gebhart/patrepeval huggingface dataset:
EPIDEMIOLOGY (2012)

BACKGROUND: Malignant pediatric brain tumors constitute a heterogeneic group of central nervous system tumors, and general markers of diagnosis and prognosis are not available. Recently, a panel of CD markers (CD15, CD24, CD29) was used to define increasing neural differentiation of embryonic stem cells. Although these CD markers have been associated with worse prognosis due to presence of tumor propagating cells, alterations in adhesion and migration in various cancer types, no studies of multiple CD markers in pediatric brain tumors have been performed. METHODS: We have collected tumors, including medulloblastomas (MB), ependymomas (EP) and juvenile astrocytomas, from >20 pediatric brain tumor patients. Frozen tumor sections and cultured tumor cells were stained for CD15, CD24 and CD29 and analyzed using fluorescence microscopy or flowcytometry. RESULTS: MB contained a mixture of cells with strong CD15 labeling inside vessels and cells with diffuse CD15 staining in the parenchyma of the tumor tissue. Cells strongly labeled with CD15 were also positive for the leukocyte marker CD45. The previously proposed association between CD15 expression and prognosis in MB could instead of reflecting abundance of tumor propagating cells depend on infiltrating immune cells. In low-grade pediatric tumors and EP, larger areas stained weakly for CD15 while few cells displayed strong staining. CD24 was expressed on the vast majority of cells in pediatric brain tumors, despite grade of malignancy. MB, however, displayed an intense and aberrant staining for CD24. Computerized image analysis of frozen tumor sections showed that proliferation of cells and the expression of CD29 correlated in a sub-group of MB. CONCLUSIONS: Our preliminary data show that CD15, CD24 and CD29 are differentially expressed in high- and low-malignant pediatric brain tumors in vivo. By defining the patterns of CD antigen expression in different pediatric tumors their relationship to biological behavior and thus prognosis can be established.
Experimental investigation of the uncontrolled higher harmonic impedances effect on the performance of high‐power microwave devices (2010)

Abstract This article assesses and quantifies the impact of higher harmonic terminations on the current and voltage waveforms of microwave devices.Previous works have shown that it is very difficult to obtain “ideal” textbook waveforms, due to the effect of higher harmonic terminations. The emergence of waveform measurement systems has made it possible to investigate the shapes of current and voltage waveforms for design purposes. This article further expands on this issue and quantifies the impact of the uncontrolled higher harmonics on the waveforms. The impact is first explained using theory and then demonstrated with simulation and actual large‐signal measurements. © 2010 Wiley Periodicals, Inc. Microwave Opt Technol Lett 52:2480–2482, 2010; View this article online at wileyonlinelibrary.com. DOI 10.1002/mop.25494
Effective Gelation of Water Using a Series of Bis-urea Dicarboxylic Acids (2000)

In Konzentrationen bis hinab zu 0.3 Gew.-% bildet eine neuartige Familie von Bisharnstoffdicarbonsäuren ein Hydrogel (siehe Bild). Der Aggregationszustand (Vesikel, Gel oder Faser) hängt ab vom pH-Wert, von der Ionenstärke und vom Molekulargewicht des Gelbildners. Somit lassen sich die Eigenschaften des Gels durch Design des Gelbildnermoleküls einstellen.
Computational intelligence and cerebellar enigmas (2002)

A three-layer cerebellar cortex presents a kind of ideal network for early perceptron theories, but its functioning is much more complicated. Three related topics connected with information coding and memorizing mechanisms in the cerebellum are considered: 1) demonstration that activity transformation by granule cells, conserves the signal continuity provided by snake-in-box type codes; 2) determining precision requirements for the standard CMAC as well as for more realistic cerebellar models to meet demands of adaptive critic based solutions for a nonlinear control problem (swinging pendulum); and 3) demonstration that the closed loop scheme for the synaptic weight adjustment provides a precise setting of cerebellar input-output relations and multiple predictions for physiological experiments.
Synthetic cADPR analogues may form only one of two possible conformational diastereoisomers (2018)

Cyclic adenosine 5'-diphosphate ribose (cADPR) is an emerging Ca<sup>2+</sup>-mobilising second messenger. cADPR analogues have been generated as chemical biology tools via both chemo-enzymatic and total synthetic routes. Both routes rely on the cyclisation of a linear precursor to close an 18-membered macrocyclic ring. We show here that, after cyclisation, there are two possible macrocyclic product conformers that may be formed, depending on whether cyclisation occurs to the "right" or the "left" of the adenine base (as viewed along the H-8 → C-8 base axis). Molecular modelling demonstrates that these two conformers are distinct and cannot interconvert. The two conformers would present a different spatial layout of binding partners to the cADPR receptor/binding site. For chemo-enzymatically generated analogues Aplysia californica ADP-ribosyl cyclase acts as a template to generate solely the "right-handed" conformer and this corresponds to that of the natural messenger, as originally explored using crystallography. However, for a total synthetic analogue it is theoretically possible to generate either product, or a mixture, from a given linear precursor. Cyclisation on either face of the adenine base is broadly illustrated by the first chemical synthesis of the two enantiomers of a "southern" ribose-simplified cIDPR analogue 8-Br-N9-butyl-cIDPR, a cADPR analogue containing only one chiral sugar in the "northern" ribose, i.e. 8-Br-D- and its mirror image 8-Br-L-N9-butyl-cIDPR. By replacing the D-ribose with the unnatural L-ribose sugar, cyclisation of the linear precursor with pyrophosphate closure generates a cyclised product spectroscopically identical, but displaying equal and opposite specific rotation. These findings have implications for cADPR analogue design, synthesis and activity.
Self-consistent electrodynamics of large-area high-frequency capacitive plasma discharge (2010)

Capacitively coupled plasmas (CCPs) generated using high frequency (3–30 MHz) and very high frequency (30–300 MHz) radio-frequency (rf) sources are used for many plasma processing applications including thin film etching and deposition. When chamber dimensions become commensurate with the effective rf wavelength in the plasma, electromagnetic wave effects impose a significant influence on plasma behavior. Because the effective rf wavelength in plasma depends upon both rf and plasma process conditions (e.g., rf power and gas pressure), a self-consistent model including both the rf power delivery system and the plasma discharge is highly desirable to capture a more complete physical picture of the plasma behavior. A three-dimensional model for self-consistently studying both electrodynamic and plasma dynamic behavior of large-area (Gen 10, &amp;gt;8 m2) CCP is described in this paper. This model includes Maxwell’s equations and transport equations for charged and neutral species, which are coupled and solved in the time domain. The complete rf plasma discharge chamber including the rf power delivery subsystem, rf feed, electrodes, and the plasma domain is modeled as an integrated system. Based on this full-wave solution model, important limitations for processing uniformity imposed by electromagnetic wave propagation effects in a large-area CCP (3.05×2.85 m2 electrode size) are studied. The behavior of H2 plasmas in such a reactor is examined from 13.56 to 200 MHz. It is shown that various rectangular harmonics of electromagnetic fields can be excited in a large-area rectangular reactor as the rf or power is increased. The rectangular harmonics can create not only center-high plasma distribution but also high plasma density at the corners and along the edges of the reactor.
Differences between human and machine perception in medical diagnosis (2020)

Deep neural networks (DNNs) show promise in image-based medical diagnosis, but cannot be fully trusted since their performance can be severely degraded by dataset shifts to which human perception remains invariant. If we can better understand the differences between human and machine perception, we can potentially characterize and mitigate this effect. We therefore propose a framework for comparing human and machine perception in medical diagnosis. The two are compared with respect to their sensitivity to the removal of clinically meaningful information, and to the regions of an image deemed most suspicious. Drawing inspiration from the natural image domain, we frame both comparisons in terms of perturbation robustness. The novelty of our framework is that separate analyses are performed for subgroups with clinically meaningful differences. We argue that this is necessary in order to avert Simpson's paradox and draw correct conclusions. We demonstrate our framework with a case study in breast cancer screening, and reveal significant differences between radiologists and DNNs. We compare the two with respect to their robustness to Gaussian low-pass filtering, performing a subgroup analysis on microcalcifications and soft tissue lesions. For microcalcifications, DNNs use a separate set of high frequency components than radiologists, some of which lie outside the image regions considered most suspicious by radiologists. These features run the risk of being spurious, but if not, could represent potential new biomarkers. For soft tissue lesions, the divergence between radiologists and DNNs is even starker, with DNNs relying heavily on spurious high frequency components ignored by radiologists. Importantly, this deviation in soft tissue lesions was only observable through subgroup analysis, which highlights the importance of incorporating medical domain knowledge into our comparison framework.
Increased Resistance of SARS-CoV-2 Variant P.1 to Antibody Neutralization (2021)

The relative resistance of SARS-CoV-2 variants B.1.1.7 and B.1.351 to antibody neutralization has been described recently. We now report that another emergent variant from Brazil, P.1, is not only refractory to multiple neutralizing monoclonal antibodies, but also more resistant to neutralization by convalescent plasma (3.4 fold) and vaccinee sera (3.8-4.8 fold). The cryo-electron microscopy structure of a soluble prefusion-stabilized spike reveals the P.1 trimer to adopt exclusively a conformation in which one of the receptor-binding domains is in the "up" position, with the functional impact of mutations appearing to arise from local changes instead of global conformational alterations. The P.1 variant threatens current antibody therapies but less so the protective efficacy of our vaccines.
Robotic myomectomy: a review of indications and techniques. (2010)

The primary surgical techniques used in myomectomy are open surgery, laparoscopic surgery, and, recently, robot-assisted ("robotic") surgery. The optimal surgical treatment of myomas is still a subject of debate because of the limitations of minimally invasive techniques and the disadvantages of laparotomy. In this article, the authors discuss the technique and the application of robotic myomectomy in the treatment of uterine fibroids.
Quantitative myocardial first-pass cardiovascular magnetic resonance perfusion imaging using hyperpolarized [1-13C] pyruvate (2018)

The feasibility of absolute myocardial blood flow quantification and suitability of hyperpolarized [1-13C] pyruvate as contrast agent for first-pass cardiovascular magnetic resonance (CMR) perfusion measurements are investigated with simulations and demonstrated in vivo in a swine model. A versatile simulation framework for hyperpolarized CMR subject to physical, physiological and technical constraints was developed and applied to investigate experimental conditions for accurate perfusion CMR with hyperpolarized [1-13C] pyruvate. Absolute and semi-quantitative perfusion indices were analyzed with respect to experimental parameter variations and different signal-to-noise ratio (SNR) levels. Absolute myocardial blood flow quantification was implemented with an iterative deconvolution approach based on Fermi functions. To demonstrate in vivo feasibility, velocity-selective excitation with an echo-planar imaging readout was used to acquire dynamic myocardial stress perfusion images in four healthy swine. Arterial input functions were extracted from an additional image slice with conventional excitation that was acquired within the same heartbeat. Simulations suggest that obtainable SNR and B0 inhomogeneity in vivo are sufficient for the determination of absolute and semi-quantitative perfusion with ≤25% error. It is shown that for expected metabolic conversion rates, metabolic conversion of pyruvate can be neglected over the short duration of acquisition in first-pass perfusion CMR. In vivo measurements suggest that absolute myocardial blood flow quantification using hyperpolarized [1-13C] pyruvate is feasible with an intra-myocardial variability comparable to semi-quantitative perfusion indices. The feasibility of quantitative hyperpolarized first-pass perfusion CMR using [1-13C] pyruvate has been investigated in simulations and demonstrated in swine. Using an approved and metabolically active compound is envisioned to increase the value of hyperpolarized perfusion CMR in patients.
Jaggies as aliasing or reconstruction phenomena: a tutorial (2014)

Jaggies (staircasing effects) along slanted lines or curved edges are omnipresent in digital imaging. They are so widespread in digital display devices that very often they are associated with the modern “computerized” world (and sometimes even intentionally introduced into artworks such as logos, advertisements, etc. to convey a modern “pixelized” look). Although this subject is not new, it still remains an important issue in the design of modern digital display and printing devices. In the classical literature, jaggies are often considered as aliasing artifacts; and yet some other references consider them instead as reconstruction artifacts. The present tutorial revisits this question and tries to elucidate the real nature of this phenomenon using Fourier-based considerations. It shows that the jaggies can be either aliasing artifacts due to poor sampling in capture, or the result of poor reconstruction; and it explains the implications thereof on the elimination of unwanted jaggies.
Diagnostic accuracy of rK28-based immunochromatographic rapid diagnostic tests for visceral leishmaniasis: a prospective clinical cohort study in Sudan (2015)

An inexpensive rK28 RDT that performs robustly with WB or serum will be valuable for diagnosing cases of VL in East Africa.
Kyphoplasty Reduction of Osteoporotic Vertebral Compression Fractures: Correction of Local Kyphosis Versus Overall Sagittal Alignment (2006)

The majority of kyphosis correction by kyphoplasty is limited to the vertebral body treated. The majority of height gained after kyphoplasty occurs in the midbody. Higher correction over longer spans of the spine can be achieved with multilevel kyphoplasty procedures, in proportion to the number of levels addressed. Notwithstanding its well-published clinical efficacy, it is unrealistic to expect a 1 or 2-level kyphoplasty to improve significantly the overall sagittal alignment after VCFs.
Image portion identification methods, image parsing methods, image parsing systems, and articles of manufacture (2023)

Image portion identification methods, image parsing methods, image parsing systems, and articles of manufacture are described. According to one embodiment, an image portion identification method includes accessing data regarding an image depicting a plurality of biological substrates corresponding to at least one biological sample and indicating presence of at least one biological indicator within the biological sample and, using processing circuitry, automatically identifying a portion of the image depicting one of the biological substrates but not others of the biological substrates.
Qualitätssicherung der patientennahen Sofortdiagnostik (Point-of-Care-Testing) im Krankenhaus: Muster für eine hausinterne Richtlinie / Quality assurance in bedside testing at the hospital: sample guidelines for internal use (2004)

Abstract The following recommendations are based on the instructions of the “Richtlinie der Bundesärztekammer zur Qualitätssicherung quantitativer laboratoriums-medizinischer Untersuchungen” according to the decision of the executive board of the Bundesärztekammer (RiliBäk) as of August 24th 2001. They have exemplary character for hospitals in which the internal quality control of point-of-care testing is under the responsibility of the central laboratory. The recommendations focus on blood glucose, but are also applicable to other analytes with only slight modifications.
A Two-Base Deletion –439delGC in the Melanocortin-4 Receptor Promoter Associated with Early-Onset Obesity (2006)

We report an MC4R promoter mutation, -439delGC, associated with early-onset obesity and show that transcription factor Nhlh2 recognises this site in vitro. Nhlh2 mutations unlikely underlie severe human obesity.
Antitumor activity of an allosteric inhibitor of centromere-associated protein-E (2010)

Centromere-associated protein-E (CENP-E) is a kinetochore-associated mitotic kinesin that is thought to function as the key receptor responsible for mitotic checkpoint signal transduction after interaction with spindle microtubules. We have identified GSK923295, an allosteric inhibitor of CENP-E kinesin motor ATPase activity, and mapped the inhibitor binding site to a region similar to that bound by loop-5 inhibitors of the kinesin KSP/Eg5. Unlike these KSP inhibitors, which block release of ADP and destabilize motor-microtubule interaction, GSK923295 inhibited release of inorganic phosphate and stabilized CENP-E motor domain interaction with microtubules. Inhibition of CENP-E motor activity in cultured cells and tumor xenografts caused failure of metaphase chromosome alignment and induced mitotic arrest, indicating that tight binding of CENP-E to microtubules is insufficient to satisfy the mitotic checkpoint. Consistent with genetic studies in mice suggesting that decreased CENP-E function can have a tumor-suppressive effect, inhibition of CENP-E induced tumor cell apoptosis and tumor regression.
Low-dose X-ray radiation induces structural alterations in proteins. (2014)

International audience
New Insights into Water Control - A Review of the State of the Art – Part II (2002)

Abstract It could be argued today that oil companies would be better described as water companies. Total worldwide oil production averages some 75 million barrels per day and, while estimates vary, this is associated with the production of 300 – 400 million barrels of water per day. These values of approximately 5 – 6 barrels of water for every barrel of oil are quite conservative. In the United States, where many fields are depleted, the ratio of water-to-oil production is closer to 9 to 1. In some areas around the world, fields remain on production when the ratio is as high as 50 to 1. Water production is a harbinger of problems in an oil well. It can cause scaling problems in susceptible wells, induce fines migration or sandface failure, increase corrosion of tubulars, and kill wells by hydrostatic loading, amongst other things. Thus, while water production is an inevitable consequence of oil production, it is usually desirable to defer its onset, or its rise, for as long as possible. Numerous strategies, both mechanical and chemical, have been employed over the years in attempts to achieve this. Simple shut-off techniques, using cement, mechanical plugs and cross-linked gels have been widely used. Exotic concepts, like relative permeability modification (RPM), have also been applied with varying degrees of success. This paper is a continuation of a previous one, which reviewed the traditional techniques and proposed some new methodologies and technologies that can be used in the design of RPM treatments, in particular.1 Additional new insights offered in this paper include the extension of matrix RPM treatments to more extreme well conditions, such as heavy (viscous) oil and low pH environments. It also introduces the concept and reviews several case histories of the usage of RPM systems to perform hydraulic fracturing treatments to simultaneously stimulate oil and control water. This conformance-fracture technique could significantly impact the development strategies of many fields worldwide.
Smoking Doubles the Mortality Risk in COVID-19: A Meta-Analysis of Recent Reports and Potential Mechanisms (2020)

Introduction Studies have reported conflicting results regarding the effect of smoking on outcome in coronavirus disease 2019 (COVID-19) patients, but the results have been conflicting. In this meta-analysis, we systematically examined the association between smoking and mortality in COVID-19. Methods PubMed database was searched to look for relevant articles. Inclusion criteria were as follows: (1) cohort studies or case series studies; (2) study population included individuals with a confirmed COVID-19 infection; (3) the status of smoking was reported, regardless if it was current or in the past; and (4) mortality among smokers was reported in the study or could be calculated and compared to non-smokers. Mortality rates were pooled using a random effects model. Risk ratio (RR) and its 95% confidence interval (CI) were also calculated using the same model. Another meta-analysis was then performed to assess the difference in mortality between current and former smokers. Results Ten studies with a total of 11,189 patients were included. Mortality among smokers was 29.4% compared to 17.0% among non-smokers. RR was 2.07 (95% CI: 1.59, 2.69). Based on analysis of four studies (532 patients), there was no difference in mortality risk between current and former smokers (RR: 1.03; 95% CI: 0.75, 1.40). Conclusions Smoking, current or past, is associated with higher mortality in COVID-19 patients. Mortality among current smokers was about 50% greater than former smokers, but the difference was not statistically significant.
Type 1 and P pili of uropathogenic Escherichia coli. (2014)

<title>Abstract</title> In uropathogenic <italic>Escherichia coli</italic> (UPEC), type 1 pili (T1P) and P pili enable the bacterium to bind to host epithelial cells within the urinary tract, which can lead to a urinary tract infection. This chapter reviews the genetics, structure and functions of UPEC T1P and P pili. It also describes the mechanisms by which T1P and P pili contribute to UPEC pathogenesis and host immune response.