gebhart/patrepeval huggingface dataset:
Endothelial Cells Recruit Macrophages and Contribute to a Fibrotic Milieu in Bleomycin Lung Injury (2013)

Systemic sclerosis (SSc) is a systemic autoimmune disease that causes inflammation, vasculopathy, and fibrosis of the skin and internal organs. One of the most severe complications of SSc involves the development of pulmonary fibrosis. Endothelial cell injury precedes the development of fibrosis, and is believed to be an initiating event. Therefore, we aimed to characterize the role of endothelial cells in the progression of pulmonary fibrosis, using a well-established bleomycin (BLM) model of pulmonary fibrosis. Endothelial cells were isolated by cell sorting, and the analysis of gene expression was performed with quantitative RT-PCR. Endothelial injury was induced between the first and second week, as shown by the elevated expression of the vascular injury markers matrix metallopeptidase-12 and von Willebrand factor. After injury, endothelial activation was indicated by the up-regulation of selectins, CCL chemokines, and inflammatory mediators, including complement anaphylatoxin receptors (C3aR and C5aR), oncostatin M, and leukemia inhibitory factor. The endothelial cell overexpression of fibrotic mediators, including connective tissue growth factor, plasminogen activator inhibitor-1, osteopontin, fibronectin, and fibroblast specific protein-1, was observed in the second and fourth weeks. This study suggests that endothelial cells actively contribute to the disease process via multiple mechanisms, including the recruitment of inflammatory cells and the establishment of a profibrotic environment during the development of BLM-induced pulmonary fibrosis.
An Assessment of the Potential to Produce Commercially Valuable Lipids on Highway Right-of-Way Land Areas Located Within the Southeastern United States (2020)

Right-of-way (ROW) land areas are required for all publicly owned transportation roadways representing over 40 million acres within the US alone. These relatively unused land assets could support potential farming land for plants and algae that contain high levels of lipids that could be used in the energy industry as an alternative fuel source. This process would offer many benefits including more efficient use of public land, eliminating mowing maintenance, increasing the bioenergy use in the US, providing visually appealing viewscapes, and helping to naturally reduce localized carbon dioxide. This paper analyzed the feasibility and potential optimization strategies of using this concept in the South-Eastern United States by scaling and comparing many of the benefits and risks associated with the selected lipid sources (soybeans, flax, sunflowers, Tung trees, Chinese tallow tree, and microalgae). Based on this assessment, the most attractive option appears to be growing flax in the winter and sunflowers in the summer with Tung Trees grown year-round as an alternative option. This would maximize lipids output while preserving and enhancing right-of-way land areas.
A Gene Trap Strategy for Identifying the Gene Expressed in the Embryonic Nervous System (1996)

An efficient gene trap strategy was devised for identifying the genes that are expressed in the mouse developing nervous system. Mouse embryonic stem (ES) cell lines that carried independent integrations of a gene trap vector, pSneolN/acZA, were allowed to differentiate in a suspension culture system. To select cells containing neurons, astrocytes or neuron-glia precursors, cell lines were immunohistochemically examined with antibodies against neuron-specific proteins (neurofilament protein 150 kD and microtubule associated protein 2), glial fibrillary acidic protein or nestin. Three cell clones (GT3-8, 11 and 12) were immunoreactive to either of the antibodies employed and at the same time positive for beta-galactosidase activity. When chimeric embryos were generated by the use of the above 3 cell lines, some cells in their nervous system showed X-gal staining. Thus the major advantage of the present gene trap method lies in its prescreening step of manipulated ES cells prior to generation of chimeric animals. This method holds promise as a useful tool for investigating the genes involved in the development of the nervous system.
Quantitative analysis of spiral ganglion projections to the cat cochlear nucleus (1997)

A quantitative examination of the tonotopic organization of primary afferent projections to the cochlear nucleus (CN) in adult cats was conducted by using focal extracellular injections of Neurobiotin (NB) into the spiral ganglion of the basal cochlea. One to three injections separated by intervals of at least 2 mm were positioned along the basal one-third of the cochlea. Each injection produced discrete projection laminae that appeared as parallel horizontal sheets of labeled axons terminals distributed sequentially dorsally to ventrally across each major CN subdivision: the anteroventral, posteroventral, and dorsal cochlear nucleus, (AVCN, PVCN, and DCN, respectively). The length (rostrocaudal dimension), width (mediolateral dimension), thickness (dorsoventral dimension), and relative placement of 18 "frequency-band" laminae were measured in 10 adult cochlear nuclei. The average AVCN projection thickness was approximately twice that of the PVCN and DCN projections. In double injection cases, the center-to-center separation between AVCN laminae was also approximately twice that in the PVCN and equal to that in the DCN. Lamina thickness did not differ significantly as a function of frequency representation. However, in both width and length, mid-frequency laminae were up to two times larger than high-frequency laminae. Thus, the results indicate that DCN projections are the most discrete (i.e., are the thinnest and have the least overlap between adjacent frequency projections), whereas the AVCN projections are the largest but are as discrete as PVCN projections. In addition, high-frequency projections are smaller and more discrete than mild-frequency projections, which are larger and have greater overlap with adjacent frequency projections.
Immune recognition of fungal β-glucans (2005)

The recognition of conserved microbial structures is a key aspect of metazoan immunity, and beta-glucans are emerging as a major target for the recognition of fungal pathogens. A number of receptors for these carbohydrates have been identified, which upon recognition, trigger a variety of immune responses. In contrast to many other systems, there is little apparent conservation in these mechanisms between vertebrates and invertebrates. In this review, we will highlight all the known receptors for beta-glucans and will discuss the various immune responses they can initiate, with reference to fungal infection, in both vertebrates and invertebrates.
Amlodipine reduces cyclosporin-induced hyperuricaemia in hypertensive renal transplant recipients (2003)

Amlodipine could be more appropriate than tertatolol for CsA-induced hypertension and hyperuricaemia in renal transplant recipients.
Anti-oxidative Effect of Kojic Acid Derivatives. I. (1970)

It seems very interesting to study antioxidative effect of kojic acid and its related compounds which are non-toxic. As to the oxidation inhibiting activities of kojic acid and palmitoyl kojic acid, it was found that they were almost ineffective against oxidation of corn oil by Anderson et al. This report presents the results of oxidation inhibiting tests of O-acyl kojic acid and alkyl kojic acid obtained from the oxidation of lard, whale and soybean oils.Introduction of acyl or alkyl groups into kojic acid increases its solubility in oil. The tested acyl groups are butyroil, capryloyl and lauroyl while alkyl groups are butyl, capryl and lauryl (Table-1, 2). Their antioxidative effects for experimented oils are compared by the A.O.M. or Schaal oxidative tests as summarized in Fig.-1, 2.
H2‐D2 exchange reaction with MgCl2‐supported Ziegler catalyst by stopped‐flow method (1996)

Abstract The effect of hydrogen on the chain transfer reaction in the initial stage of propene polymerization with MgCl 2 ‐supported Ziegler catalyst was studied through H 2 ‐D 2 exchange reaction using the stopped‐flow method. When the exchange reaction was carried out with various catalyst components at room temperature for 5 min, HD was produced only in case of using the catalyst with Al(C 2 H 5 ) 3 . In case of the stopped‐flow method (reaction time ca. 0.1 s), the catalyst without pre‐treatment with Al(C 2 H 5 ) 3 showed no activity for the H 2 ‐D 2 exchange reaction (no HD produced), while the catalyst with pre‐treatment had exchange activity. As the chain transfer activity of H 2 in propene polymerization shows the same tendency, it is evident that chain transfer with H 2 occurs via atomic hydrogen generated on the pre‐treated catalyst.
EP50* Catheter tip distensibility substantially influences the aspiration force of thrombectomy devices (2021)

<h3>Introduction</h3> A direct aspiration first pass thrombectomy is a fast-growing technique for which a broad catalog of catheters that provide a wide range of aspiration forces can be used. <h3>Objectives</h3> To characterize different catheters´ aspiration performance on stiff clots in an in vitro vascular model. <h3>Aims</h3> To demonstrate that labeled catheter inner diameter (labeled-ID) is not the only parameter that affects the aspiration force (asp-F) and that thrombus-catheter tip interaction and distensibility also play a major role. <h3>Methods</h3> We designed an experimental setup consisting of a 3D-printed carotid artery immersed in water. We measured asp-F and distensibility of catheter tips when performing ADAPT on a stiff clot analog larger than catheter labeled-ID. Correlations between asp-F, catheter ID, and tip distensibility were statistically assessed. <h3>Results</h3> Experimental asp-F and catheter labeled-ID were correlated (r=0.9601; P&lt;0.01). The relative difference between experimental and theoretical asp-F (obtained by the product of the tip’s section area by the vacuum pressure) correlated with tip’s distensibility (r=0.9050; P&lt;0.01), evidencing that ADAPT performance is highly influenced by catheter tip shape-adaptability to the clot and that the effective ID (eff-ID) may differ from the labeled-ID specified by manufacturers. Eff-ID showed the highest correlation with experimental asp-F (r=0.9944; P&lt;0.01), confirming that eff-ID rather than labeled-ID should be considered to better estimate the device efficiency. <h3>Conclusions</h3> Catheter tip distensibility can induce a significant impact on ADAPT performance when retrieving a stiff clot larger than the device ID. Our findings might contribute to optimizing thrombectomy strategies. <h3>References</h3> Spiotta AM, Fargen KM, Chaudry MI, Turner R, Turk AS. ADAPT: a direct aspiration first pass technique. <i>Stroke</i> 2016;<b>15</b>(2):68–70. Froehler MT. Comparison of vacuum pressures and forces generated by different catheters and pumps for aspiration thrombectomy in acute ischemic stroke. <i>Interv Neurol</i> 2017;<b>6</b>(3–4):199–206. doi: 10.1159/000475478 Yaeger K, <i>et al</i>. A technical comparison of thrombectomy vacuum aspiration systems. J Neurointerv Surg 2020;<b>12</b>(1):72–76. doi:10.1136/neurintsurg-2019–014929 <h3>Disclosure</h3> Nothing to disclose
Pharmacokinetic analysis of new synthetic antimalarial N-251 (2019)

N-251 has been selected as a potent antimalarial candidate. We found that N-251 showed short half-life in plasma, and AUCs increased proportionally to dose. With multiple doses of N-251, the plasma level of N-251 was greater than 10 ng/mL in normal-fed mice, and accumulation of N-251 was not observed; however, multiple treatments with N-251 are required for the complete cure of parasite-infected mice. Determining the appropriate dosage was an important step in the clinical applications of N-251.
TISSUE THROMBOMODULIN CORRELATES WITH LUNG INJURY IN A RAT MODEL OF ARDS (1999)

s Of Papers To Be Presented At The Fifty-Ninth Annual Meeting Of The American Association For The Surgery Of Trauma; Marriott Copley Place Hotel, Boston, Massachusetts; September 16-18, 1999
Reaction dynamics studied via positron and electron spectroscopy (1986)

The dynamics of collisions between very heavy ions have been studied via their influence on the positron and \ensuremath{\delta}-electron spectra using the Tori spectrometer, a new magnetic transport system which is able to measure positrons and electrons simultaneously. The spectra obtained in coincidence with elastic scattering agree well at all measured energies with theory based on Rutherford trajectories, while a steeper slope is observed in spectra measured in coincidence with dissipative collisions. These spectra can only be described by calculations taking into account a nuclear contact time of up to 2\ifmmode\times\else\texttimes\fi{}${10}^{\mathrm{\ensuremath{-}}21}$ s in the collision process.
Selective Inhibition of Dipeptidyl Peptidase I, Not Caspases, Prevents the Partial Processing of Procaspase-3 in CD3-activated Human CD8+ T Lymphocytes (2002)

Activation of primary human T cells by anti-CD3 and interleukin-2 resulted in partial processing of procaspase-3 in activated nonapoptotic (Delta Psi(m)high) CD8(+) T cells but not in CD4(+) T cells. Apical caspases-8 and -9 were not activated, and Bid was not processed to truncated Bid. Boc-D.fmk, a broad spectrum caspase inhibitor, did not prevent this process, whereas GF.dmk, a selective inhibitor of dipeptidyl peptidase I, was effective. Dipeptidyl peptidase I is required for the activation of granule-associated serine proteases. It is enriched in the cytolytic granules of cytotoxic lymphocytes, where it promotes the proteolytic activation of progranzymes A and B. Inhibition of granzyme B (GrB)-like serine proteases by Z-AAD.cmk prevented partial processing of procapase-3, whereas inhibition of GrA activity by D-FPR.cmk had no effect. Specific inhibitors of other lysosomal proteases such as cathepsins B, L, and D did not interfere in this event. Patients with Chediak-Higashi syndrome or with perforin deficiency also displayed partial processing of procaspase-3, excluding the involvement of granule exocytosis for the delivery of the serine protease in cause. The p20/p12 processing pattern of procaspase-3 in our model points to GrB, the sole serine protease with caspase activity. Small amounts of GrB were indeed exported from cytolytic granules to the cytosol of a significant fraction of GrB-positive cells.
Tropical and Extratropical Influences on the Variability of the Southern Hemisphere Wintertime Subtropical Jet (2021)

Abstract Interannual variability of the Southern Hemisphere subtropical jet (STJ) is assessed using atmospheric reanalyses during 1979–2018. The focus is on the austral winter season when the STJ is strongest and most distinct from the midlatitude eddy-driven jet (EDJ). Variations in the intensity and latitudinal position of the STJ are diagnosed using an index developed to discriminate between variations associated with the EDJ. STJ intensity and position variations are found to be tied to different mechanisms. An intensification of the STJ is associated with enhanced divergent outflow from diabatic heating over the equatorial Pacific Ocean, primarily resulting from eastern Pacific or canonical El Niño. This intensification is associated with a narrowing of the STJ and an in-place weakening of the EDJ. An equatorward-shifted STJ, however, appears to be eddy driven and is associated with an acceleration and poleward displacement of the EDJ, which projects onto the positive polarity of the southern annular mode. As has previously been reported, El Niño Modoki (or central Pacific El Niño) can act to shift the EDJ poleward during austral winter; thus, a possible pathway for changes in the position of the STJ is via tropically forced changes in the position of the EDJ. In contrast to previous studies, we also highlight a weakening and poleward shift of the STJ in association with an expansion of the Hadley circulation.
Complement activation on a model biomaterial surface: Binding of C3b via the alternative amplification loop to plasma proteins adsorbed to the surface (2005)

Complement activation on a model biomaterial surface: Binding of C3b via the alternative amplification loop to plasma proteins adsorbed to the surface
Quantitative HAADF Imaging of Crystals Containing Heavy Elements: A Comparison with Theory (2009)

Extended abstract of a paper presented at Microscopy and Microanalysis 2009 in Richmond, Virginia, USA, July 26 – July 30, 2009
Positive Darwinian selection is a driving force for the diversification of terpenoid biosynthesis in the genus Oryza (2014)

In this study, we found that positive Darwinian selection is a driving force for the functional divergence of OryzaTPS1. This finding suggests that the diverged sesquiterpene blend produced by the Oryza species containing DAS may be adaptive, likely in the attraction of the natural enemies of insect herbivores.
Alterations in the Immunohistochemical Expression of Das-1 and CG-3 in Colonic Mucosal Biopsy Specimens Helps Distinguish Ulcerative Colitis From Crohn Disease and From Other Forms of Colitis (2008)

Distinction between ulcerative colitis (UC) and Crohn disease (CD) in mucosal biopsies is often difficult. Das-1 and CG-3 are monoclonal antibodies directed against an unknown colonic epithelial protein and human tropomyosin isoform-5, respectively, both show altered expression in patients with UC. In this study, we evaluated the utility of Das-1 and CG-3 in distinguishing UC from CD and from other types of colitis. One colonic biopsy specimen from each of 85 patients with confirmed UC (n=25), CD (n=15), lymphocytic (n=15), collagenous (n=15), and ischemic (n=15) colitis, and also 10 samples from normal controls, were stained for Das-1 and CG-3 using standard techniques. Reactivity for Das-1 and CG-3 was noted to be absent or present, and the location (ie, surface+/-crypt epithelium) and degree (weak or strong) of CG-3 staining was recorded. Loss of Das-1 staining occurred more frequently in UC (96%) compared with CD (20%), lymphocytic (20%), collagenous (13%), and ischemic colitis (0%) cases, as well as controls (10%, P<0.001 for all comparisons). CG-3 positivity in crypt epithelium was significantly more common in UC (52%) compared with the other groups (P< or =0.02 for all comparisons). The combination of strong crypt CG-3 staining and loss of Das-1 staining was noted in 44% of UC cases, but not in any other type of colitis (P=0.003 for all comparisons). We conclude that the patterns of Das-1 and CG-3 staining in colonic mucosal biopsies may be clinically useful in distinguishing UC from CD and from other colitidies.
De novo CD5‐positive primary cardiac diffuse large B‐cell lymphoma diagnosed by pleural fluid cytology (2012)

Primary cardiac lymphomas are exceedingly rare. The presence and extent of the intracardiac mass is determined by echocardiography, computed tomography (CT), or magnetic resonance imaging (MRI); however, the diagnosis is established by endomyocardial biopsy or by pericardial or pleural effusion cytology. We describe the pleural effusion cytologic features of a primary cardiac lymphoma in a 55-year-old woman who presented with progressive shortness of breath, fatigue, mild dizziness, dull chest ache, and lower extremity edema. Transthoracic echocardiography, CT, and MRI showed a large mass centered in the right atrium and extending into the right ventricle, associated with pericardial effusion and bilateral pleural effusions. Cytologic examination of the pleural fluid showed very large pleomorphic malignant cell, some of which were binucleated and multinucleated and had anaplastic features. Flow cytometry showed a kappa monotypic population of large cells coexpressing CD5, CD19, and CD20; and immunoperoxidase stains performed on the cell block sections showed that the large neoplastic cells were positive for CD20, PAX5, CD5, and MUM1 and showed a very high proliferation rate (over 90%) by Ki67 staining. The cytologic, flow cytometry, and immunohistochemistry findings established the diagnosis of de novo CD5-positive primary cardiac diffuse large B-cell lymphoma (DLBCL), anaplastic variant, which was confirmed by the subsequent endomyocardial biopsy. This is, to the best of our knowledge, the first report of de novo CD5-positive primary cardiac diffuse large B-cell lymphoma, and the first report of the anaplastic variant of DLBCL diagnosed by effusion cytology.
Response to Richard Rosen (2021)

Global economic production, or the GDP, has risen steadily relative to world primary energy demands, suggesting technological change is driving a gradual decoupling of society from its resource needs and associated pollution. Here show that in each of the 50 years following 1970 for which reliable data are available, one Exajoule of world energy was consumed to sustain each 5.50 ± 0.21 trillion constant 2019 US dollars, not of yearly production or physical capital, but of running cumulative production summed over human history. The half-century for which this fixed ratio held covers two thirds of historical growth in energy demands, so assuming its persistence, the implication is that society is not in fact decoupling from resource needs. Rather, it can be expected that future environmental impacts will be more strongly guided by past activities, or inertia, than is generally permitted within economic and climate modeling prescriptions that allow for policy to spur more rapid change.
Effects of aged garlic extract (AGE) on colorectal adenomas: a double-blinded study. (2004)

Aged garlic extract (AGE) is a material that has the possibility of a cancer-preventive effect according to epidemiologic and animal studies. In order to confirm the effects of AGE on colorectal adenomas, we conducted a double-blinded randomized study using high-AGE (AGE 2.4 ml/day) and low-AGE (AGE 0.16 ml/day) doses 1 groups. Fifty-one patients who were diagnosed as having colorectal adenomas by colonoscopy were randomly assigned to the high-AGE and low-AGE groups. The number and size of adenomas before intake (0 month) and 6 and 12 months after intake were measured using colonoscopy. In 37 patients chosen as efficacy evaluated subjects, 47.4% (9/19) in the high-AGE and 66.7% (12/18) in the low-AGE group had at least one new adenoma for the first and second interval (0 to 12 months after intake), and its relative risk was 0.71. The decrease rate of at least one adenoma was 50.0% (7/14) in the high-AGE group for the second interval (6 to 12 months after intake), whereas there was no decrease in subjects in the low-AGE group (p=0.02). The difference from the base-line for total size of adenomas increased in the low-AGE group, whereas an increase in the high-AGE group was suppressed for the second interval (p=0.04). The difference from the base-line for the total size of adenomas in subjects who had adenomas on the base-line increased in the low-AGE group and decreased in the high-AGE group for the second interval (p=0.03). The results of this study suggest the possibility of preventive and therapeutic effects of AGE on colorectal adenomas, though it is necessary to investigate these in larger-scale and longer-term trials.
Low Porosity Metallic Periodic Structures with Negative Poisson's Ratio (2013)

Auxetic behavior in low porosity metallic structures is demonstrated via a simple system of orthogonal elliptical voids. In this minimal 2D system, the Poisson's ratio can be effectively controlled by changing the aspect ratio of the voids. In this way, large negative values of Poisson's ratio can be achieved, indicating an effective strategy for designing auxetic structures with desired porosity.
Technical Note: Deep learning based MRAC using rapid ultrashort echo time imaging (2018)

The proposed MRAC method utilizing deep learning with transfer learning and an efficient dRHE acquisition enables reliable PET quantitation with accurate and rapid pseudo CT generation.