gebhart/patrepeval huggingface dataset:
Interference of Copper Sulphate in Growth of <i>Erwinia amylovora</i> (1999)

Abstract To understand the toxicity of copper salts on Erwinia amylovora , which are used in the control of fire blight, bacterial growth and cell metabolism was assayed with copper sulphate in the presence or absence of complex‐forming compounds such as various amino acids or citrate. In minimal medium without amino acids copper sulphate strongly interfered with the growth of E. amylovora. A concentration of 15 μ m CuSO 4 resulted in about 50% growth inhibition. In contrast to a strong effect of streptomycin, copper ions barely killed the cells when incubated in minimal medium for 1 h. The addition of 4 g asparagine per litre relieved a‘bacteriostatic’effect of copper ions and allowed growth of the bacteria at 2 m m CuSO 4 . Other amino acids had a similar effect in the protection of E. amylovora against copper ions. This was in contrast to glycine betain, which was unable to suppress growth inhibition by CuSO 4 . Presumably, the free ammonium groups of amino acids participated in the protective effect. The addition of citrate, exceeding the amount of copper‐ions, was also protective. Bioluminescence of E. amylovora cells was expressed via a constitutive promoter from the lux ‐operon of Vibrio fischeri. The light emission is dependent on active cell metabolism. In a novel approach to determine the immediate response of E. amylovora after the addition of copper sulphate, the change of bioluminescence was determined. Addition of copper ions to MM3 medium strongly affected the bioluminescence, but no change in light production was noticed, when citrate or asparagine were present in addition to copper sulphate. A decrease of bioluminescence to 50% was observed for 50 μ m CuSO 4 in the absence of amino acids.
Supplementary Figure 1 from Plasmacytoid Dendritic Cells Promote Immunosuppression in Ovarian Cancer via ICOS Costimulation of Foxp3&lt;sup&gt;+&lt;/sup&gt; T-Regulatory Cells (2023)

&lt;p&gt;PDF file - 54K, Plasmacytoid dendritic cells do not correlate with ICOS- Foxp3+ T regulatory cells in the tumor microenvironment. Percentages of plasmacytoid dendritic cells (pDC) and percentages of ICOS- Foxp3+ T regulatory cells as analyzed by FACS show no correlation within the tumor microenvironment of ovarian cancer&lt;/p&gt;
Intention estimation from gaze and motion features for human-robot shared-control object manipulation (2022)

Shared control can help in teleoperated object manipulation by assisting with the execution of the user's intention. To this end, robust and prompt intention estimation is needed, which relies on behavioral observations. Here, an intention estimation framework is presented, which uses natural gaze and motion features to predict the current action and the target object. The system is trained and tested in a simulated environment with pick and place sequences produced in a relatively cluttered scene and with both hands, with possible hand-over to the other hand. Validation is conducted across different users and hands, achieving good accuracy and earliness of prediction. An analysis of the predictive power of single features shows the predominance of the grasping trigger and the gaze features in the early identification of the current action. In the current framework, the same probabilistic model can be used for the two hands working in parallel and independently, while a rule-based model is proposed to identify the resulting bimanual action. Finally, limitations and perspectives of this approach to more complex, full-bimanual manipulations are discussed.
3D voxel construction based on epipolar geometry (2003)

In this paper, we propose an approach for construction of a projective 3D voxel space based on epipolar geometry obtained with weak calibration. This concept of voxel space defines the epipolar lines following to the coordinate axis. In the field of computer vision, it is common to reconstruct 3D geometry data based on camera calibration data and disparities of matching points in each image. In the case that the goal of the system is generating the images from another point of view, complete 3D geometry reconstruction is not presently required. However, detecting the consistent matching points in several pairs of images without complete 3D geometry information is difficult. This paper describes the concept of projective 3D voxel, which makes it possible to handle 3D geometric data without complete 3D geometry information.
Salix eriocephala Michx. (1989)

https://thekeep.eiu.edu/herbarium_specimens_byname/13182/thumbnail.jpg
Interparticle Phase-Separation Dynamics in Dense Agglomerates of Lithium Iron Phosphate Nanoparticles (2013)

Abstract not Available.
A Second Order Virtual Node Method for Poisson Interface Problems on Irregular Domains (2009)

We present a second order accurate, geometrically flexible and easy to implement method for solving the variable coefficient Poisson equation with interfacial discontinuities on an irregular domain. We discretize the equations using an embedded approach on a uniform Cartesian grid employing virtual nodes at interfaces and boundaries. A variational method is used to define numerical stencils near these special virtual nodes and a Lagrange multiplier approach is used to enforce jump conditions and Dirichlet boundary conditions. Our combination of these two aspects yields a symmetric positive definite discretization. In the general case, we obtain the standard 5-point stencil away from the interface. For the specific case of interface problems with continuous coefficients, we present a discontinuity removal technique that admits use of the standard 5-point finite difference stencil everywhere in the domain. Numerical experiments indicate second order accuracy in L∞.
Data from Antitumor Efficacy of the Novel RAF Inhibitor GDC-0879 Is Predicted by BRAF&lt;sup&gt;V600E&lt;/sup&gt; Mutational Status and Sustained Extracellular Signal-Regulated Kinase/Mitogen-Activated Protein Kinase Pathway Suppression (2023)

&lt;div&gt;Abstract&lt;p&gt;Oncogenic activation of the BRAF serine/threonine kinase has been associated with initiation and maintenance of melanoma tumors. As such, development of pharmacologic agents to target RAF proteins or their effector kinases is an area of intense investigation. Here we report the biological properties of GDC-0879, a highly selective, potent, and orally bioavailable RAF small-molecule inhibitor. We used extracellular signal-regulated kinase (ERK)-1/2 and mitogen-activated protein kinase/ERK kinase (MEK)-1/2 phosphorylation as biomarkers to explore the relationship between tumor outcome and pharmacodynamic inhibition of the RAF-MEK-ERK pathway. In GDC-0879–treated mice, both cell line– and patient-derived BRAF&lt;sup&gt;V600E&lt;/sup&gt; tumors exhibited stronger and more sustained pharmacodynamic inhibition (&gt;90% for 8 hours) and improved survival compared with mutant KRAS–expressing tumors. Despite the involvement of activated RAF signaling in RAS-induced tumorigenesis, decreased time to progression was observed for some KRAS-mutant tumors following GDC-0879 administration. Moreover, striking differences were noted for RAF and MEK inhibition across a panel of 130 tumor cell lines. Whereas GDC-0879–mediated efficacy was associated strictly with BRAF&lt;sup&gt;V600E&lt;/sup&gt; status, MEK inhibition also attenuated proliferation and tumor growth of cell lines expressing wild-type BRAF (81% KRAS mutant, 38% KRAS wild type). The responsiveness of BRAF&lt;sup&gt;V600E&lt;/sup&gt; melanoma cells to GDC-0879 could be dramatically altered by pharmacologic and genetic modulation of phosphatidylinositol 3-kinase pathway activity. These data suggest that GDC-0879–induced signaling changes are dependent on the point of oncogenic activation within the RAS network. Taken together, these studies increase our understanding of the molecular determinants for antitumor efficacy resulting from RAF pathway inhibition and have implications for therapeutic intervention in the clinic. [Cancer Res 2009;69(7):3042–51]&lt;/p&gt;&lt;/div&gt;
In vitro selection of resistance in Escherichia coli and Klebsiella spp. at in vivo fluoroquinolone concentrations (2010)

Among the tested fluoroquinolones, levofloxacin was the most capable of limiting the occurrence of resistance.
Plasmodium vivax: who cares? (2008)

More attention is being focused on malaria today than any time since the world's last efforts to achieve eradication over 40 years ago. The global community is now discussing strategies aimed at dramatically reducing malarial disease burden and the eventual eradication of all types of malaria, everywhere. As a consequence, Plasmodium vivax, which has long been neglected and mistakenly considered inconsequential, is now entering into the strategic debates taking place on malaria epidemiology and control, drug resistance, pathogenesis and vaccines. Thus, contrary to the past, the malaria research community is becoming more aware and concerned about the widespread spectrum of illness and death caused by up to a couple of hundred million cases of vivax malaria each year. This review brings these issues to light and provides an overview of P. vivax vaccine development, then and now. Progress had been slow, given inherent research challenges and minimal support in the past, but prospects are looking better for making headway in the next few years. P. vivax, known to invade the youngest red blood cells, the reticulocytes, presents a strong challenge towards developing a reliable long-term culture system to facilitate needed research. The P. vivax genome was published recently, and vivax researchers now need to coordinate efforts to discover new vaccine candidates, establish new vaccine approaches, capitalize on non-human primate models for testing, and investigate the unique biological features of P. vivax, including the elusive P. vivax hypnozoites. Comparative studies on both P. falciparum and P. vivax in many areas of research will be essential to eradicate malaria. And to this end, the education and training of future generations of dedicated "malariologists" to advance our knowledge, understanding and the development of new interventions against each of the malaria species infecting humans also will be essential.
Filgrastim as an Alternative to Donor Leukocyte Infusion for Relapse After Allogeneic Stem-Cell Transplantation (2000)

The use of filgrastim with rapid discontinuation of immunosuppression results in response rates that are similar to results using DLI. Filgrastim could be considered as an alternative or an adjunct to DLI for relapses after alloSCT.
The degradation of arabinoxylan-rich cell walls in digesta obtained from piglets fed wheat-based diets varies depending on digesta collection site, type of cereal, and source of exogenous xylanase (2012)

The objective of the present study was to compare the ability of experimental and commercial xylanases to degrade, in vitro, the arabinoxylan (AX) fraction in digesta from 28-d-old piglets fed a wheat (Triticum aestivum)-based diet (49% wheat). Pigs were euthanized at 1, 2, 3, or 4 h after feeding; stomach and ileum contents were isolated and frozen and later used for the in vitro studies. Xylan solubilization provided information regarding the ability of the enzymes to degrade AX during the harsh in vivo conditions prevailing in the gastrointestinal tract. The hydrolytic capacity of a commercial xylanase was compared with that of an experimental xylanase using stomach digesta (pH 1.8) obtained at 4 h after feeding. Relative to the control, both enzymes increased (P < 0.001) xylan solubilization 3-fold. In the ileal digesta (1 h), xylan solubilization was increased by 36% (P < 0.001). Inclusion of arabinofuranosidases (Ara f) with xylanases increased xylan solubilization in stomach samples (P = 0. 007 and P = 0. 030) but not in ileal samples (P = 0.873 and P = 0.997). Our results illustrate clearly the importance of using different conditions and substrates when enzyme performance is studied in vitro as a prescreening tool for setting up in vivo trials.
A Qualitative Analysis of Android Taint-Analysis Results (2019)

In the past, researchers have developed a number of popular taint-analysis approaches, particularly in the context of Android applications. Numerous studies have shown that automated code analyses are adopted by developers only if they yield a good "signal to noise ratio", i.e., high precision. Many previous studies have reported analysis precision quantitatively, but this gives little insight into what can and should be done to increase precision further. To guide future research on increasing precision, we present a comprehensive study that evaluates static Android taint-analysis results on a qualitative level. To unravel the exact nature of taint flows, we have designed COVA, an analysis tool to compute partial path constraints that inform about the circumstances under which taint flows may actually occur in practice. We have conducted a qualitative study on the taint flows reported by FlowDroid in 1,022 real-world Android applications. Our results reveal several key findings: Many taint flows occur only under specific conditions, e.g., environment settings, user interaction, I/O. Taint analyses should consider the application context to discern such situations. COVA shows that few taint flows are guarded by multiple different kinds of conditions simultaneously, so tools that seek to confirm true positives dynamically can concentrate on one kind at a time, e.g., only simulating user interactions. Lastly, many false positives arise due to a too liberal source/sink configuration. Taint analyses must be more carefully configured, and their configuration could benefit from better tool assistance.
Identification of Quantitative Trait Loci That Regulate Arabidopsis Root System Size and Plasticity (2005)

Root system size (RSS) is a complex trait that is greatly influenced by environmental cues. Hence, both intrinsic developmental pathways and environmental-response pathways contribute to RSS. To assess the natural variation in both types of pathways, we examined the root systems of the closely related Arabidopsis ecotypes Landsberg erecta (Ler) and Columbia (Col) grown under mild osmotic stress conditions. We found that Ler initiates more lateral root primordia, produces lateral roots from a higher percentage of these primordia, and has an overall larger root system than Col under these conditions. Furthermore, although each of these parameters is reduced by osmotic stress in both ecotypes, Ler shows a decreased sensitivity to osmotica. To understand the genetic basis for these differences, QTL for RSS under mild osmotic stress were mapped in a Ler x Col recombinant inbred population. Two robust quantitative trait loci (QTL) were identified and confirmed in near-isogenic lines (NILs). The NILs also allowed us to define distinct physiological roles for the gene(s) at each locus. This study provides insight into the genetic and physiological complexity that determines RSS and begins to dissect the molecular basis for naturally occurring differences in morphology and developmental plasticity in the root system.
Efficient photoinduced second-harmonic generation in Ce-doped lead germanate glasses (1994)

Efficient photoinduced second-harmonic generation in Ce-doped bulk lead germanate glasses is observed. A linear increase of photoinduced second-order nonlinearity with Ce concentration is obtained. The reported glasses can be encoded for frequency doubling with extremely low (as little as 30 W of peak power at 1.064 microm) preparation intensities.
SMARCB1 deficient sinonasal carcinoma (2023)

SMARCB1 deficient sinonasal carcinomas are rare neoplasms, classified under sinonasal undifferentiated carcinomas by the fourth edition of the World Health Organization (WHO) classification of head and neck tumors. It is characterized immunohistochemically by loss of SMARCB1(INI1) expression. We are reporting the case of a 63-year-old man who was evaluated for nasal stuffiness of 3 months duration in another hospital where a radiological evaluation showed a polypoidal soft tissue lesion in the right maxillary sinus extending to the right nasal cavity and spheno-ethmoidal sinus. He underwent excision biopsy which was reported as non- keratinizing nasopharyngeal carcinoma. He was referred to our center with residual disease in spheno-ethmoidal recess for which radiotherapy was given. After completion of radiotherapy, the primary site had no residual disease, but while on follow-up he developed left sided neck nodes within 4 months of completion of treatment. Excision of the lesion was done and histopathological and immunohistochemical analysis revealed it to be metastasis from SMARCB1 deficient sinonasal carcinoma and not nasopharyngeal carcinoma as diagnosed from the other center. This case is being reported to highlight the diagnostic challenge associated with this rare entity.
Chirality induction from chiral molecules to adsorbed monolayers (2001)

Monolayer structures of a chiral mesogen, (R)- or (S)-[4′-(1-methylheptyloxy)-3′-nitrobiphenyl-4yl] 4-(trans-5-decenyloxy) benzoate, adsorbed on graphite were investigated by molecular dynamics simulations to clarify the mechanism of chirality inductions from chiral mesogens to chiral monolayers. We propose a molecular model that is based on coupling between the up-down symmetry breaking and the molecular tilt direction symmetry breaking of the monolayer. From the proposed model, we further predict alternative reversal of the two dimensional chirality of the monolayer when the chiral carbon is shifted along alkyl chain. This is a two-dimensional analogue of the “odd-even” effect on twist sense reversal in bulk chiral nematic systems.
Hermitian Splines for Modeling Biological Soft Tissue Systems That Exhibit Nonlinear Force-Elongation Curves (2011)

Numerical simulation of soft tissue mechanical properties is a critical step in developing valuable biomechanical models of live organisms. A cubic Hermitian spline optimization routine is proposed in this paper to model nonlinear experimental force-elongation curves of soft tissues, in particular when modeled as lumped elements. Boundary conditions are introduced to account for the positive definiteness and the particular curvature of the experimental curve to be fitted. The constrained least-square routine minimizes user intervention and optimizes fitting of the experimental data across the whole fitting range. The routine provides coefficients of a Hermitian spline or corresponding knots that are compatible with a number of constraints that are suitable for modeling soft tissue tensile curves. These coefficients or knots may become inputs to user-defined component properties of various modeling software. Splines are particularly advantageous over the well-known exponential model to account for the traction curve flatness at low elongations and to allow for more flexibility in the fitting process. This is desirable as soft tissue models begin to include more complex physical phenomena.
A Swine Model of Changes in the Neuronal Electromagnetic Field After Traumatic Brain Injury: A Pilot Study (2023)

Background Traumatic brain injury (TBI) is a global cause of disability and mortality. Treatment depends on mitigation of secondary injury resulting in axonal injury, necrosis, brain dysfunction, and disruption of electrical and chemical signaling in neural circuits. To better understand TBI, translational models are required to study physiology, diagnostics, and treatments in homologous species, such as swine. Electromagnetic fields (EMFs) from altered neural circuits can be measured and historically have been reliant on expensive shielding and supercooling in magnetoencephalography. Using proprietary induction sensors, it has been found that a non-invasive, non-contact approach with an engineered Mu-metal and copper mesh-shielded helmet effectively measures EMFs. This has not yet been investigated in swine models. We wished to evaluate the efficacy of this technology to assess TBI-dependent EMF changes in swine to describe the efficacy of these sensors and this model using a gravity-dependent controlled cortical impact (CCI). Methods A Yucatan miniswine was evaluated using non-contact, non-invasive proprietary induction sensors with an engineered dual-layer Mu-metal and interlaced copper mesh helmet with sensors within EMF channels connected to a helmet. Swine EMF recordings were obtained prior to induced gravity-dependent CCI followed by post-TBI measurements. Behavioral changes and changes in EMF measurements were assessed. EMF measurements were evaluated with an artificial intelligence (AI) model. Results Differences between room "noise" EMF measurements and pre-TBI swine electromagnetic field measurements were identified. Morphological characteristics between pre-injury and post-injury measurements were noted. AI modeling differentiated pre-injury and post-injury patterns in the swine EMF. Frequently identified frequencies seen post-injury were peaks at 2.5 Hz and 6.5 Hz and a valley at 11 Hz. The AI model identified less changes in the slope and thus decreased variation of EMF measurements post-TBI between 4.5 Hz and 7 Hz. Conclusions For the first time, it was identified that cortical function in a swine can be appropriately measured using novel induction sensors and shielding isolated to a helmet and EMF channels. The swine model can be appropriately differentiated from the external noise signal with identifiably different pre-injury and post-injury EMFs. Patterns can be recognized within the post-injury EMF due to altered neural circuits that can be measured using these sensors continuously, non-invasively, and in real time.
Amination with PdNHC Complexes: Rate and Computational Studies Involving Substituted Aniline Substrates (2011)

The amination of aryl chlorides with various aniline derivatives using the N-heterocyclic carbene-based Pd complexes Pd-PEPPSI-IPr and Pd-PEPPSI-IPent (PEPPSI=pyridine, enhanced precatalyst, preparation, stabilization, and initiation; IPr=diisopropylphenylimidazolium derivative; IPent= diisopentylphenylimidazolium derivative) has been studied. Rate studies have shown a reliance on the aryl chloride to be electron poor, although oxidative addition is not rate limiting. Anilines couple best when they are electron rich, which would seem to discount deprotonation of the intermediate metal ammonium complex as being rate limiting in favour of reductive elimination. In previous studies with secondary amines using PEPPSI complexes, deprotonation was proposed to be the slow step in the cycle. These experimental findings relating to mechanism were corroborated by computation. Pd-PEPPSI-IPr and the more hindered Pd-PEPPSI-IPent catalysts were used to couple deactivated aryl chlorides with electron poor anilines; while the IPr catalysis was sluggish, the IPent catalyst performed extremely well, again showing the high reactivity of this broadly useful catalyst.