>a</i> = 9.1442(2) Å, <i>b</i> = 12.0872(3) Å, <i>c</i> = 14.1223(4) Å, <i>α</i> = 102.1700(10)°, <i>β</i> = 97.4190(10)°, <i>γ</i> = 99.1600(10)°, and V = 1484.81(7) Å<sup>3</sup>. There are two molecules per unit cell and one formula unit per asymmetric unit. Hirshfeld analysis was used to study the molecular packing of the heterocyclic hybrid. H···H (50.8%), H···C (14.2%), Cl···H (8.9%), O···H (7.3%), and N···H (5.1%) are the most dominant intermolecular contacts in the crystal structure. O···H, N···H, H···C, F···H, F···C, and O···O are the only contacts that have the characteristic features of short and significant interactions. AIM study indicated predominant covalent characters for the Fe-C interactions. Also, the electron density (ρ(r)) at the bond critical point correlated inversely with the Fe-C distances.