gebhart/patrepeval huggingface dataset:
In Situ Localization of Gelatinolytic Activity in the Extracellular Matrix of Metastases of Colon Cancer in Rat Liver Using Quenched Fluorogenic DQ-gelatin (2003)

Matrix metalloproteinases (MMPs) such as gelatinases are believed to play an important role in invasion and metastasis of cancer. In this study we investigated the possible role of MMP-2 and MMP-9 in an experimental model of colon cancer metastasis in rat liver. We demonstrated with gelatin zymography that the tumors contained MMP-2 and MMP-9, but only MMP-2 was present in the active form. Immunolocalization of MMP-2 showed that the protein was localized at basement membranes of colon cancer cells and in intratumor stroma, associated with extracellular matrix (ECM) components. However, zymography and immunohistochemistry (IHC) do not provide information on the localization of MMP activity. Therefore, we developed an in situ zymography technique using the quenched fluorogenic substrate DQ-gelatin in unfixed cryostat sections. The application of DQ-gelatin in combination with a gelled medium allows precise localization of gelatinolytic activity. Fluorescence due to gelatinolytic activity was found in the ECM of tumors and was localized similarly to both MMP-2 protein and collagen type IV, its natural substrate. The localization of MMP-2 activity and collagen type IV at similar sites suggests a role of MMP-2 in remodeling of ECM of stroma in colon cancer metastases in rat liver.
Fold recognition aided by constraints from small angle X-ray scattering data (2005)

We performed a systematic exploration of the use of structural information derived from small angle X-ray scattering (SAXS) measurements to improve fold recognition. SAXS data provide the Fourier transform of the histogram of atomic pair distances (pair distribution function) for a given protein and hence can serve as a structural constraint on methods used to determine the native conformational fold of the protein. Here we used it to construct a similarity-based fitness score with which to evaluate candidate structures generated by a threading procedure. In order to combine the SAXS scores with the standard energy scores and other 1D profile-based scores used in threading, we made use both of a linear regression method and of a neural network-based technique to obtain optimal combined fitness scores and applied them to the ranking of candidate structures. Our results show that the use of SAXS data with gapless threading significantly improves the performance of fold recognition.
Ultrastructural Changes of Mitochondria in the Skeletal Muscle of Patients with Amyotrophic Lateral Sclerosis (2002)

Functional defects and morphological changes of mitochondria have been reported to be in the skeletal muscle of patients with amyotrophic lateral sclerosis (ALS). Recent studies suggested that mitochondrial abnormalities are related to the pathogenesis of ALS. The purpose of this study is to evaluate the ultrastructural changes of muscle mitochondria in ALS patients. The authors examined 49 cases of diagnostic muscle biopsy samples with definite or probable ALS by electron microscopy. Of the 49 cases, 5 (10%) had ultrastructural abnormalities of muscle mitochondria, including giant mitochondria, paracrystalline inclusions, and abnormal cristae. These abnormal mitochondria were mainly observed among subsarcolemmal mitochondrial aggregates.
Temperature Dependence of Spin Transfer Switching in Nanosecond Regime (2006)

We present a micromagnetic modeling study of spin transfer (ST) switching in magnetic tunneling junctions (MTJs) and its dependence on thermal effects due to a finite temperature of the MTJ. It is shown that the major effect of temperature is the introduction of nonzero distribution of local magnetization deviation from the easy axis of the free layer. The study of asymmetry between antiparallel (AP) to parallel (P) and P to AP switching is presented.
Multicentre randomized controlled trial comparing ferric(III)carboxymaltose infusion with oral iron supplementation in the treatment of preoperative anaemia in colorectal cancer patients (2015)

ClincalTrials.gov: NCT02243735 .
The porcine 2A10 antigen is homologous to human CD163 and related to macrophage differentiation. (1999)

The mAb 2A10 recognizes a 120-kDa protein with sequence homology to the human CD163 and whose expression is restricted to the cells of the porcine monocyte/macrophage lineage. While most of tissue macrophages express high levels of 2A10 Ag, bone marrow cells and a subset of blood monocytes are negative for this marker. The percentage of 2A10+ blood monocytes ranges between 5-50% depending on the donor. The phenotypic analysis indicates that these cells are more similar to mature macrophages than 2A10- monocytes. 2A10+ monocytes express higher levels of swine histocompatibility leukocyte Ag II, CD16, and the adhesion molecules very late Ag-4 (CD49d) and LFA-1 (CD11a) than 2A10- monocytes, while CD14 and SWC1 expression is lower. Both monocyte subsets also differ in their functional capabilities. 2A10+ monocytes induce a greater allogeneic response on T lymphocytes than 2A10- cells. LPS-stimulated 2A10+ and 2A10- monocytes both produce proinflammatory cytokines (TNF-alpha and IL-1alpha), but antiinflammatory IL-10 is only detected on the latter population. When 2A10- monocytes were cultured in medium containing pig serum, they acquired some phenotypic features of 2A10+ cells, expressing the 2A10 Ag. In contrast, when they were cultured in the presence of L929 supernatant as a source of GM-CSF, the 2A10 Ag expression remained low, scarcely increasing over basal levels. 2A10+ cells cultured with pig serum developed features that resemble monocyte-derived dendritic cells. These results indicate that 2A10+ monocytes could constitute a cell population in a more advanced maturation stage than 2A10- circulating monocytes.
A human tumor necrosis factor (TNF) alpha mutant that binds exclusively to the p55 TNF receptor produces toxicity in the baboon. (1994)

A number of recent studies have demonstrated that cellular responses to tumor necrosis factor (TNF) mediated by the p55 and the p75 TNF receptors are distinct. To evaluate the relative in vivo toxicities of wild-type TNF alpha (wtTNF alpha) and a novel p55 TNF selective receptor agonist, healthy, anesthetized baboons (Papio sp.) were infused with a near-lethal dose of either wtTNF alpha or a TNF alpha double mutant (dmTNF alpha) that binds specifically to the p55, but not to the p75, TNF receptor. Both wtTNF alpha and dmTNF alpha produced comparable acute hypotension, tachycardia, increased plasma lactate, and organ dysfunction in Papio. However, administration of wtTNF alpha produced a marked granulocytosis and loss of granulocyte TNF receptors, whereas little if any changes in neutrophil number or cell surface TNF receptor density were seen after dmTNF alpha mutant administration. Infusion of dmTNF alpha resulted in a plasma endogenous TNF alpha response that peaked after 90-120 min. We conclude that selective p55 TNF receptor activation is associated with early hemodynamic changes and the autocrine release of endogenous TNF alpha. Significant systemic toxicity results from p55 TNF receptor activation, but the role of the p75 TNF receptor in systemic TNF toxicity requires further study.
Insight into the Catalytic Mechanism of DNA Polymerase β:  Structures of Intermediate Complexes, (2001)

The catalytic reaction mediated by DNA polymerases is known to require two Mg(II) ions, one associated with dNTP binding and the other involved in metal ion catalysis of the chemical step. Here we report a functional intermediate structure of a DNA polymerase with only one metal ion bound, the DNA polymerase beta-DNA template-primer-chromium(III).2'-deoxythymidine 5'-beta,gamma-methylenetriphosphate [Cr(III).dTMPPCP] complex, at 2.6 A resolution. The complex is distinct from the structures of other polymerase-DNA-ddNTP complexes in that the 3'-terminus of the primer has a free hydroxyl group. Hence, this structure represents a fully functional intermediate state. Support for this contention is provided by the observation of turnover in biochemical assays of crystallized protein as well as from the determination that soaking Pol beta crystals with Mn(II) ions leads to formation of the product complex, Pol beta-DNA-Cr(III).PCP, whose structure is also reported. An important feature of both structures is that the fingers subdomain is closed, similar to structures of other ternary complexes in which both metal ion sites are occupied. These results suggest that closing of the fingers subdomain is induced specifically by binding of the metal-dNTP complex prior to binding of the catalytic Mg(2+) ion. This has led us to reevaluate our previous evidence regarding the existence of a rate-limiting conformational change in Pol beta's reaction pathway. The results of stopped-flow studies suggest that there is no detectable rate-limiting conformational change step.
Interplay of IKK/NF-κB signaling in macrophages and myofibers promotes muscle degeneration in Duchenne muscular dystrophy (2007)

Duchenne muscular dystrophy (DMD) is a lethal X-linked disorder associated with dystrophin deficiency that results in chronic inflammation and severe skeletal muscle degeneration. In DMD mouse models and patients, we find that IkappaB kinase/NF-kappaB (IKK/NF-kappaB) signaling is persistently elevated in immune cells and regenerative muscle fibers. Ablation of 1 allele of the p65 subunit of NF-kappaB was sufficient to improve pathology in mdx mice, a model of DMD. In addition, conditional deletion of IKKbeta in mdx mice elucidated that NF-kappaB functions in activated macrophages to promote inflammation and muscle necrosis and in skeletal muscle fibers to limit regeneration through the inhibition of muscle progenitor cells. Furthermore, specific pharmacological inhibition of IKK resulted in improved pathology and muscle function in mdx mice. Collectively, these results underscore the critical role of NF-kappaB in the progression of muscular dystrophy and suggest the IKK/NF-kappaB signaling pathway as a potential therapeutic target for DMD.
An Improved Total Synthesis of Triciribine: A Tricyclic Nucleoside with Antineoplastic and Antiviral Properties (2004)

We describe an efficient total synthesis of triciribine, a tricyclic nucleoside with antineoplastic and antiviral properties, starting from 4-amino-6-bromo-5-cyanopyrrolo[2,3-d]pyrimidine.
Spatial phase-shifting technique in large image-shearing electronic speckle pattern interferometry (2007)

A technique for deformation measurement by carrier is presented, which is based on large image-shearing shearography. A reference object is fixed on the side of a test object. They are all illuminated by one expanded laser beam. When a large image-shearing Wollaston crystal is used in front of a charge-coupled device (CCD) camera, one image of the object is superposed by one image of the reference surface. The carrier can be introduced by tilting the reference surface at a small angle. When Fourier transform is used to demodulate the modulated fringe pattern, the phase of deformation can be calculated and the deformation can be measured accurately. The principle of spatial carrier frequency modulation in large-shearing electronic speckle pattern interferometry (ESPI) is discussed. A typical experiment using a centrally loaded clamped circular plate is completed. Some experimental results are presented. The experimental results prove that the method can modulate a speckle pattern very well and the displacement fields can be measured effectively.
Retaining the 3D Framework of Zinc Sponge Anodes upon Deep Discharge in Zn–Air Cells (2014)

We fabricate three-dimensional zinc electrodes from emulsion-cast sponges of Zn powder that are thermally treated to produce rugged monoliths. This highly conductive, 3D-wired aperiodic scaffold achieves 740 mA h gZn(-1) when discharged in primary Zn-air cells (>90% of theoretical Zn capacity). We use scanning electron microscopy and X-ray diffraction to monitor the microstructural evolution of a series of Zn sponges when oxidized in Zn-air cells to specific depths-of-discharge (20, 40, 60, 80% DOD) at a technologically relevant rate (C/40; 4-6 mA cm(-2)). The Zn sponges maintain their 3D-monolithic form factor at all DOD. The cell resistance remains low under all test conditions, indicating that an inner core of metallic Zn persists that 3D-electrically wires the electrode, even to deep DOD.
Low affinity binding of an LFA-3/IgG1 fusion protein to CD2+T cells is independent of cell activation (1999)

Quantitative analysis of binding of the bivalent recombinant soluble fusion protein, LFA-3/IgG1, shows that the fusion protein binds to human CD2+ PBLs primarily through low affinity (KD approximately 140 microM) but also through high avidity (90 nM) interactions. The concentration dependence for LFA-3/IgG1 PBL binding took the form of two overlapping bell-shaped curves separated by a clear and reproducible minimum. This was accounted for in part by minor heterogeneity in the LFA-3/IgG1 preparations, and potentially by the ability of the ligand to bind to both CD2 and Fc receptors (FcR), best evidenced by the distinct binding properties of the fusion protein to NK and T cells. The low affinity LFA-3/ IgG1 binding to T cells is consistent with binding to CD2 only, and is in agreement with the low affinity reported for interactions between soluble forms of LFA-3 and CD2 by surface plasmon resonance technology. Moreover, as the low affinity determinations are similar for CD2 on resting and activated T cells, although the CD2 molecule has been reported to be altered to reveal new epitopes upon T cell activation, the binding data argue against multiple cell activation-dependent affinity states of CD2 for LFA-3 binding. This is distinct from that observed with other adhesion partners, and suggests that the different adhesion pathways utilize distinct mechanisms to mediate cell adhesion.
General asymmetric synthesis of isoquinoline alkaloids. Enantioselective hydrogenation of enamides catalyzed by BINAP-ruthenium(II) complexes (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTGeneral asymmetric synthesis of isoquinoline alkaloids. Enantioselective hydrogenation of enamides catalyzed by BINAP-ruthenium(II) complexesMasato Kitamura, Yi Hsiao, Masako Ohta, Masaki Tsukamoto, Tetsuo Ohta, Hidemasa Takaya, and Ryoji NoyoriCite this: J. Org. Chem. 1994, 59, 2, 297–310Publication Date (Print):January 1, 1994Publication History Published online1 May 2002Published inissue 1 January 1994https://pubs.acs.org/doi/10.1021/jo00081a007https://doi.org/10.1021/jo00081a007research-articleACS PublicationsRequest reuse permissionsArticle Views2124Altmetric-Citations128LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Composition and Topography of Structural Polypeptides of Bovine Rotavirus (1981)

The composition and topography of the structural polypeptides of bovine rotavirus was studied by polyacrylamide gel electrophoresis of radioactively labelled virus grown in LLC-MK2 cells and by lactoperoxidase-catalysed iodination of single- and double- capsid particles. Bovine rotavirus was found to possess at least six structural polypeptides, three of them associated with the inner capsid (p102K, p91K and p45K) and the others with the outer capsid (p84K, p37K and p34K). The most abundant polypeptide of the inner capsid was p45K, which accounted for approx, 80% of the protein mass, followed by p91K (approx, 20% of the protein mass) and p102K (approx. 1% of the protein mass). Polypeptide 45K is not readily available for iodination, indicating that it is partially covered by p91K, which is the most exposed polypeptide of the inner capsid. The number of polypeptide molecules per single capsid particle (calculated on the basis of an RNA content of 16%) was estimated to be approx. 6 molecules of p102K, 140 of p91K and 989 of p45K. The stoichiometry and degree of exposure of outer capsid polypeptides was more difficult to establish, even when it appears that p84K and p34K are the most exposed components.
Mutations in an integration host factor-binding site: effect on lambda site-specific recombination and regulatory implications (1986)

The manner in which integration host factor (IHF) regulates lambda site-specific recombination has been analyzed by examining the behavior of both wild-type and mutant DNAs in integrative and excisive recombination as well as in protein binding. While integrative recombination of an attP with two base changes in the H1 site required 8-fold more IHF than did wild type, binding to this site was lowered at least 500-fold, suggestive of cooperative interactions. A mutant attP with nine base changes did not integrate at all in vitro, with the defect being less severe in vivo. IHF inhibition of excisive recombination was relieved by both mutations in vitro and in vivo. These results imply that occupancy of the H1 site is critical for determining the direction of recombination. It is proposed that IHF inhibition of excision provides a monitor of the strength of the induction stimulus and the nutritional state of the cell; this would allow the prophage to excise selectively in conditions which favor successful completion of the lytic cycle.
Ultrashort, Strongly Focused Laser Pulses in Free Space (2010)

Technological advances in ultrafast optics now allow the generation of laser pulses whose duration is as short as a few optical cycles of the electric field; furthermore, these pulses can be focused to a spot size comparable to the wavelength. These strongly focused, ultrashort laser pulses have found applications, for instance, in high-resolution microscopy, particle trapping and electron acceleration. In order to characterize the spatiotemporal behavior of such ultrashort, tightly focused pulses, one needs the expressions of their electromagnetic fields. Ultrafast nonparaxial pulsed beams must be modeled as exact solutions to Maxwell's equations. Many studies on the propagation of a pulsed beam are based on a scalar paraxial theory, which provides an accurate description of the pulsed beam propagation when the beam divergence angle is small and the beam spot size is much larger than the wavelength for each spectral component. However, the analysis of tightly focused laser beams requires expressions of optical beams that extend beyond the paraxial approximation. Moreover, the vector nature of light cannot be neglected to properly describe tightly focused beams. Also, the appropriate spectrum amplitude must be employed in order to model ultrashort pulses. Many authors have proposed expressions for the electromagnetic fields of laser pulsed beams, but most of these models are incomplete. For example, Wang and co-workers presented scalar paraxial pulsed Gaussian beams that have a Gaussian spectrum (Wang et al., 1997), but their expressions are not suitable to describe ultrashort pulses, as reported by Porras (Porras, 1998). Caron and Potvliege suggested forms of spectra, which are appropriate to characterize pulses of very small duration, but the expressions for their vectorial nonparaxial ultrashort pulses are written in terms of numerically calculated angular spectra (Caron & Potvliege, 1999). Lin et al. presented closed-form expressions for subcycle pulsed focused vector beams that are exact solutions to Maxwell’s equations obtained in the context of the so-called complex-source point method, but they used an unsuitable Gaussian spectrum (Lin et al., 2006). Recently, an der Brugge and Pukhov have provided solutions for ultrashort focused electromagnetic pulses found with a more appropriate spectral amplitude, but the expressions hold true only in the paraxial regime (an der Brugge & Pukhov, 2009). The aim of this chapter is to provide a simple and complete strategy to correctly model strongly focused, ultrashort laser pulses. Three main tools are employed to find the expressions for the fields of such pulsed beam. First, the Hertz potential method is used in
Rapidly Forming Apatitic Mineral in an Osteoblastic Cell Line (UMR 106—01 BSP) (1995)

This study evaluated a rapid biomineralization phenomenon exhibited by an osteoblastic cell line, UMR 106-01 BSP, when treated with either organic phosphates [beta-glycerophosphate (beta-GP), Ser-P, or Thr-P], inorganic phosphate (P(i)), or calcium. In a dose-dependent manner, these agents (2-10 mM) stimulated confluent cultures to deposit mineral in the cell layer (ED50 of approximately 4.6 mM for beta-GP (30 +/- 2 nmol Ca2+/microgram DNA) and approximately 3.8 mM (29 +/- 2 nmol Ca2+/microgram DNA) for P(i)) with a plateau in mineral formation by 20 h (ET50 approximately 12-15 h). beta-GP or P(i) treatment yielded mineral crystals having an x-ray diffraction pattern similar to normal human bone. Alizarin red-S histology demonstrated calcium mineral deposition in the extracellular matrix and what appeared to be intracellular paranuclear staining. Electron microscopy revealed small, needle-like crystals associated with fibrillar, extracellular matrix deposits and intracellular spherical structures. Mineral formation was inhibited by levamisole (ED50 approximately 250 microM), pyrophosphate (ED50 approximately 1-10 microM), actinomycin C1 (500 ng/ml), cycloheximide (50 micrograms/ml), or brefeldin A (1 microgram/ml). These results indicate that UMR 106-01 BSP cells form a bio-apatitic mineralized matrix upon addition of supplemental phosphate. This process involves alkaline phosphatase activity, ongoing RNA and protein synthesis, as well as Golgi-mediated processing and secretion.
Reliability and Validity of the Massachusetts General Hospital Cognitive and Physical Functioning Questionnaire (2009)

In summary, the CPFQ is a unifactorial scale, with strong internal consistency, good temporal stability and sensitivity to change with treatment. Further studies will be needed to assess the validity and reliability of this instrument in other psychiatric and neuropsychiatric conditions associated with cognitive dysfunction.