gebhart/patrepeval huggingface dataset:
Whole Mitochondrial and Plastid Genome SNP Analysis of Nine Date Palm Cultivars Reveals Plastid Heteroplasmy and Close Phylogenetic Relationships among Cultivars (2014)

Date palm is a very important crop in western Asia and northern Africa, and it is the oldest domesticated fruit tree with archaeological records dating back 5000 years. The huge economic value of this crop has generated considerable interest in breeding programs to enhance production of dates. One of the major limitations of these efforts is the uncertainty regarding the number of date palm cultivars, which are currently based on fruit shape, size, color, and taste. Whole mitochondrial and plastid genome sequences were utilized to examine single nucleotide polymorphisms (SNPs) of date palms to evaluate the efficacy of this approach for molecular characterization of cultivars. Mitochondrial and plastid genomes of nine Saudi Arabian cultivars were sequenced. For each species about 60 million 100 bp paired-end reads were generated from total genomic DNA using the Illumina HiSeq 2000 platform. For each cultivar, sequences were aligned separately to the published date palm plastid and mitochondrial reference genomes, and SNPs were identified. The results identified cultivar-specific SNPs for eight of the nine cultivars. Two previous SNP analyses of mitochondrial and plastid genomes identified substantial intra-cultivar ( = intra-varietal) polymorphisms in organellar genomes but these studies did not properly take into account the fact that nearly half of the plastid genome has been integrated into the mitochondrial genome. Filtering all sequencing reads that mapped to both organellar genomes nearly eliminated mitochondrial heteroplasmy but all plastid SNPs remained heteroplasmic. This investigation provides valuable insights into how to deal with interorganellar DNA transfer in performing SNP analyses from total genomic DNA. The results confirm recent suggestions that plastid heteroplasmy is much more common than previously thought. Finally, low levels of sequence variation in plastid and mitochondrial genomes argue for using nuclear SNPs for molecular characterization of date palm cultivars.
Complex Nano-objects Displaying Both Magnetic and Catalytic Properties: A Proof of Concept for Magnetically Induced Heterogeneous Catalysis (2015)

Addition of Co2(Co)9 and Ru3(CO)12 on preformed monodisperse iron(0) nanoparticles (Fe(0) NPs) at 150 °C under H2 leads to monodisperse core-shell Fe@FeCo NPs and to a thin discontinuous Ru(0) layer supported on the initial Fe(0) NPs. The new complex NPs were studied by state-of-the-art transmission electron microscopy techniques as well as X-ray diffraction, Mössbauer spectroscopy, and magnetic measurements. These particles display large heating powers (SAR) when placed in an alternating magnetic field. The combination of magnetic and surface catalytic properties of these novel objects were used to demonstrate a new concept: the possibility of performing Fischer-Tropsch syntheses by heating the catalytic nanoparticles with an external alternating magnetic field.
[Hyperaldosteronism sensitive to dexamethasone with adrenal adenoma. Clinical, biological and genetic study]. (1995)

The simplicity and rapidity of genetic testing allows early diagnosis of this disease among families with early onset hypertension and associated hyperaldosteronism with or without adrenal hyperplasia and/or a tumoral formation.
Regeneración neuronal y recuperación funcional tras la lesión del sistema nervioso periférico (2004)

It is concluded that there is a gradient of functional adaptability in motoneurons to the role of new motor targets depending on their affinity in embryologic origins and functional properties. It is remarked the importance that, for a proper recovery of the lost function, have the compensatory processes started by synergistic motor systems not affected directly by the lesion.
The effect of random copolymer on the characteristic dimensions of cylinder-forming PS-<i>b</i>-PMMA thin films (2011)

The block copolymer self-assembly approach has received great attention in recent years as a possible way to overcome the limits of conventional lithography and to fabricate sub-22 nm structures. At this level, precise nanometric control is crucial for technological applications and the search for a flexible and reproducible protocol is a great challenge. The polystyrene-b-poly(methylmethacrylate) (PS-b-PMMA) system, with a styrene fraction of 0.71, spontaneously separates into a periodic array of hexagonally packed PMMA cylinders embedded in a matrix of PS and, under suitable processing conditions, this is perpendicularly oriented with respect to the underlying substrate. The selective removal of the PMMA allows us to obtain a nanoporous PS matrix with well-defined pore dimensions. Perpendicular orientation of the PMMA cylinders requires surface neutralization by means of a suitable PS-r-PMMA random copolymer. The choice of the random copolymer is not trivial, because different PS-r-PMMA copolymers strongly affect the characteristics of the PS-b-PMMA film deposited on it. In this paper the effects of the selected PS-r-PMMA on the arrangement as well as on the peculiar dimensions (pore diameter, pore to pore distance) of the final nanoporous PS thin film are studied. Reliable protocols for the fabrication of a disposable polymeric mask are proposed in view of its application in advanced lithographic processes.
(Invited) Charge Separation in Tetrapyrrole-Graphene and Tetrapyrrole-Slgo-Fullerene Hybrids (2013)

Abstract not Available.
Quantitative PET/CT in clinical practice (2017)

Excellent correlation has been found between two tested software reading platforms for all PET-derived metrics in a dual-reader analysis. Overall, the SULmax and SULpeak values had less bias and better precision compared with the MTV and TLG.
Isolation and Characterization of Carbene Derivatives of La@C<sub>82</sub>(<i>C</i><i><sub>s</sub></i>) (2008)

The photochemical reaction of La@C82(Cs) with 2-adamantane-2,3-[3H]-diazirine (1) affords the adduct 2 of La@C82(Cs) with adamantylidene (Ad:) in a high selectivity. The two isomers of La@C82(Cs)(Ad), 2a and 2b, are isolated by HPLC and characterized by electron spin resonance, mass, and UV-vis-near-infrared spectroscopies. The electronic properties of 2a and 2b are very similar to that of the pristine La@C82(Cs), suggesting that 2a and 2b retain the essential electronic and structural character of La@C82(Cs).
Spectroscopic Studies of Electron Injection in Quantum Dot Sensitized Mesoporous Oxide Films (2010)

Optimization of interfacial charge transfer in quantum dot (QD) sensitized mesoporous oxide films is crucial for the efficient design of QD sensitized solar cells (QDSSC). We employ TeraHertz time-domain spectroscopy (THz-TDS), transient absorption (TA) and time-resolved luminescence measurements, combined with transmission electron microscopy (TEM) and current−voltage measurements to study injection of electrons from PbSe QDs that are chemically linked to mesoporous oxide films. We illustrate that the interpretation of injection experiments is ambiguous for time-resolved optical measurements (TA and time-resolved luminescence) because nonradiative recombination processes at the oxide−QD interface have the same spectroscopic signature as electron injection. Complementary THz-TDS and current−voltage measurements demonstrate electron injection from the 1Se level of PbSe QDs into SnO2 mesoporous films, but injection into TiO2 films is not observed, although the time-resolved optical measurements could be interpreted as indicating injection. That injection takes place into SnO2 but not into TiO2 can be explained by the energy alignment of the 1Se level of the PbSe QD, which is energetically favorable and unfavorable respectively with respect to the oxide conduction band edges of SnO2 and TiO2. THz-TDS experiments demonstrate that electron injection from 5.5 nm PbSe QDs into SnO2 occurs on a time scale of 125 ± 40 ps. THz-TDS experiments further reveal a subensemble of photogenerated carriers in these QD−oxide systems that recombine within 10 ps after photoexcitation. These carriers are likely located in QD clusters formed on the oxide surface that are apparent from TEM images and where efficient nonradiative recombination processes occur. Control of QD cluster formation is therefore essential in the optimization of QDSSC devices because the time scale of carrier recombination in the QD clusters is shorter than the time scale of electron injection into the mesoporous oxide film.
Toward an early diagnosis of lung cancer: An autoantibody signature for squamous cell lung carcinoma (2008)

Serum-based diagnosis offers the prospect of early lung carcinoma detection and of differentiation between benign and malignant nodules identified by CT. One major challenge toward a future blood-based diagnostic consists in showing that seroreactivity patterns allow for discriminating lung cancer patients not only from normal controls but also from patients with non-tumor lung pathologies. We addressed this question for squamous cell lung cancer, one of the most common lung tumor types. Using a panel of 82 phage-peptide clones, which express potential autoantigens, we performed serological spot assay. We screened 108 sera, including 39 sera from squamous cell lung cancer patients, 29 sera from patients with other non-tumor lung pathologies, and 40 sera from volunteers without known disease. To classify the serum groups, we employed the standard Naïve Bayesian method combined with a subset selection approach. We were able to separate squamous cell lung carcinoma and normal sera with an accuracy of 93%. Low-grade squamous cell lung carcinoma were separated from normal sera with an accuracy of 92.9%. We were able to distinguish squamous cell lung carcinoma from non-tumor lung pathologies with an accuracy of 83%. Three phage-peptide clones with sequence homology to ROCK1, PRKCB1 and KIAA0376 reacted with more than 15% of the cancer sera, but neither with normal nor with non-tumor lung pathology sera. Our study demonstrates that seroreactivity profiles combined with statistical classification methods have great potential for discriminating patients with squamous cell lung carcinoma not only from normal controls but also from patients with non-tumor lung pathologies.
Automation of Integrated Perfusion Control Simplifying Process Intensification of Mammalian Biomanufacturing in Single‐Use Bioreactors (2022)

Abstract Production of biopharmaceuticals needs to become faster, more flexible, and efficient. Perfusion processes allow to operate cell cultivations at higher cell concentrations, shorten their process time and increase their productivity. Still, either customized software solutions or third‐party stand‐alone control devices are often used for perfusion control. Its integration into a bioreactor automation platform will simplify the implementation and application of perfusion processes in the future. In this study, the automation of an integrated perfusion control strategy for a scalable single‐use bioreactor family is demonstrated. The control strategy is illustrated by means of a CHO cell N–1 perfusion process in a 50‐L bioreactor. Accurate control allowed to achieve 80 · 10 6 c mL −1 within five days. Furthermore, also DO and pH setpoints were precisely controlled throughout the N–1 perfusion process. Finally, the advantage of this process strategy is exemplified by comparing fed‐batch processes inoculated from N–1 perfusion vs. N–1 batch processes.
Machine learning for recovery factor estimation of an oil reservoir: a\n tool for de-risking at a hydrocarbon asset evaluation (2020)

Well known oil recovery factor estimation techniques such as analogy,\nvolumetric calculations, material balance, decline curve analysis, hydrodynamic\nsimulations have certain limitations. Those techniques are time-consuming,\nrequire specific data and expert knowledge. Besides, though uncertainty\nestimation is highly desirable for this problem, the methods above do not\ninclude this by default. In this work, we present a data-driven technique for\noil recovery factor estimation using reservoir parameters and representative\nstatistics. We apply advanced machine learning methods to historical worldwide\noilfields datasets (more than 2000 oil reservoirs). The data-driven model might\nbe used as a general tool for rapid and completely objective estimation of the\noil recovery factor. In addition, it includes the ability to work with partial\ninput data and to estimate the prediction interval of the oil recovery factor.\nWe perform the evaluation in terms of accuracy and prediction intervals\ncoverage for several tree-based machine learning techniques in application to\nthe following two cases: (1) using parameters only related to geometry,\ngeology, transport, storage and fluid properties, (2) using an extended set of\nparameters including development and production data. For both cases model\nproved itself to be robust and reliable. We conclude that the proposed\ndata-driven approach overcomes several limitations of the traditional methods\nand is suitable for rapid, reliable and objective estimation of oil recovery\nfactor for hydrocarbon reservoir.\n
Monitoring trucks, cars and joggers on the horsetail falls bridge using fiber optic grating strain sensors (2000)

Blue Road Research installed fiber optic grating sensors on the Horsetail Falls bridge in 1998 to monitor static strain in support of health monitoring of the bridge. In November 1999 Blue Road Research utilized high speed, high sensitivity fiber grating demodulation systems on this bridge to monitor the weight arid speed of traffic. Sensitivity levels used were sufficiently high that joggers could be detected easily as well as people walking on the bridge. This paper provides an overview of these recent tests that show both health monitoring and traffic monitoring functions can be performed on a bridge using the same set of fiber grating strain sensors.
Magnetic Resonance Imaging of Sports Injuries Involving the Ankle (2015)

Understanding of ankle injuries has evolved for the past few decades, influenced by capability to visualize ligaments, tendons, and bone marrow on magnetic resonance imaging (MRI). Natural history of injury progression, complications, and healing has also been characterized using MRI. Stress injury is particularly common at the ankle in athletes and "weekend warriors" alike. This article will discuss manifestations of ankle injury on MRI as well as associated findings that should be addressed.
LGG-11. ESTABLISHMENT OF A HUMAN 3-DIMENSIONAL LOW-GRADE GLIOMA TUMOR MODEL IN INDUCED PLURIPOTENT STEM CELL DERIVED BRAIN ORGANOIDS (2019)

INTRODUCTION: Low-grade glioma (LGG) are the most common pediatric brain tumors. Preclinical models are still scarce. We used human induced pluripotent stem cell (hiPSC) derived brain organoids for human LGG disease modeling. METHODS: Brain organoids were generated from hiPSC cells using the STEMdiff™ Cerebral Organoid Kit (Stem Cell Technologies), based on the Lancaster et al. (Nature, 2013). LGG tumor spheres were generated from pilocytic astrocytoma cells DKFZ-BT66. High-grade glioma (HGG) tumor spheres were derived from U-87 cells. Brain organoids were co-cultured with either LGG or HGG tumor spheres. Co-cultures were formalin-fixed and paraffin-embedded for H&E and immunohistochemistry for analysis. RESULTS: Neuronal rosettes in the brain organoids represented immature and proliferating progenitor cells which were positive for MIB1. From day 30 to day 45, numbers of mature neurons expressing MAP2 increased. Organoids were focally expressing GFAP and S-100. After co-culturing tumor spheres with brain organoids (size ratio 1:1) we observed a partial or complete fusion of both tissues within the first three days. Red fluorescent protein expressing LGG cells migrated into the organoids. Their morphology resembled bipolar astrocytes and they invaded without destroying the normal organoid architecture. LGG cells strongly expressed MAP2 showing their differentiated character. In contrast, U-87 HGG cells massively spread around the organoids and showed a highly proliferating and invading biology. It was not possible to clearly discern remaining organoid tissue from HGG cells. Furthermore, we found a high rate of apoptotic cells. Co-cultured U-87 cells only expressed MIB1, especially in the outer cell layers, and no mature glial markers. CONCLUSIONS: We established the first human 3-dimensional LGG model in developing brain organoids, that allows animal free 3D LGG research. To better characterize the inter- and intracellular biology we will apply single-cell analysis.
Quasi-Three-Dimensional Approach to Transient Analysis of I2L Devices (1981)

Quasi-Three-Dimensional modeling, where a device is represented by several one-dimensional model units and the network which connects them, is extended to the transient analysis of I2L devices. Even at high current levels good agreement between the computed delay time and the measured one is obtained. Moreover, we establish quantitatively the effect of lateral voltage drops on the delay time.
Impact of containment and deposition method on sub-micron chip-to-wafer self-assembly yield (2012)

3D technologies need a high speed high alignment accuracy chip-to-wafer hybridation technique. This paper will focus on chip-to-wafer self assembly processes coupled with direct bonding hybridation. Submicronic alignment accuracy and a 90 per cent self-assembly process yield are obtained. The self-assembly process yield is analyzed in term of alignment accuracy and direct bonding quality. The impact of the chip's surface state (hydrophilic, hydrophobic, and mixed) on fluid containment efficiency and self-assembly process yield will be discussed. Topological containment (canthotaxis effect) is also evaluated with regards to structures height. Finally, the alignment yield as a function of deposition parameters will be described.
Bypass surgery for ruptured dissecting aneurysms of the proximal posterior cerebral artery: illustrative case (2022)

Surgical trapping using STA-PCA bypass could be a treatment of choice for proximal PCA dissecting aneurysms, considering its potential for cure and prevention of ischemic complications.
Expression of the G1-S Modulators in Hepatitis B Virus-Related Hepatocellular Carcinoma and Dysplastic Nodule: Association of Cyclin D1 and p53 Proteins with the Progression of Hepatocellular Carcinoma (2001)

Deranged expression of cell cycle modulators has been reported to contribute to the development and progression of hepatocellular carcinoma (HCC). However, their expression patterns remain poorly understood in hepatitis B virus (HBV)-related HCC, which constitutes about 65-70% of HCC in Korea. The aims of this study were to evaluate the expressions of G1-S modulators in HBV-related HCCs and dysplastic nodules (DNs), and to correlate with the histopathologic features of HCCs. Immunohistochemical expressions of cyclin D1, cyclin E, p53, p27, p21, p16, Rb, and PCNA proteins were investigated in 80 HCCs and 22 DNs. Cyclin D1 overexpression showed positive relationships with advanced tumor stage, poor differentiation, larger tumor size, microvascular invasion, intrahepatic meta-stasis, no tumor capsule formation, infiltrative growth, aberrant p53 expression, and high PCNA labeling index (LI) of HCC (p<0.05). Aberrant p53 expression showed positive relationship with poor differentiation of HCC (p<0.01). Expression of cyclin D1 or p53 was not observed in DNs. The p27 LI and p16 LI were lower in HCCs with intrahepatic metastasis (p<0.05). Cyclin D1 overexpression and aberrant p53 expression could be associated with the progression of HBV-related HCC, and might have a less crucial role in the DN-HCC sequence. In addition, elevated expression of p27 and p16 proteins might have inhibitory action to the intrahepatic metastasis of HBV-related HCC.
Gene expression profiling of samples of limited RNA amounts by the NGS application whole transcriptome AmpliSeq-RNA on the Ion Torrent platform offers straightforward, fast, and affordable analysis of human T cell subpopulations. (2017)

Abstract The diversity of T cell subpopulations demands a growing number of biomarkers to be studied from small samples. To bridge the gap between multicolor flow cytometry or classical qPCR and RNA-Seq, we applied highly multiplexed whole transcriptome AmpliSeq-RNA with 20,803 genes to perform sensitive and specific gene expression profiling (GEP). This study analyzed untouched primary human naïve and memory T cells and compared results to microarrays. Method 8 T cell subsets were isolated by FACS from 4 healthy donors without restimulation: CD4+ or CD8+ naïve (CCR7+CD45RA+), central memory (CCR7+CD45RA−), effector memory TEM (CCR7−CD45RA−) and TEMRA (CCR7−CD45RA+). AmpliSeq transcriptome human gene expression kit (Thermo Fisher) generated barcoded libraries from total RNA. 8–10 samples multiplexed per Ion 540 chip were sequenced on an Ion S5 System. Samples were also analyzed by Affymetrix HG-U133 Plus 2 genechips. Results The resulting Excel matrix of normalized reads [RPM = reads per million reads] had a dynamic range of more than 5 log units. Biological replicates of T cell subsets showed high correlation with r ≥ 0.925. Technical replicates (same libraries) demonstrated high reproducibility with r ≥ 0.995. A high concordance with genechip data were found for expression pattern of analyzed markers. For several very high or low abundant genes the AmpliSeq-RNA data were more sensitive and more specific than the hybridization-based genechip data. Conclusion AmpliSeq-RNA (counting PCR products by NGS) is an interesting alternative to perform straightforward GEP. The analysis of phenotypically well-defined T cell subsets without artificial in vitro stimulation allows more precise determination of in vivo relevant functions.
MALDI‐TOF mass spectrometry analysis of proteins and lipids in <i>Escherichia coli</i> exposed to copper ions and nanoparticles (2016)

Escherichia coli (E. coli) is one of the most important foodborne pathogens to the food industry responsible for diseases as bloody diarrhea, hemorrhagic colitis and life-threatening hemolytic-uremic syndrome. For controlling and eliminating E. coli, metal nano-antimicrobials (NAMs) are frequently used as bioactive systems for applications in food treatments. Most NAMs provide controlled release of metal ions, eventually slowing down or completely inhibiting the growth of undesired microorganisms. Nonetheless, their antimicrobial action is not totally unraveled and is strongly dependent on metal properties and environmental conditions. In this work, we propose the use of matrix-assisted laser desorption ionization time-of-flight (MALDI TOF) mass spectrometry as a powerful tool for direct, time efficient, plausible identification of the cell membrane damage in bacterial strains exposed to copper-based antimicrobial agents, such as soluble salts (chosen as simplified AM material) and copper nanoparticles. E. coli ATCC 25922 strain was selected as 'training bacterium' to set up some critical experimental parameters (i.e. cell concentration, selection of the MALDI matrix, optimal solvent composition, sample preparation method) for the MS analyses. The resulting procedure was then used to attain both protein and lipid fingerprints from E. coli after exposure to different loadings of Cu salts and NPs. Interestingly, bacteria exposed to copper showed over-expression of copper binding proteins and degradation of lipids when treated with soluble salt. These findings were completed with other investigations, such as microbiological experiments. Copyright © 2016 John Wiley & Sons, Ltd.