gebhart/patrepeval huggingface dataset:
Purification and characterization of a hemolysin produced by a clinical isolate of Kanagawa phenomenon-negative Vibrio parahaemolyticus and related to the thermostable direct hemolysin (1988)

A clinical isolate (strain 4037) of Kanagawa phenomenon-negative Vibrio parahaemolyticus was studied. Although the strain was judged to be Kanagawa phenomenon-negative by various conventional tests, it produced a new hemolysin (named Vp-TRH, for thermostable direct hemolysin [Vp-TDH]-related hemolysin) that was related to the Vp-TDH produced by ordinary Kanagawa phenomenon-positive V. parahaemolyticus. Vp-TRH was purified by ammonium sulfate fractionation and successive column chromatographies on DEAE-cellulose, hydroxyapatite, and Mono Q. The molecular weight of Vp-TRH was estimated as 48,000 by Sephadex G-100 gel filtration, and the molecular weight of the subunit was estimated to be 23,000 by sodium dodecyl sulfate-slab gel electrophoresis. Thus, like Vp-TDH, Vp-TRH seems to be composed of two subunits. The isoelectric point of Vp-TRH was determined to be 4.6. Vp-TRH showed lytic activities different from those of Vp-TDH on erythrocytes from various animals, especially those from calves, chickens, and sheep. The hemolytic activity of Vp-TRH was labile on heat treatment at 60 degrees C for 10 min, unlike that of Vp-TDH. The immunological similarities, but not the identities of Vp-TRH and Vp-TDH, were demonstrated by Ouchterlony, neutralization, and latex agglutination tests. Thus, we conclude that this clinical isolate of Kanagawa phenomenon-negative V. parahaemolyticus produces a new type of hemolysin that is similar, but not identical, to Vp-TDH, which is usually produced by Kanagawa phenomenon-positive V. parahaemolyticus.
Probing site-specific conformational distributions in protein folding with solid-state NMR (2005)

We demonstrate an experimental approach to structural studies of unfolded and partially folded proteins in which conformational distributions are probed at a site-specific level by 2D solid-state 13C NMR spectroscopy of glassy frozen solutions. Experiments on chemical denaturation of the 35-residue villin headpiece subdomain, a model three-helix-bundle protein with a known folded structure, reveal that 13C-labeled residues in the three helical segments of the folded state have markedly different conformational distributions in the unfolded state. Moreover, the 2D solid-state NMR line shapes near the unfolding midpoint do not fit a simple two-state model, in which the conformational distributions of the unfolded component are assumed to be independent of denaturant concentration. Comparison with solid-state NMR spectra of peptides containing the individual helical segments suggests an alternative two-step description of conformational distributions in partially folded states of the helical villin headpiece subdomain, in which chemical denaturation is viewed as a disruption of tertiary contacts followed by equilibration of local secondary structure according to the intrinsic helical propensities of individual segments.
Evaluation of very highly pixellated crystal blocks with SiPM readout as candidates for PET/MR detectors in a small animal PET insert (2012)

Arrays of silicon photo-multipliers (SiPMs) are good candidates for the readout of detectors in PET MR inserts due to their high packing density, efficiency, low bias voltage and insensitivity to magnetic fields. In this study we report the readout performance of SensL SiPM arrays in terms of their ability to resolve all elements of pixellated lutetium oxyorthosilicate (LYSO) crystals their energy resolution, and coincidence response function. Two SensL SPMarray-4 were used as light sensors. Two L YSO crystal blocks consisting of a arrays of 8 × 8 1.2 mm × 1.2 mm × 6.0 mm crystals on the lower layer and 7 × 7 1.2 mm × 1.2 mm × 4.0 mm crystals on the upper layer (which is offset by Yz the crystal width) were mounted on the SensL arrays. A second study was performed with single layer arrays of 8 × 8 1.2 mm × 1.2 mm × 10.0 mm crystals. All of the crystals in the dual layer block were easily identified with a peak to valley ratio of 7.2 while the single layer blocks had a peak to valley ratio of 11.2. The crystal dots were more uniformly spaced in the dual layer arrays suggesting that the inter-layer connection affords some useful light sharing. The average energy resolution for all 113 crystals was 16.3 ± 2.3%. The coincidence response to a 0.25 mm Na-22 source in plastic was 0.97 ± 0.12 mm for normally incident gamma rays with the detectors 120 mm apart. These results indicate that it should be possible to achieve a spatial resolution of about one millimetre near the center of the field of view.
Evaluation of Stereo Matching Costs on Images with Radiometric Differences (2008)

Stereo correspondence methods rely on matching costs for computing the similarity of image locations. We evaluate the insensitivity of different costs for passive binocular stereo methods with respect to radiometric variations of the input images. We consider both pixel-based and window-based variants like the absolute difference, the sampling-insensitive absolute difference, and normalized cross correlation, as well as their zero-mean versions. We also consider filters like LoG, mean, and bilateral background subtraction (BilSub) and nonparametric measures like Rank, SoftRank, Census, and Ordinal. Finally, hierarchical mutual information (HMI) is considered as pixelwise cost. Using stereo data sets with ground-truth disparities taken under controlled changes of exposure and lighting, we evaluate the costs with a local, a semiglobal, and a global stereo method. We measure the performance of all costs in the presence of simulated and real radiometric differences, including exposure differences, vignetting, varying lighting, and noise. Overall, the ranking of methods across all data sets and experiments appears to be consistent. Among the best costs are BilSub, which performs consistently very well for low radiometric differences; HMI, which is slightly better as pixelwise matching cost in some cases and for strong image noise; and Census, which showed the best and most robust overall performance.
Tumour Cell Labelling by Magnetic Nanoparticles with Determination of Intracellular Iron Content and Spatial Distribution of the Intracellular Iron (2013)

Magnetically labelled cells are used for in vivo cell tracking by MRI, used for the clinical translation of cell-base therapies. Studies involving magnetic labelled cells may include separation of labelled cells, targeted delivery and controlled release of drugs, contrast enhanced MRI and magnetic hyperthermia for the in situ ablation of tumours. Dextran-coated super-paramagnetic iron oxide (SPIO) ferumoxides are used clinically as an MR contrast agents primarily for hepatic imaging. The material is also widely used for in vitro cell labelling, as are other SPIO-based particles. Our results on the uptake by human cancer cell lines of ferumoxides indicate that electroporation in the presence of protamine sulphate (PS) results in rapid high uptake of SPIO nanoparticles (SPIONs) by parenchymal tumour cells without significant impairment of cell viability. Quantitative determination of cellular iron uptake performed by colorimetric assay is in agreement with data from the literature. These results on intracellular iron content together with the intracellular distribution of SPIONs by magnetic force microscopy (MFM) following in vitro uptake by parenchymal tumour cells confirm the potential of this technique for clinical tumour cell detection and destruction.
Optical constants of magnetron-sputtered boron carbide thin films from photoabsorption data in the range 30 to 770 eV (2008)

This work discusses the experimental determination of the optical constants (refractive index) of DC-magnetron-sputtered boron carbide films in the 30-770 eV photon energy range. Transmittance measurements of three boron carbide films with thicknesses of 54.2, 79.0, and 112.5 nm were performed for this purpose. These are believed to be the first published experimental data for the refractive index of boron carbide films in the photon energy range above 160 eV and for the near-edge x-ray absorption fine structure regions around the boron K (188 eV), carbon K (284.2 eV), and oxygen K (543.1 eV) absorption edges. The density, composition, surface chemistry, and morphology of the films were also investigated using Rutherford backscattering, x-ray photoelectron spectroscopy, atomic force microscopy, scanning electron microscopy, and extreme ultraviolet reflectance measurements.
Electrical bistable behaviors of organic materials in a single-layer structure (2003)

The electrical bistable behavior of two organic materials, 2-amino-4, 5-imidazole-dicarbonitrile (AIDCN) and 2-(4-Diphenylamino-benzylidene)-malononitrile (DBMN) were investigated. Samples were prepared in a single layer structure, namely Al electrode/ organic material layer/ Al electrode. The Al electrodes and the AIDCN layer were formed with vacuum evaporation, and the DBMN layer was formed with spin coating. The specimens were initially electrical insulators (off-state) at low applied voltage. Beyond a critical value of voltage, the current suddenly increased by several orders. They remained in the low impedance state (on-state) even when the voltage was lowered below the critical value. The results of the surface observations with an atomic force microscope and the structure analysis with X-ray diffraction indicated that the AIDCN layer was composed of multi-crystalline grains, whereas the DBMN layer was amorphous. The on-state current was proportional to the square of the applied voltage, which suggested it was limited by space charge in the organic layer. The on/off transition behaviors and the surface morphology suggested that the transition of AIDCN would be due to tunneling charge injection caused by the charge accumulation at the interface between the organic layer and the metal electrode. The transition of DBMN would be the one between the states of almost equal energy levels, such as a change of polarization direction.
Detection of Lymph Node Micrometastases by Gene Promoter Hypermethylation in Samples Obtained by Endosonography- Guided Fine-Needle Aspiration Biopsy (2004)

Endoscopic ultrasound-guided fine-needle aspiration (EUS-FNA) has become a fundamental procedure for gastrointestinal and lung cancer staging. However, there is growing evidence that micrometastases are present in lymph nodes, which cannot be detected with standard pathological methods. The aim of this study was to evaluate whether hypermethylation gene promoter analysis was feasible on samples obtained by EUS-FNA from lymph nodes, as well as to establish the usefulness of this strategy for the detection of micrometastases in patients with gastrointestinal and non-small cell lung cancer. Suspicious lymph nodes based on EUS findings from consecutive patients with esophageal, gastric, rectal, and non-small cell lung cancer were sampled by EUS-FNA. Hypermethylation analysis of the MGMT, p16(INK4a), and p14(ARF) gene promoter CpG islands were performed by methylation-specific PCR. Effectiveness of conventional cytology, methylation analysis, and their combination were established with respect to the definitive diagnosis. Twenty-seven patients were included, thus representing a total of 42 lymph nodes (esophageal cancer, n = 11; rectal cancer, n = 7; gastric cancer, n = 3; and lung cancer, n = 21). According to definitive diagnosis, 21 (50%) corresponded to metastatic lymph nodes. Sensitivity, specificity, and overall accuracy of conventional cytology were 76%, 100%, and 88%, respectively, whereas the corresponding values for the methylation analysis were 81%, 67%, and 74%, respectively. Combination of both techniques increased sensitivity (90%) but decreased specificity (67%) with respect to conventional cytology. In conclusion, it is feasible to detect occult neoplastic cells in EUS-FNA samples by hypermethylation gene promoter analysis. Moreover, addition of methylation analysis to conventional cytology may increase its sensitivity at the expenses of a decrease in its specificity.
Note on Transliteration (2013)

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Phyllotaxis (1994)

Phyllotaxis, the study of the patterns exhibited by leaves and other organs of plants, raises some of the deepest questions of plant morphogenesis. What principles of biological organisation produce these dynamical geometric systems? The constant occurrence of the Fibonacci sequence in such systems is a phenomenon that has fascinated botanists and mathematicians for centuries. In this book, first published in 1994, the many facets of phyllotaxis are dealt with in an integrated manner for the first time. The author describes a unified concept of phyllotaxis based on experimental, anatomical, cellular, physiological and paleontological observations. The book provides a framework for formal analyses of botanical data and emphasises the relevance of the phyllotactic paradigm in the study of other structures, such as crystals and proteins. It is of interest to cystallographers and physicists as well as to botanists and mathematicians.
Beta-catenin signaling regulates barrier-specific gene expression in circumventricular organ and ocular vasculatures (2019)

The brain, spinal cord, and retina are supplied by capillaries that do not permit free diffusion of molecules between serum and parenchyma, a property that defines the blood-brain and blood-retina barriers. Exceptions to this pattern are found in circumventricular organs (CVOs), small midline brain structures that are supplied by high permeability capillaries. In the eye and brain, high permeability capillaries are also present in the choriocapillaris, which supplies the retinal pigment epithelium and photoreceptors, and the ciliary body and choroid plexus, the sources of aqueous humor and cerebrospinal fluid, respectively. We show here that (1) endothelial cells in these high permeability vascular systems have very low beta-catenin signaling compared to barrier-competent endothelial cells, and (2) elevating beta-catenin signaling leads to a partial conversion of permeable endothelial cells to a barrier-type state. In one CVO, the area postrema, high permeability is maintained, in part, by local production of Wnt inhibitory factor-1.
Human fetuses are able to mount an adultlike CD8 T-cell response (2002)

Fetal/neonatal immune responses generally are considered to be immature and weaker than that of adults. We have studied the cord-blood T cells of newborns congenitally infected with Trypanosoma cruzi, the protozoan agent of Chagas disease. Our data demonstrate a predominant activation of CD8 T cells expressing activation markers and armed to mediate effector functions. The analysis of the T-cell receptor beta chain variable repertoire shows the oligoclonal expansion of these T lymphocytes, indicating that activation was driven by parasite antigens. Indeed, we have detected parasite-specific CD8 T cells secreting interferon-gamma after coincubation with live T cruzi. This response is enhanced in the presence of recombinant interleukin-15, which limits the T-cell spontaneous apoptosis. These findings point out that the fetal immune system is more competent than previously appreciated, since fetuses exposed to live pathogens are able to develop an adultlike immune CD8 T-cell response.
Minocycline Reduces Neuronal Death and Attenuates Microglial Response after Pediatric Asphyxial Cardiac Arrest (2009)

The mechanisms leading to delayed neuronal death after asphyxial cardiac arrest (ACA) in the developing brain are unknown. This study aimed at investigating the possible role of microglial activation in neuronal death in developing brain after ACA. Postnatal day-17 rats were subjected to 9 mins of ACA followed by resuscitation. Rats were randomized to treatment with minocycline, (90 mg/kg, intraperitoneally (i.p.)) or vehicle (saline, i.p.) at 1 h after return of spontaneous circulation. Thereafter, minocycline (22.5 mg/kg, i.p.) was administrated every 12 h until sacrifice. Microglial activation (evaluated by immunohistochemistry using ionized calcium-binding adapter molecule-1 (Iba1) antibody) coincided with DNA fragmentation and neurodegeneration in CA1 hippocampus and cortex (assessed by deoxynucleotidyltransferase-mediated dUTP nick-end labeling (TUNEL), Fluoro-Jade-B and Nissl stain). Minocycline significantly decreased both the microglial response and neuronal degeneration compared with the vehicle. Asphyxial CA significantly enhanced proinflammatory cytokine and chemokine levels in hippocampus versus control (assessed by multiplex bead array assay), specifically tumor necrosis factor-alpha (TNF-alpha), macrophage inflammatory protein-1alpha (MIP-1alpha), regulated upon activation, normal T-cell expressed and secreted (RANTES), and growth-related oncogene (GRO-KC) (P<0.05). Minocycline attenuated ACA-induced increases in MIP-1alpha and RANTES (P<0.05). These data show that microglial activation and cytokine production are increased in immature brain after ACA. The beneficial effect of minocycline suggests an important role for microglia in selective neuronal death after pediatric ACA, and a possible therapeutic target.
Ultralight and highly flexible aerogels with long cellulose I nanofibers (2011)

Ultralight and highly flexible aerogels with long cellulose I nanofibers (CNFs) were produced viapurification and defibrillation of wood fibers into CNF hydrogels, followed by freeze-drying. The aerogels had a web-like entangled structure, low density, and high water uptake capability. With the increase of CNF content in hydrogels from 0.1 to 1.5%, the bulk density of the aerogels increased from 1.3 × 10−3 to 17.0 × 10−3 g cm−3, whereas the water uptake ratio (WUR) decreased from 155 to 54. The microstructure of the aerogels can be transformed from open 3D porous nanofibrillar network to 2D sheet-like skeletons by adjusting the CNF content of the hydrogels. A possible assembly mechanism was proposed based on this transformation. When the transparent supernatant fraction, which has ∼0.018% solid content obtained viacentrifugation of the hydrogels, was subjected to freeze-drying, ultra-low density aerogels (0.2 × 10−3 g cm−3) consisting of nanofibers with lengths above 1 mm and a width range of 40–180 nm, were successfully produced due to the self-assembled of the tiny CNFs and their bundles along the longitudinal direction.
Discovery of the First Series of Small Molecule H5N1 Entry Inhibitors (2009)

The occurrence of highly pathogenic avian influenza virus H5N1 highlights the urgent need for new classes of antiviral drugs. Inhibition of H5N1 entry into cells may be an effective strategy. We report the first three small molecule inhibitors saponins with 3-O-beta-chacotriosyl residue, which showed potent inhibitory activity with IC(50) of 7.22-9.25 microM. The subsequent SAR studies showed the 3-O-beta-chacotriosyl residue was essential for the activity, and the aglycone structure also affected the activity.
Noxious stimulation decreases substance P binding in rat spinal dorsal horn (1994)

To determine the participation of NK-1 receptors in mediating inputs from noxious thermal stimulation, sustained noxious stimulation was applied to anaesthetized rats by immersing one hind paw in water for 1.5 min at different temperatures. After sacrificing the animal, lumbar spinal cords were removed and 20 microns sections were incubated with [125I]BH-substance P. Compared with unstimulated controls, binding was the least in rats given a 55 degrees C stimulus and sacrificed 1 min after the stimulus; the greatest reduction was found in the superficial dorsal horn. Rats sacrificed at 10 min showed intermediate binding levels. Groups given less intense stimuli showed smaller decreases in binding. It is suggested that the decrease in binding was due to occupation of receptors by endogenous ligand, which is consistent with the idea that noxious stimulation evokes the release of substance P at the spinal level.
Gibraltar, Controles en la verja y Nuevo diálogo AD HOC: La UE se involucra en la controversia. (2014)

La crisis con Gibraltar ha motivado una fuerte conflictividad por los controles de frontera exterior en la verja, en un contexto de busqueda de un nuevo formato de negociacion ad hoc entre las partes interesadas y de progresiva involucracion institucional y normativa de la UE en ciertos aspectos de la controversia.
The Psychology of Names (1992)

A name is a simple thing; it is a label — although there is also an element of mystery and magic about it. If we give a name to something which did not have one before it is like bringing that thing into existence for the first time. It seems to add an extra dimension to anything if we give it a name. A name is also capable, with familiarity and repetition, of being a kind of incantation.
Berbamine Inhibits the Growth of Liver Cancer Cells and Cancer-Initiating Cells by Targeting Ca2+/Calmodulin-Dependent Protein Kinase II (2013)

Liver cancer is the third leading cause of cancer deaths worldwide but no effective treatment toward liver cancer is available so far. Therefore, there is an unmet medical need to identify novel therapies to efficiently treat liver cancer and improve the prognosis of this disease. Here, we report that berbamine and one of its derivatives, bbd24, potently suppressed liver cancer cell proliferation and induced cancer cell death by targeting Ca(2+)/calmodulin-dependent protein kinase II (CAMKII). Furthermore, berbamine inhibited the in vivo tumorigenicity of liver cancer cells in NOD/SCID mice and downregulated the self-renewal abilities of liver cancer-initiating cells. Chemical inhibition or short hairpin RNA-mediated knockdown of CAMKII recapitulated the effects of berbamine, whereas overexpression of CAMKII promoted cancer cell proliferation and increased the resistance of liver cancer cells to berbamine treatments. Western blot analyses of human liver cancer specimens showed that CAMKII was hyperphosphorylated in liver tumors compared with the paired peritumor tissues, which supports a role of CAMKII in promoting human liver cancer progression and the potential clinical use of berbamine for liver cancer therapies. Our data suggest that berbamine and its derivatives are promising agents to suppress liver cancer growth by targeting CAMKII. Mol Cancer Ther; 12(10); 2067-77. ©2013 AACR.