gebhart/patrepeval huggingface dataset:
Cytosine Methylation Enhances DNA Damage Produced by Groove Binding and Intercalating Enediynes:  Studies with Esperamicins A1 and C (1997)

Methylation of the C5 position of cytosine in CG dinucleotides represents an important element in the control of gene expression in eukaryotic cells. This major groove modification of DNA causes changes in DNA conformation that are recognized by DNA-binding proteins and DNA-damaging chemicals. We have observed that CG methylation affects the DNA damage produced by the enediyne esperamicin A1 and its analog lacking the intercalating anthranilate, esperamicin C. Fragments of the human phosphoglycerate kinase gene (PGK1) and the plasmid pUC19 were methylated with SssI methylase and subjected to damage by esperamicins A1 and C. Damage produced by esperamicin A1 was enhanced 1.5-2-fold near a single CG sequence at position -101 in PGK1 and in a region containing several methylated CG dinucleotides between positions -120 and -131. Esperamicin C-induced damage was enhanced to a similar degree in PGK1 but only at the site that contained multiple CG dinucleotides. There was enhancement of damage for both drugs in the pUC19 fragment at several sites near CG sequences. Analysis of the chemistry of esperamicin-induced DNA damage suggests that cytosine methylation does not affect the identity of drug-abstracted hydrogen atoms. The damage chemistry was also used to identify the DNA binding orientation of the esperamicins. The anthranilate of esperamicin A1 is predicted to intercalate in a CT step four base pairs in a 3'-direction to the CG sequence at -101 in PGK1 and in a CG dinucleotide at the site containing multiple CGs (positions -120 to -131). These observations are consistent with other studies that indicate a long range effect of cytosine methylation on DNA conformation.
Navigation by optical flow (2003)

A new navigation method based on measurements of image token positions and Kalman filtering is presented. An image token is the central projection of a landmark, a point on the terrain surface. This surface being described by a topographical map, the Kalman filter processes the measurements to update estimates of camera position and orientation, and landmark positions. Tests of an implementation for aeroplane navigation indicate a performance comparable to, or better than, that of satellite navigation systems. The implemented algorithm also seems to have a high tolerance against noise and modelling errors.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Nanoparticles of Conjugated Methotrexate-Human Serum Albumin: Preparation and Cytotoxicity Evaluations (2010)

Methotrexate-human serum albumin conjugates were developed by a simple carbodiimide reaction. Methotrexate-human serum albumin conjugates were then crosslinked with 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide HCl (EDC) to form nanoparticles. The size of nanoparticles determined by laser light scattering and TEM was between 90–150 nm. Nanoparticles were very stable at physiologic conditions (PBS pH 7.4, ) and after incubation with serum. The effect of amount of EDC used for crosslinking on the particle size and free amino groups of nanoparticles was examined. The amount of crosslinker showed no significant effect on the size of nanoparticles but free amino groups of nanoparticles were decreased by increasing the crosslinker. The physicochemical interactions between methotrexate and human serum albumin were investigated by differential scanning calorimetry (DSC). Nanoparticles were more cytotoxic on T47D cells compared to free methotrexate. Moreover, methotrexate-human serum albumin nanoparticles decreased the IC50 value of methotrexate on T47D cells in comparison with free methotrexate.
Atopic and non‐atopic allergic disorders: current insights into the possible involvement of free immunoglobulin light chains (2008)

Allergic diseases have become a serious global health problem in the developed world. IgE interacting with its high-affinitiy receptor FcepsilonRI is considered a major contributing factor to most types of allergies, but depending on the type of allergy, however, a subgroup of patients displays common symptoms and yet lack elevated levels of total serum IgE and/or antigen-specific IgE. Novel therapeutic strategies such as anti-IgE therapy may therefore not be applicable to these patients. It is clear, however, that these patients do display activation of mast cells. In several patients suffering from immunological disorders, an increase in free immunoglobulin (IG) light chain levels can be detected. Previously, we have described the capability of free light chains to elicit immediate hypersensitivity responses. In this Opinion article, we will discuss the role of IgE- and non-IgE-mediated mechanisms in allergic disorders and point out a possible role of free IG light chains in the pathogenesis of the non-atopic types of these allergies.
Epidemiology of complex regional pain syndrome: a retrospective chart review of 134 patients (1999)

Complex regional pain syndrome (CRPS) remains a poorly understood chronic pain disorder. Little data has been published assessing the epidemiology of CRPS (and reflex sympathetic dystrophy, RSD). This study assessed epidemiological variables in 134 CRPS patients evaluated at a tertiary chronic pain clinic in the US, including demographic, health care utilization and legal/workman's compensation measures. In addition, the frequency of physician-imposed immobilization of the CRPS limb was assessed, as was physical examination evidence of myofascial dysfunction. This study found that these patients had seen on average 4.8 different physicians before referral to the pain center and had received an average of five different kinds of treatments both prior to and during pain clinic treatment. The mean duration of CRPS symptoms prior to pain center evaluation was 30 months. Seventeen percent had a lawsuit and 54% had a worker compensation claim related to the CRPS. Fifty-one patients received a bone scan, but only 53% of which were interpreted as consistent with the diagnosis of RSD/CRPS. Forty-seven percent had a history of physician-imposed immobilization, and 56% had a myofascial component present at evaluation. The duration of CRPS symptoms and the involvement of the upper extremity was significantly associated with the presence of myofascial dysfunction. Thus, this study found that most CRPS patients are referred to a pain specialty clinic after several years of symptoms and many failed therapies. The data also suggest the lack of utility of a diagnostic bone scan and highlight the prominence of myofascial dysfunction in a majority of CRPS patients.
piggyBac is a flexible and highly active transposon as compared to Sleeping Beauty , Tol2 , and Mos1 in mammalian cells (2006)

A nonviral vector for highly efficient site-specific integration would be desirable for many applications in transgenesis, including gene therapy. In this study we directly compared the genomic integration efficiencies of piggyBac, hyperactive Sleeping Beauty (SB11), Tol2, and Mos1 in four mammalian cell lines. piggyBac demonstrated significantly higher transposition activity in all cell lines whereas Mos1 had no activity. Furthermore, piggyBac transposase coupled to the GAL4 DNA-binding domain retains transposition activity whereas similarly manipulated gene products of Tol2 and SB11 were inactive. The high transposition activity of piggyBac and the flexibility for molecular modification of its transposase suggest the possibility of using it routinely for mammalian transgenesis.
The 3DP: a processor architecture for three-dimensional applications (1992)

The 3DP (3-Dimensional Processor), a parallel-computing architecture that targets problems that have a 3-D numerical structure and require numerous calculations on 3-D vectors, is described. The 3DP architecture differs from traditional scalar architectures in that it operates directly on vectors. It differs from general parallel architectures in that it can solve problems that predict the behavior of highly coupled systems, and it differs from vector architectures in that it runs efficiently on length-3 vectors. Object-oriented programming on the 3DP and programming the 3DP in C++ are discussed. 3DP performance is reviewed, and the current implementation of the 3DP architecture, as an attached processor that plugs directly into Sun host VMEbus, is described.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A coherent computational approach to model bottom-up visual attention (2006)

Visual attention is a mechanism which filters out redundant visual information and detects the most relevant parts of our visual field. Automatic determination of the most visually relevant areas would be useful in many applications such as image and video coding, watermarking, video browsing, and quality assessment. Many research groups are currently investigating computational modeling of the visual attention system. The first published computational models have been based on some basic and well-understood Human Visual System (HVS) properties. These models feature a single perceptual layer that simulates only one aspect of the visual system. More recent models integrate complex features of the HVS and simulate hierarchical perceptual representation of the visual input. The bottom-up mechanism is the most occurring feature found in modern models. This mechanism refers to involuntary attention (i.e., salient spatial visual features that effortlessly or involuntary attract our attention). This paper presents a coherent computational approach to the modeling of the bottom-up visual attention. This model is mainly based on the current understanding of the HVS behavior. Contrast sensitivity functions, perceptual decomposition, visual masking, and center-surround interactions are some of the features implemented in this model. The performances of this algorithm are assessed by using natural images and experimental measurements from an eye-tracking system. Two adequate well-known metrics (correlation coefficient and Kullbacl-Leibler divergence) are used to validate this model. A further metric is also defined. The results from this model are finally compared to those from a reference bottom-up model.
<title>Four-dimensional coronary morphology and computational hemodynamics</title> (2001)

Conventional reconstructions from intravascular ultrasound (IVUS) stack the frames as acquired during the pullback of the catheter to form a straight three-dimensional volume, thus neglecting the vessel curvature and merging images from different heart phases. We are developing a comprehensive system for fusion of the IVUS data with the pullback path as determined from x-ray angiography, to create a geometrically accurate 4-D (3-D plus time) model of the coronary vasculature as basis for computational hemodynamics. The overall goal of our work is to correlate shear stress with plaque thickness. The IVUS data are obtained in a single pullback using an automated pullback device; the frames are afterwards assigned to their respective heart phases based upon the ECG signal. A set of 3-D models is reconstructed by fusion of IVUS and angiographic data corresponding to the same ECG-gated heart phase; methods of computational fluid dynamics (CFD) are applied to obtain important hemodynamic data. Combining these models yields the final 4-D reconstruction. Visualization is performed using the platform-independent VRML standard for a user-friendly manipulation of the scene. An extension for virtual angioscopy allows an easy assessment of the vessel features within their local context. Validation was successfully performed both in-vitro and in-vivo.
Cloning and expression of the cDNA for E6-AP, a protein that mediates the interaction of the human papillomavirus E6 oncoprotein with p53. (1993)

The E6 oncoproteins of the cancer-associated or high-risk human papillomaviruses (HPVs) target the cellular p53 protein. The association of E6 with p53 leads to the specific ubiquitination and degradation of p53 in vitro, suggesting a model by which E6 deregulates cell growth control by the elimination of the p53 tumor suppressor protein. Complex formation between E6 and p53 requires an additional cellular factor, designated E6-AP (E6-associated protein), which has a native and subunit molecular mass of approximately 100 kDa. Here we report the purification of E6-AP and the cloning of its corresponding cDNA, which contains a novel open reading frame encoding 865 amino acids. E6-AP, translated in vitro, has the following properties: (i) it associates with wild-type p53 in the presence of the HPV16 E6 protein and simultaneously stimulates the association of E6 with p53, (ii) it associates with the high-risk HPV16 and HPV18 E6 proteins in the absence of p53, and (iii) it induces the E6- and ubiquitin-dependent degradation of p53 in vitro.
Apoptosis mediates the decrease in cellularity during the transition between granulation tissue and scar. (1995)

Granulation tissue formation and contraction is an important step of second intention wound healing. Granulation tissue develops from the connective tissue surrounding the damaged or missing area and its cellular components are mainly small vessel and inflammatory cells as well as fibroblasts and myofibroblasts. As the wound closes and evolves into a scar, there is an important decrease in cellularity; in particular myofibroblasts disappear. The question arises as to which process is responsible for this cellular loss. During a previous investigation on the expression of alpha-smooth muscle actin in myofibroblasts (Darby I, Skalli O, Gabbiani G, Lab Invest, 1990, 63:21-29), we have observed that in late phases of wound healing, many myofibroblasts show changes compatible with apoptosis and suggested that this type of cell death could be responsible for the disappearance of myofibroblasts. We have now tested this hypothesis by means of morphometry at the electron microscopic level and by in situ end labeling of fragmented DNA. Our results indicate that the number of myofibroblastic and vascular cells undergoing apoptosis increases as the wound closes and support the assumption that this is the mechanism of granulation tissue evolution into a scar. The regulation of apoptotic phenomena during wound healing may be important in scar establishment and development of pathological scarring.
G protein-coupled signal transduction pathways for interleukin-8 (1993)

Interleukin-8 (IL-8) is one of the major mediators of the inflammatory response. The pathways by which IL-8 activates inositide-specific phospholipase C (PLC) were investigated by co-expression of different components of the guanosine triphosphate binding protein (G protein) pathway in COS-7 cells. Two distinct IL-8 receptors reconstituted ligand-dependent activation of endogenous PLC when transfected together with the G protein alpha subunits G alpha 14, G alpha 15, or G alpha 16. However, reconstitution was not observed with cells that overexpressed G alpha q or G alpha 11. Furthermore, IL-8 receptors interacted with endogenous pertussis toxin-sensitive G proteins or with the recombinant G protein Gi to release free beta gamma subunits that could then specifically activate the beta 2 isoform of PLC. These findings suggest that IL-8 acts through signal-transducing pathways that are limited to specific heterotrimeric G proteins and effectors. These may provide suitable targets for the development of anti-inflammatory agents.
Effect of protease inhibitors on angiotensin-converting enzyme activity in human T-lymphocytes (2000)

The purpose of these investigations was to determine whether the aminopeptidase B and leucine aminopeptidase inhibitor bestatin, the chymase inhibitor chymostatin, the calpain inhibitor E-64, and the neutral serine protease inhibitor leupeptin affect the angiotensin converting enzyme (ACE) activity in T-lymphocytes. ACE activity in homogenates of T-lymphocytes or in intact T-lymphocytes in suspension was measured by determining fluorimetrically histidyl-leucine, formed from the conversion of hippuryl-histidyl-leucine, coupled with ophtaldialdehyde. The effect of various concentrations (10(-9) to 10(-3) mol/L) of the angiotensin-converting enzyme inhibitors lisinopril and captopril and of the various protease inhibitors on ACE activity was studied. Lisinopril and captopril reduced the ACE activity in homogenates of T-lymphocytes in a concentration-dependent manner. Lisinopril exhibited a more pronounced inhibition of ACE in T-lymphocytes than did captopril. Chymostatin and E-64 had no effect on the ACE activity in T-lymphocytes, whereas leupeptin inhibited its activity in a dose-dependent fashion. Bestatin, on the contrary, increased the ACE activity in homogenates of T-lymphocytes as well as in intact T-lymphocytes in proportion to the concentration. Our data showed that the ACE activity in T-lymphocytes was stimulated by bestatin and inhibited by leupeptin, whereas chymostatin and E-64 did not affect the ACE activity in T-lymphocytes.
Transient Enol Isomers of Dibenzoylmethane and Avobenzone as Efficient Hydrogen Donors toward a Nitroxide Pre-fluorescent Probe† (2007)

Dibenzoylmethane and avobenzone photochemistry involves the formation of transient enol isomers (Z and E). Conjugation of the OH group with the carbonyl group in these transient isomers reduces the OH bond energy. A fast reduction of the pre-fluorescent probe (C343T) was observed after addition to photolysed DBM samples in nonpolar solvents. This can be attributed to a hydrogen transfer reaction from the transient E accumulated. While no quenching for Z by TEMPO was detected in the laser flash photolysis timescale. Theoretical calculations of spin densities distribution of the radical formed from Z and E showed a more delocalized distribution that would indicate a low reactivity towards oxygen. Our results suggest that DBM and avobenzone can effectively behave as photoantioxidants or photoactivated antioxidants under conditions where its enol isomers can be accumulated.
Generation of a Transplantable Erythropoietin-Producer Derived From Human Mesenchymal Stem Cells (2008)

Differentiation of autologous stem cells into functional transplantable tissue for organ regeneration is a promising regenerative therapeutic approach for cancer, diabetes, and many human diseases. Yet to be established, however, is differentiation into tissue capable of producing erythropoietin (EPO), which has a critical function in anemia. We report a novel EPO-producing organ-like structure (organoid) derived from human mesenchymal stem cells. Using our previously established relay culture system, a human mesenchymal stem cell-derived, human EPO-competent organoid was established in rat omentum. The organoid-derived levels of human EPO increased in response to anemia induced by rapid blood withdrawal. In addition, the presence of an organoid in rats suppressed for native (rat) EPO production enhanced recovery from anemia when compared with control animals lacking the organoid. Together these results confirmed the generation of a stem cell-derived organoid that is capable of producing EPO and sensitive to physiological regulation.
Urban agriculture : an opportunity for environmentally sustainable development in Sub-Saharan Africa (1996)

Urban agriculture (UA) can play an important role in sustaining sub-Saharan African (SSA) cities. Ranging from informal garden plots to large agribusiness corporations, UA can be an important source of food, fuel, and income. It can also promote natural resource conservation, and in some cases, better living conditions for urban populations, particularly the poor. This paper aims to examine how urban agricultural activities can contribute to sustainable development in SSA and how the Bank can expand its involvement in UA in the future. Chapter 1 discusses the nature and extent of UA world wide, and summarizes UA's role in sustainable development. Subsequent chapters examines urbanization trends in SSA and the nature and extent of urban agricultural activities in SSA (chapter 2). Key factors that constrain UA in Africa's urban and peri-urban areas (chapter 3), how the Bank has addressed UA (chapter 4), and the various means by which the Bank can promote or support UA as part of its strategy for sub-Saharan Africa (chapter 5).
3-Formylchromones, Acylpyruvates, and Chalcone as Valuable Substrates for the Syntheses of Fused Pyridines (2010)

The reaction of electron-rich aminoheterocycles with 1,3-CCC-dielectrophiles, such as 3-formylchromones, acylpyruvates, and chalcone, provided diversely fused pyridines. Starting from 5-amino-1-(2,3-O-isopropylidene-β-d-ribofuranosyl)-1H-pyrazole, nucleosides containing a pyrazolo[3,4-b]pyridine fragment were obtained, which can be considered as adenosine deaminase (ADA) inhibitors.
Extrafollicular CD4+ T-B interactions are sufficient for inducing autoimmune-like chronic graft-versus-host disease (2017)

Chronic graft-versus-host disease (cGVHD) is an autoimmune-like syndrome mediated by pathogenic CD4<sup>+</sup> T and B cells, but the function of extrafollicular and germinal center CD4<sup>+</sup> T and B interactions in cGVHD pathogenesis remains largely unknown. Here we show that extrafollicular CD4<sup>+</sup> T and B interactions are sufficient for inducing cGVHD, while germinal center formation is dispensable. The pathogenesis of cGVHD is associated with the expansion of extrafollicular CD44<sup>hi</sup>CD62<sup>lo</sup>PSGL-1<sup>lo</sup>CD4<sup>+</sup> (PSGL-1<sup>lo</sup>CD4<sup>+</sup>) T cells. These cells express high levels of ICOS, and the blockade of ICOS/ICOSL interaction prevents their expansion and ameliorates cGVHD. Expansion of PSGL-1<sup>lo</sup>CD4<sup>+</sup> T cells is also prevented by BCL6 or Stat3 deficiency in donor CD4<sup>+</sup> T cells, with the induction of cGVHD ameliorated by BCL6 deficiency and completely suppressed by Stat3 deficiency in donor CD4<sup>+</sup> T cells. These results support that Stat3- and BCL6-dependent extrafollicular CD4<sup>+</sup> T and B interactions play critical functions in the pathogenesis of cGVHD.Chronic graft-versus-host disease (cGVHD) is mediated by specific CD4 and B cells, but the relative contribution of extrafollicular and germinal centre (GC) T-B interaction is unclear. Here the authors show that the extrafollicular expansion of a specific CD4 T subset is sufficient for inducing cGVHD while GC is dispensable.