gebhart/patrepeval huggingface dataset:
First Report of Infection of Honeydew with Acidovorax avenae subsp. citrulli (1997)

Honeydew fruits (Cucumis melo var. inodorus Jacq. 'Morning Ice,' 'Honeybrew,' and 'Green Flesh') with circular, 3- to 10-mm-diameter lesions that did not extend into the flesh of the fruit were collected from a field in Frio County, TX, in October 1996. Lesions were either water-soaked or had a scabby center with a water-soaked edge. Non-fluorescent, gram-negative bacteria were consistently isolated from lesions. Eleven representative bacterial strains had 0.835 to 0.950 similarity to Acidovorax avenae subsp. citrulli, using Biolog GN Microplates and the MicroLog data base release 3.50 (Biolog, Hayward, CA). Strains were tested for pathogenicity on watermelon (C. lanatus (Thunb.) Matsum. & Nakai 'Royal Sweet') and honeydew seedlings (cv. Morning Ice) by daubing suspensions (approximately 10<sup>8</sup> CFU/ml) of bacteria onto cotyledons of 1-week-old transplants. Water soaking, followed by necrosis, occurred after 3 to 5 days. A. avenae subsp. citrulli, the causal agent of bacterial fruit blotch of watermelon, was reisolated from lesions. Detached fruit of honeydew (various cultivars) and watermelon (cv. Emperor) were surface disinfested with 70% ethanol, injected sub-epidermally with bacterial suspensions in blemish-free areas, and incubated at 24°C. Water-soaked lesions developed on fruit 10 to 14 days later and the bacteria were reisolated from inoculated fruit. Fruit inoculated with sterile water did not develop symptoms. Female flowers of honeydew plants (cv. Honeybrew) were inoculated at the time of pollination with a suspension of bacteria daubed on the fruit surface. Pollinated fruits were sealed in a moist chamber for 48 h. Circular, water-soaked spots developed 10 to 14 days later. A. avenae subsp. citrulli was reisolated from these lesions. The affected 44-ha field utilized center pivot irrigation and the incidence of diseased fruit exceeded 50%. The source of the pathogen is unknown. Bacterial fruit blotch was identified in watermelon grown under overhead irrigation 0.8 km from this honeydew field 9 weeks earlier. In past years, bacterial fruit blotch has occurred in watermelon fields in Frio County (1). Honeydew from other fields in the vicinity, including one that was also sprinkler irrigated, did not show these symptoms. This is the first report of A. avenae subsp. citrulli causing a disease of honeydew fruit. Reference: M. C. Black et al. Plant Dis. 78:831, 1994.
A soluble domain of the membrane-anchoring chain of influenza virus hemagglutinin (HA2) folds in Escherichia coli into the low-pH-induced conformation. (1995)

The extensive refolding of the membrane-anchoring chain of hemagglutinin (HA) of influenza virus (termed HA2) in cellular endosomes, which initiates viral entry by membrane fusion, suggests that viral HA is meta-stable. HA2 polypeptide residues 38-175 expressed in Escherichia coli are reported here to fold in vivo into a soluble trimer. The structure appears to be the same as the low-pH-induced conformation of viral HA2 by alpha-helical content, thermodynamic stability, protease dissection, electron microscopy, and antibody binding. These results provide evidence that the structure of the low-pH-induced fold of viral HA2 (TBHA2) observed crystallographically is the lowest-energy-state fold of the HA2 polypeptide. They indicate that the HA2 conformation in viral HA before low pH activation of its fusion potential is metastable and suggest that removal of the receptor-binding chain (HA1) is enough to allow HA2 to adopt the stable state. Further, they provide direct evidence that low pH is not required to form the membrane-fusion conformation but acts to make this state kinetically accessible in viral HA.
LIVE, ORALLY GIVEN POLIOVIRUS VACCINE (1960)

The phenomenon of viral interference must be taken into account in planning the use of live poliovirus vaccine in areas where conditions favor the extensive dissemination of naturally occurring polioviruses. Experience with feeding a trivalent vaccine to 26,033 children in a tropical city of 100, 000 population led to the conclusion that interference was overcome by mass feeding of vaccine to 86% of all children under 11 years within a period of about four days, and that, because dissemination of the poliovirus was self-limited, a second feeding of trivalent vaccine was necessary to achieve immunization of almost all children. Recommendations are here formulated for the eradication of poliomyelitis, but they apply only to subtropical and tropical regions with extensive dissemination of various enteric viruses and not to temperate zones with good sanitation and hygiene during certain periods of the year and under conditions of low or absent dissemination of enteric viruses.
Linear coupling between cerebral blood flow and oxygen consumption in activated human cortex (1999)

The aim of this study was to test the hypothesis that, within a specific cortical unit, fractional changes in cerebral blood flow (CBF) and cerebral metabolic rate of oxygen consumption (CMR(O(2))) are coupled through an invariant relationship during physiological stimulation. This aim was achieved by simultaneously measuring relative changes in these quantities in human primary visual cortex (V1) during graded stimulation with patterns designed to selectively activate different populations of V1 neurons. Primary visual cortex was delineated individually in each subject by using phase-encoded retinotopic mapping. Flow-sensitive alternating inversion recovery MRI, in conjunction with blood oxygenation-sensitive MRI and hypercapnic calibration, was used to monitor CBF and CMR(O(2)). The stimuli used included (i) diffuse isoluminant chromatic displays; (ii) high spatial-frequency achromatic luminance gratings; and (iii) radial checkerboard patterns containing both color and luminance contrast modulated at different temporal rates. Perfusion responses to each pattern were graded by varying luminance and/or color modulation amplitudes. For all stimulus types, fractional changes in blood flow and oxygen uptake were found to be linearly coupled in a consistent ratio of approximately 2:1. The most potent stimulus produced CBF and CMR(O(2)) increases of 48 +/- 5% and 25 +/- 4%, respectively, with no evidence of a plateau for oxygen consumption. Estimation of aerobic ATP yields from the observed CMR(O(2)) increases and comparison with the maximum possible anaerobic ATP contribution indicate that elevated energy demands during brain activation are met largely through oxidative metabolism.
Biosynthesis of the Peptidoglycan of Bacterial Cell Walls (1970)

Abstract A particulate d-alanine carboxypeptidase present in Bacillus subtilis has been studied. This enzyme has a pH optimum near 5, and is activated by Zn+2 cations. The enzyme is inactivated by penicillin G and activity cannot be restored by washing or by treating it with penicillinase. 14C-Penicillin G is also bound to this particulate enzyme. Both the binding of penicillin G and the inactivation of the carboxypeptidase by penicillin G are reversed by treatment with neutral hydroxylamine, and the kinetics of these two processes is identical. d-Alanine carboxypeptidase activity is also inhibited by sulfhydryl reagents such as iodoacetate in a manner similar to their inhibition of penicillin binding. The possibility that the particulate d-alanine carboxypeptidase may be an uncoupled transpeptidase is discussed.
Extracellular Matrix Composition and Remodeling in Human Abdominal Aortic Aneurysms: A Proteomics Approach (2011)

Abdominal aortic aneurysms (AAA) are characterized by pathological remodeling of the aortic extracellular matrix (ECM). However, besides the well-characterized elastolysis and collagenolysis little is known about changes in other ECM proteins. Previous proteomics studies on AAA focused on cellular changes without emphasis on the ECM. In the present study, ECM proteins and their degradation products were selectively extracted from aneurysmal and control aortas using a solubility-based subfractionation methodology and analyzed by gel-liquid chromatography-tandem MS and label-free quantitation. The proteomics analysis revealed novel changes in the ECM of AAA, including increased expression as well as degradation of collagen XII, thrombospondin 2, aortic carboxypeptidase-like protein, periostin, fibronectin and tenascin. Proteomics also confirmed the accumulation of macrophage metalloelastase (MMP-12). Incubation of control aortic tissue with recombinant MMP-12 resulted in the extensive fragmentation of these glycoproteins, most of which are novel substrates of MMP-12. In conclusion, our proteomics methodology allowed the first detailed analysis of the ECM in AAA and identified markers of pathological ECM remodeling related to MMP-12 activity.
Isolation of a cell surface receptor protein for laminin from murine fibrosarcoma cells. (1983)

We used affinity chromatography to isolate a specific laminin-binding protein from murine fibrosarcoma cells. These cells bind exogenous laminin to their surface with high affinity (Kd = 2 X 10(-9)M for laminin) with approximately 5 X 10(4) sites per cell. Laminin affinity chromatography of [35S]methionine-labeled cell extracts produced two distinct proteins. One was identified as Type IV (basement membrane) collagen based on its migration pattern on SDS gels and bacterial collagenase sensitivity. The other protein, which migrates as a single band or closely spaced doublet on reduced SDS gels, has a reduced molecular weight of 69,000. Using a nitrocellulose filter disk assay, we found that the latter protein specifically bound 125I-laminin with the same high affinity (Kd = 2 X 10(-9)M for laminin) as did intact fibrosarcoma cells. By iodinating intact cells, we demonstrated that this laminin-binding protein is on the cell surface. We conclude that this protein with reduced molecular weight of 69,000 is a subunit or component of a larger cell surface receptor protein for laminin in this fibrosarcoma model. This laminin receptor may mediate the interaction of the cell with its extracellular matrix.
Finite amplitude distortion-based inhomogeneous pulse echo ultrasonic imaging (1997)

Ultrasonic pulse echo imaging in inhomogeneous media suffers from significant lateral and contrast resolution losses due to the defocusing effects of the inhomogeneities. The losses in lateral and contrast resolution are associated with increases in the width of the mainbeam and increases in sidelobe levels, respectively. These two forms of resolution loss represent significant hurdles to improving the clinical utility of biomedical ultrasonic imaging. A number of research efforts are currently under way to investigate the defocusing effects of tissue and to consider corrective measures. All of these efforts assume linear propagation, and base the image-formation process on the reception of the transmitted pulse. A novel pulse echo imaging scheme in which the image is formed using the finite amplitude distortion components of the received pulse is considered here. Alternatively, this could be described as image formation using the nonlinearly-generated higher harmonics. In homogeneous beam propagations, it has been established that the sidelobes of nonlinearly-generated higher harmonics are much lower than their linear counterparts. Computations considered here suggest that this relationship also holds for the case of propagations through abdominal wall and breast wall tissue. These computations also suggest that the lateral resolution limits imposed by abdominal wall and breast wall tissue are slightly smaller for nonlinearly-generated second harmonics than for their linear counterparts. The resulting potential of these higher harmonics to improve image resolution is investigated.
Antigen‐specific B cell detection reagents: Use and quality control (2008)

Tests for immunoglobulin reactivity with specific antigens are some of the oldest and most used assays in immunology. With efforts to understand B cell development, B cell dysregulation in autoimmunity, and to generate B cell vaccines for infectious agents, investigators have found the need to understand the ontogeny and regulation of epitope-specific B cell responses. The synchrony between surface and secreted antibodies for individual B cells has led to the development of reagents and techniques to identify antigen-specific B cells via reagent interactions with the B cell receptor complex. B cell antigen-specific reagents have been reported for model systems of haptens, for whole proteins, and for identification of double stranded (ds) DNA antibody-producing B cells using peptide mimics. Here we provide an overview of reported techniques for the detection of antigen-specific B cell responses via secreted antibody or by the surface B cell receptor and briefly discuss our recent work developing a panel of reagents to probe the B cell response to HIV-1 envelope. We also present an analysis of strengths and weaknesses of various methods for flow cytometric analysis of antigen-specific B cells.
Abstract 5414: Macrophage Migration Inhibitory Factor Inhibits C-jun N Terminal Kinase And Prevents Cardiac Injury During Acute Ischemia Reperfusion (2008)

Macrophage migration inhibitory factor (MIF) is a pro-inflammatory cytokine, which is expressed in multiple organs including the heart. Plasma MIF is elevated after myocardial infarction. MIF is released from the heart during ischemia and has an autocrine/paracrine effect to positively modulate AMP-activated protein kinase (AMPK). Genetic deficiency in MIF (MIF−/−) attenuates AMPK activation, leading to cardiac dysfunction and injury during ischemia/reperfusion (IR). MIF also inhibits c-Jun N-terminal kinase (JNK) activation in HeLa cells, but its action in the heart is not known. In Langendorff perfused WT hearts, MIF content was reduced after global ischemia (15 min) and reperfusion (30 min). JNK activation and downstream c-Jun phosphorylation were greater (p in viv o augmented MKK4, JNK and c-Jun phosphorylation in MIF−/− vs. WT mice. MIF−/− hearts showed more necrosis on TTC staining after LAD occlusion and reperfusion than WT. Increased cardiac injury following IR was associated with less BAD phosphorylation and more cellular apoptosis in MIF−/− hearts. Administration of SP600125 (1mg/kg, IP) prior to ischemia also limited injury in MIF−/− mice. In vitro studies showed that the JNK activator, anisomycin, stimulated the JNK pathway in H9C2 cells in a dose-dependent manner and MIF (50 ng/ml) inhibited anisomycin-activation of MKK4, JNK, and c-Jun. Thus, cardiac-derived MIF inhibits activation of the JNK pathway, which may protect the heart from injury following IR. This research has received full or partial funding support from the American Heart Association, AHA Founders Affiliate (Connecticut, Maine, Massachusetts, New Hampshire, New Jersey, New York, Rhode Island, Vermont).
X-tolerant signature analysis (2005)

Stochastic coding is used to design X-tolerant signature analyzers that can detect defective chips even in the presence of unknown logic values (X's). These signature analyzers can be used for built-in-self-test applications and test data compression. Application of this technique to industrial designs shows that thousands of X's can be tolerated while reducing test response data volume by 50 to 2,000 times compared to traditional scan, with practically no impact on test quality.
Current status and prospects of studies on human genetic alleles associated with hepatitis B virus infection (2003)

Chronic hepatitis B virus (HBV) infection can cause a broad spectrum diseases, including from asymptomatic HBV carriers or cryptic hepatitis, to acute hepatitis, chronic hepatitis, Liver cirrhosis and primary hepatocellular carcinoma. The variable pattern and clinical outcome of the infection were mainly determined by virological itself factors, host immunological factors and genetic factors as well as the experimental factors. Among the human genetic factors, major candidate or identified genes involved in the process of HBV infection fall into the following categories: (1) genes that mediate the processes of viral entry into hepatocytes, including genes involved in viral binding, fusion with cellular membrane and transportation in target cells; (2) genes that modulate or control the immune response to HBV infection; (3) genes that participate in the pathological alterations in liver tissue; (4) genes involved in the development of liver cirrhosis and hepatocellular carcinoma associated with chronic HBV infection, including genes related to mother-to-infant transmission of HBV infection; and (5) those that contribute to resistance to antiviral therapies. Most of the reports of human genes associated with HBV infection have currently focused on HLA associations. For example, some investigators reported the association of the HLA class II alleles such as DRB1*1302 or HLA-DR13 or DQA1*0501-DQB1*0301-DQB1*1102 haplotypes with acute and/or chronic hepatitis B virus infection, respectively. Several pro-inflammatory cytokines such as Th1 cytokines (including IL-2 and IFN-gamma) and TNF-alpha have been identified to participate the process of viral clearance and host immune response to HBV. In contrast, the Th2 cytokine IL-10 serves as a potent inhibitor of Th1 effector cells in HBV diseases. The MBP polymorphisms in its encoding region were found to be involved in chronic infection. Thus, reports from various laboratories have shown some inconsistencies with regard to the effects of host genetic factors on HBV clearance and persistence. Since genetic interactions are complex, it is unlikely that a single allelic variant is responsible for HBV resistance or susceptibility. However, the collective influence of several single nucleotide polymorphisms (SNPs) or haplotype (s) may underlie the natural combinational or synergistic protection against HBV. The future study including the multi-cohort collaboration will be needed to clarify these preliminary associations and identify other potential candidate genes. The ongoing study of the distributions and functions of the implicated allele polymorphisms will not only provide insight into the pathogenesis of HBV infection, but may also provide a novel rationale for new methods of diagnosis and therapeutic strategies.
BUCCAL MUCOSAL X-CHROMATIN FREQUENCY AND PREGNANCY (1996)

International audience
Effects of Diffusion on Free Precession in Nuclear Magnetic Resonance Experiments (1954)

Nuclear resonance techniques involving free precession are examined, and, in particular, a convenient variation of Hahn's spin-echo method is described. This variation employs a combination of pulses of different intensity or duration ("90-degree" and "180-degree" pulses). Measurements of the transverse relaxation time ${T}_{2}$ in fluids are often severely compromised by molecular diffusion. Hahn's analysis of the effect of diffusion is reformulated and extended, and a new scheme for measuring ${T}_{2}$ is described which, as predicted by the extended theory, largely circumvents the diffusion effect. On the other hand, the free precession technique, applied in a different way, permits a direct measurement of the molecular self-diffusion constant in suitable fluids. A measurement of the self-diffusion constant of water at 25\ifmmode^\circ\else\textdegree\fi{}C is described which yields $D=2.5(\ifmmode\pm\else\textpm\fi{}0.3)\ifmmode\times\else\texttimes\fi{}{10}^{\ensuremath{-}5}$ ${\mathrm{cm}}^{2}$/sec, in good agreement with previous determinations. An analysis of the effect of convection on free precession is also given. A null method for measuring the longitudinal relaxation time ${T}_{1}$, based on the unequal-pulse technique, is described.
The Single Frame Stereo Vision System for Reliable Obstacle Detection Used during the 2005 DARPA Grand Challenge on TerraMax (2006)

Autonomous driving in off-road environments requires an exceptionally capable sensor system, especially given that the unstructured environment does not provide many of the cues available in on-road environments. This paper presents a variable-width-baseline (up to 1.5 meters) single-frame stereo vision system for obstacle detection that can meet the needs of autonomous navigation in extreme environments. Efforts to maximize computational speed <b xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">o</b> th in the attention given to accurate and stable calibration and the exploitation of the processors MMX and SSE instruction sets - allow a guaranteed 15 fps rate. Along with the assured speed, the system proves very robust against false positives. The system has been field tested on the TerraMax vehicle, one of only five vehicles to complete the 2005 DARPA Grand Challenge course and the only one to do so using a vision system for obstacle detection
Mitotic Activity in Expanded Human Skin (1993)

In 20 patients subjected to breast reconstruction by means of tissue expansion, a skin biopsy was obtained at the vertex of the breast before and the day after expansion. Samples were incubated in [3H]thymidine, and the number of labeled cells were counted. A statistically significant rise in the number of labeled basal and supra-basal keratinocytes was seen after expansion. The findings suggest a net gain of tissue not only by stretching but also by formation of new tissue generated by tissue expansion.
Binding of Submaximal C1q Promotes Complement-Dependent Cytotoxicity (CDC) of B Cells Opsonized with Anti-CD20 mAbs Ofatumumab (OFA) or Rituximab (RTX): Considerably Higher Levels of CDC Are Induced by OFA than by RTX (2009)

The CD20 mAb ofatumumab (OFA) is more effective than rituximab (RTX) in promoting complement-dependent cytotoxicity (CDC) of B cells via the classical pathway (CP) of complement. CP activation is initiated by C1q binding to cell-bound IgG. Therefore, we examined the role of C1q in the dynamics of complement activation and CDC of B cell lines and primary cells from patients with chronic lymphocytic leukemia, reacted with OFA or RTX. C1q binding, complement activation, and colocalization of C1q with cell-bound mAbs were determined by flow cytometry and high-resolution digital imaging. C1q binds avidly to OFA-opsonized Raji and Daudi cells (K(D) = 12-16 nM) and colocalizes substantially with cell-bound OFA. Cells opsonized with OFA undergo high levels of complement activation and CDC in C1q-depleted serum supplemented with low concentrations of C1q. Under comparable conditions, RTX-opsonized cells bind less C1q; in addition, even when higher concentrations of C1q are used to achieve comparable C1q binding to RTX-opsonized cells, less complement activation and CDC are observed. Greater CDC induced by OFA may occur because C1q is bound in close proximity and with high avidity to OFA, resulting in effective CP activation. Moreover, OFA binds to the small, extracellular CD20 loop, placing the mAb considerably closer to the cell membrane than does RTX. This may facilitate effective capture and concentration of activated complement components closer to the cell membrane, potentially shielding them from inactivation by fluid phase agents and promoting efficient generation of the membrane attack complex.