gebhart/patrepeval huggingface dataset:
Early coagulation events induce acute lung injury in a rat model of blunt traumatic brain injury (2016)

Acute lung injury (ALI) and systemic coagulopathy are serious complications of traumatic brain injury (TBI) that frequently lead to poor clinical outcomes. Although the release of tissue factor (TF), a potent initiator of the extrinsic pathway of coagulation, from the injured brain is thought to play a key role in coagulopathy after TBI, its function in ALI following TBI remains unclear. In this study, we investigated whether the systemic appearance of TF correlated with the ensuing coagulopathy that follows TBI in ALI using an anesthetized rat blunt trauma TBI model. Blood and lung samples were obtained after TBI. Compared with controls, pulmonary edema and increased pulmonary permeability were observed as early as 5 min after TBI without evidence of norepinephrine involvement. Systemic TF increased at 5 min and then diminished 60 min after TBI. Lung injury and alveolar hemorrhaging were also observed as early as 5 min after TBI. A biphasic elevation of TF was observed in the lungs after TBI, and TF-positive microparticles (MPs) were detected in the alveolar spaces. Fibrin(ogen) deposition was also observed in the lungs within 60 min after TBI. Additionally, preadministration of a direct thrombin inhibitor, Refludan, attenuated lung injuries, thus implicating thrombin as a direct participant in ALI after TBI. The results from this study demonstrated that enhanced systemic TF may be an initiator of coagulation activation that contributes to ALI after TBI.
Enhancement of insulin sensitivity by troglitazone lowers blood pressure in diabetic hypertensives (1995)

The association of hypertension with insulin resistance has been reported. Troglitazone (CS-045) is a newly developed antidiabetic agent that enhances insulin sensitivity. Its antidiabetic effects have been confirmed in diabetic animals and patients. The present study was performed to evaluate whether the amelioration of hyperinsulinemia by troglitazone lowers blood pressure in essential hypertensives. Troglitazone was administered orally to 18 outpatients with essential hypertension complicated by mild diabetes at a dose of 200 mg twice a day for 8 weeks. Blood pressure was decreased from 164 +/- 3/94 +/- 2 mm Hg to 146 +/- 3 (P < .001)/82 +/- 3 (P < .05) mm Hg at 8 weeks of the treatment period. Pulse rate did not change. Fasting plasma glucose changed from 159 +/- 10 mg/dL to 144 +/- 14 mg/dL at 8 weeks (P < .05). Plasma insulin (IRI) levels changes from 9.1 +/- 1.2 microU/mL to 6.3 +/- 0.8 microU/mL at the endpoint of treatment (P < .1). Decrease in mean blood pressure from the control period to the endpoint of the treatment correlated significantly with decrease in IRI (r = 0.59, P < .05). In summary, troglitazone treatment induces improvement in both glucose metabolism and blood pressure control in essential hypertensive patients with diabetes mellitus. These results suggest that insulin resistance or plasma insulin level plays a role in the pathogenesis of essential hypertension.
Activation of a chicken embryonic globin gene in adult erythroid cells by 5-azacytidine and sodium butyrate. (1984)

Adult White Leghorn chickens were rendered anemic by injection with 1-acetyl-2-phenylhydrazine and then treated with parenteral 5-azacytidine, and levels of embryonic globin RNA in circulating reticulocytes were measured. A very small but detectable amount of correctly initiated embryonic p-type globin RNA was detected in reticulocytes from birds treated with 5-azacytidine, while none was detected in reticulocytes from those receiving only phenylhydrazine or phenylhydrazine plus 1-beta-D-arabinofuranosylcytosine (cytosine arabinonucleoside). An attempt to increase embryonic globin RNA induction by treatment with parenteral sodium butyrate after 7 days of 5-azacytidine administration resulted in a 5- to 10-fold increase in the level of embryonic globin RNA. However, sodium butyrate did not induce embryonic gene expression when given alone or after treatment with cytosine arabinonucleoside. Sodium butyrate treatment also caused a DNase I-hypersensitive site to be exposed at the 5' end of the rho-globin gene only after 5-azacytidine induced demethylation of several CpG sites in and around the gene. The implications of this model of gene activation in vivo are discussed in the context of multistep gene regulation.
<title>Automated calculation of the axial orientation of intravascular ultrasound images by fusion with biplane angiography</title> (1999)

This paper presents an approach for fusion of the two major cardiovascular imaging modalities, angiography and intravascular ultrasound (IVUS). While the path of the IVUS catheter, which follows the vessel curvature during pullback, is reconstructed from biplane angiograms, cross-sectional information about the vessel is derived from IVUS. However, after mapping of the IVUS frames into their correct 3-D locations along the catheter path, their orientations remain ambiguous. We determine the relative catheter twisting analytically, followed by a statistical method for finding the absolute orientation from the out-of-center position of the IVUS catheter. Our results as obtained from studies with cadaveric pig hearts and from three patients undergoing routine coronary intervention showed a good match of the absolute orientation by the algorithm. In all tested cases, the method determined the visually correct orientations of the IVUS frames. Local distortions were reliably identified and discarded.
Identification of renal cathepsin B as a human prorenin-processing enzyme (1991)

Prorenin, the inactive biosynthetic precursor of renin, is proteolytically cleaved in the renal juxtaglomerular cells to renin. The activity of renin is rate-limiting for generation of angiotensin II in the circulation. We identified a renal thiol protease which activates and accurately cleaves the 43-amino acid prosegment of human recombinant prorenin. In the current studies, 6.5 mg of this protease was purified from human renal cortex using a three-step procedure dependent upon Leu-Leu-arginyl affinity chromatography. This represented an overall 766-fold purification and resulted in three protein bands on sodium dodecyl sulfate-polyacrylamide gel electrophoresis of molecular weights 30,000, 25,000, and 24,000. All three bands cross-reacted with an anti-human liver cathepsin B antibody upon immunoblot analysis; electrolution of each band and amino-terminal sequence analysis confirmed that the Mr 30,000 protein was mature cathepsin B and the Mr 25,000 and 24,000 bands were cathepsin B subunits. The pH optimum for the hydrolysis of pure human recombinant prorenin by pure renal cathepsin B was 6, and the Michaelis-Menten constant, Km, of the reaction was 1.4 x 10(-9) M. Immunostaining of human kidney using a sheep anti-human cathepsin B antibody demonstrated the presence of cathepsin B in the juxtaglomerular areas of the kidney, as well as in the renal proximal tubules. Electron microscopic immunohistochemistry using the same antibody demonstrated cathepsin B in dense secretory granules of the juxtaglomerular cells. Renin was also shown to be present in these granules. This study provides both biochemical and morphological evidence that renal cathepsin B is a human prorenin-processing enzyme.
Improving Digestibility of Straws for Ruminant Feed by Aqueous Ammonia (1972)

Digestibility and nutritive value of straws can be improved by treatment with aqueous ammonia at ordinary room temperature in a confined system. Experiments indicate that optimal process conditions are to treat rice straw with 5% of added ammonia (by wt) and 30% of added water (by wt) for about 30 days at ambient temperatures. Under these conditions, enzymatic digestibility is increased 10% and nitrogen content is increased 133%. In vivo digestibility trials also show enhanced digestibility of treated rice straw. Other cellulosic wastes respond to ammonia treatment in a similar manner.
Environmental, economic, and energetic costs and benefits of biodiesel and ethanol biofuels (2006)

Negative environmental consequences of fossil fuels and concerns about petroleum supplies have spurred the search for renewable transportation biofuels. To be a viable alternative, a biofuel should provide a net energy gain, have environmental benefits, be economically competitive, and be producible in large quantities without reducing food supplies. We use these criteria to evaluate, through life-cycle accounting, ethanol from corn grain and biodiesel from soybeans. Ethanol yields 25% more energy than the energy invested in its production, whereas biodiesel yields 93% more. Compared with ethanol, biodiesel releases just 1.0%, 8.3%, and 13% of the agricultural nitrogen, phosphorus, and pesticide pollutants, respectively, per net energy gain. Relative to the fossil fuels they displace, greenhouse gas emissions are reduced 12% by the production and combustion of ethanol and 41% by biodiesel. Biodiesel also releases less air pollutants per net energy gain than ethanol. These advantages of biodiesel over ethanol come from lower agricultural inputs and more efficient conversion of feedstocks to fuel. Neither biofuel can replace much petroleum without impacting food supplies. Even dedicating all U.S. corn and soybean production to biofuels would meet only 12% of gasoline demand and 6% of diesel demand. Until recent increases in petroleum prices, high production costs made biofuels unprofitable without subsidies. Biodiesel provides sufficient environmental advantages to merit subsidy. Transportation biofuels such as synfuel hydrocarbons or cellulosic ethanol, if produced from low-input biomass grown on agriculturally marginal land or from waste biomass, could provide much greater supplies and environmental benefits than food-based biofuels.
Synthesis and Evaluation of Bivalent NDP-α-MSH(7) Peptide Ligands for Binding to the Human Melanocortin Receptor 4 (hMC4R) (2007)

We demonstrate the potential utility of multivalent ligands as targeting agents for cancer imaging or therapy by determining the binding of homobivalent ligands to their corresponding receptors. This manuscript details the synthesis and evaluation of a series of bivalent ligands containing two copies of the truncated heptapeptide version of [Nle4-D-Phe7]-alpha-melanocyte stimulating hormone (NDP-alpha-MSH), referred to as MSH(7). These were connected with various semirigid linkers containing Pro-Gly repeats, with or without flexible poly(ethylene glycol) (PEGO) moieties at their termini. Modeling data suggest a distance of 20-50 A between the ligand binding sites of two adjacent G-protein coupled receptors, GPCRs. These bivalent ligands were observed to bind with higher affinity compared to their monovalent counterparts. Data suggest these ligands may be capable of cross-linking adjacent receptors. An optimal linker length of 25 +/- 10 A, inferred from these ligands, correlated well with the inter-receptor distance estimated through modeling. Although there was no difference in maximal binding affinities between the ligands constructed with the Pro-Gly repeats versus those constructed with the PEGO inserts, the PEGO-containing ligands bound with high affinities over a greater range of linker lengths.
Apolipoprotein A-I Conformation in Reconstituted Discoidal Lipoproteins Varying in Phospholipid and Cholesterol Content (1995)

The effects of the size and cholesterol content on the conformation of apolipoprotein A-I (apoA-I) have been studied in reconstituted discoidal lipoproteins containing two apoA-I per particle (Lp2A-I). The immunoreactivity of a series of 13 epitopes distributed along the apoA-I sequence has been evaluated in Lp2A-I with a phospholipid/apoA-I molar ratio ranging from 31 to 156 and in Lp2A-I with constant phospholipids but varying in cholesterol content from 0 to 22 molecules. The results are compatible with a three domain structure in apoA-I in which the central domain is located between residues 99 and 143 and postulated to be a hinged domain that responds differentially to changes in phospholipid and cholesterol contents. Increasing the phospholipid content results in significant changes of epitope immunoreactivity throughout the N-terminal and central domains of apoA-I with fewer modifications in the C-terminal domain. In contrast, increasing Lp2A-I of two central epitopes, A11 (residues 99-132) and 5F6 (residues 118-148), and an extreme N-terminal epitope, 4H1 (residues 2-8). Interestingly, the effects of increasing cholesterol or phospholipids on these epitopes are opposite. This suggests a specific effect of cholesterol on the central domain tertiary structure between residues 99 and 143. Competition binding assays among pairs of antibodies binding to apoA-I on Lp2A-I are best explained by invoking inter- as well as intramolecular competitions. The specificity of the intermolecular competitions suggests an N to C termini arrangement of the two apoA-I molecules around the disc. Increasing the phospholipid content of Lp2A-I mainly increases the competitions between 3G10 and antibodies binding to most adjacent epitopes. Simultaneously as Lp2A-I enlarges, several of these antibodies also enhance the binding of 3G10. This has been interpreted as evidence of a structural rearrangement of apoA-I as a result of the size increase where the alpha-helix (residues 99-121) that contains the 3G10 epitope is increasingly interacting with lipids resulting in the enhanced expression of this epitope. The increasing interactions of apoA-I helices with lipids in the enlarging disc are compatible with previous reports of a greater apoA-I stability in the large discs. By contrast, cholesterol has limited but specific effects on antibody competitions and decreases the interaction of the N-terminal domain with the domain containing 3G10, either by direct cholesterol protein interaction or by modification of the lipid phase packing.
Purification and properties of single strand DNA-binding endo-exonuclease of Neurospora crassa. (1983)

Single strand DNA-binding endo-exonucleases purified from mitochondria, vacuoles, or a mixture of these organelles had the same high specific single strand DNase activity (910 mumol of nucleotides/min/mg), and each contained a polypeptide of Mr = 31,000-33,000 which was found to be active by sodium dodecyl sulfate-DNA-gel electrophoresis. The properties of the three preparations were identical in all respects tested. The enzyme showed distributive endonuclease activity with single strand DNA, but processive exonuclease activity with double strand DNA. In the former case, 5'-phosphoryl-terminated fragments were released at early times, while in the latter case, short 5'-oligonucleotides (n = 2-4) were released. Both activities were dependent on Mg2+ (or Mn2+), but to different extents. In 0.1 mM Mg2+, superhelical bacteriophage phi X174 (replicative form (RF II) DNA and, at converted to relaxed circular (RF II) DNA and, at higher enzyme concentrations, to unit length linear (RF III) DNA. In 10 mM Mg2+, these same conversions took place rapidly, and the RF III DNA which formed was degraded to pieces shorter than unit length. At very low enzyme concentrations, long single strand tails and gaps were detected in bacteriophage T7 linear double strand DNA molecules.
Serum Neurofilament light: A biomarker of neuronal damage in multiple sclerosis (2017)

These results support the value of sNfL as a sensitive and clinically meaningful blood biomarker to monitor tissue damage and the effects of therapies in MS. Ann Neurol 2017;81:857-870.
Carnitine biosynthesis. Hydroxylation of N6-trimethyl-lysine to 3-hydroxy-N6-trimethyl-lysine (1980)

Rat kidney homogenates metabolize N6-trimethyl-lysine to N-trimethylammoniobutyrate, but not to carnitine. The first step in this conversion is the hydroxylation of trimethyl-lysine to form 3-hydroxy-N6-trimethyl-lysine. An assay system was developed in which hydroxylation of trimethyl-lysine is linear with respect to both time and homogenate protein concentration. The rate is 5 nmol of 3-hydroxy-N6-trimethyl-lysine formed/min per mg of homogenate protein. The cofactors required are ascorbate, alpha-oxoglutarate, FeSO4, and O2. Catalase and dithiothreitol give a 20% stimulation. Ca2+ produces a 2-fold increase in specific activity and cannot be replaced by Mg2+, Mn2+ or Zn2+. These last three bivalent cations lead to a decreased activity. Subcellular distribution studies demonstrate that trimethyl-lysine hydroxylase activity parallels the distribution profile of succinate dehydrogenase and citrate synthase. Thus trimethyl-lysine hydroxylase has a mitochondrial localization. Distribution of trimethyl-lysine hydroxylase activity between cortex and medulla of kidney if 67 and 33% respectively, similar to mitochondrial distribution.
An in Vivo Map of the Yeast Protein Interactome (2008)

Protein interactions regulate the systems-level behavior of cells; thus, deciphering the structure and dynamics of protein interaction networks in their cellular context is a central goal in biology. We have performed a genome-wide in vivo screen for protein-protein interactions in Saccharomyces cerevisiae by means of a protein-fragment complementation assay (PCA). We identified 2770 interactions among 1124 endogenously expressed proteins. Comparison with previous studies confirmed known interactions, but most were not known, revealing a previously unexplored subspace of the yeast protein interactome. The PCA detected structural and topological relationships between proteins, providing an 8-nanometer-resolution map of dynamically interacting complexes in vivo and extended networks that provide insights into fundamental cellular processes, including cell polarization and autophagy, pathways that are evolutionarily conserved and central to both development and human health.
Biological Effects of Sex Hormone-Binding Globulin on Androgen-Induced Proliferation and Androgen Metabolism in LNCaP Prostate Cells* (1991)

The effects of purified human sex hormone-binding globulin (SHBG) on androgen-sensitive cell proliferation were examined using a human prostatic cell line (LNCaP-FGC). Cells were grown for 5 days in medium supplemented with 10% charcoal-dextran-stripped human serum (10% CDHuS) and various concentrations of 5 alpha-dihydrotestosterone (DHT). In 10% CDHuS, without SHBG, the proliferative response of these cells to androgens was typically biphasic. At low androgen concentrations, cell yields were increased in a dose-dependent manner, reaching maximal levels at 0.3 nM DHT. However, at high androgen concentrations, cell proliferation was inhibited. Addition of purified human SHBG to the medium reduced the effectiveness of DHT on both phases of the proliferative response in a dose-dependent manner. These effects of SHBG appeared to be due primarily to the high affinity binding of DHT by SHBG. Proliferative responses induced by the synthetic androgen methyltrienolone (R1881), which binds poorly to SHBG, were not affected by added SHBG. Furthermore, analysis of the protein binding of DHT revealed that cell proliferation correlated best with the concentration of DHT not bound to SHBG. The presence of SHBG in the medium also altered the uptake and metabolism of DHT. LNCaP-FGC cells rapidly metabolized DHT to a polar glucuronidase-sensitive conjugate of DHT. In 10% CDHuS, LNCaP-FGC cells conjugated virtually all of the added DHT during the 5-day experiment. However, in medium containing SHBG, the SHBG-bound DHT remained unconjugated; more than 90% of the DHT initially bound to SHBG was present in the medium at the end of the experiment as unconjugated DHT. Uptake of radiolabeled DHT by cells was also inhibited by SHBG. In summary, these experiments provide evidence that 1) SHBG-bound DHT is not a signal for DHT-induced cell proliferation and 2) SHBG inhibits the uptake and metabolism of DHT by LNCaP-FGC cells.
Insight into the mechanism by which metoclopramide improves immune functions after trauma-hemorrhage (2000)

Although studies have shown that prolactin (Prl) and metoclopramide (Mcp) administration restores the depressed cell-mediated immune functions after hemorrhage, the underlying mechanism responsible for the immunostimulatory effects of Mcp remains unknown. We hypothesized that Mcp improves immune responses by upregulating the secretion of Prl. To test this hypothesis, male C3H/HeN mice were subjected to sham operation or laparotomy (i.e., soft tissue trauma) and hemorrhagic shock (Hem; 35 +/- 5 mmHg for 90 min) and then resuscitated. Plasma Prl levels were determined 30 min after Mcp (1 microgram/g body wt sc at end of Hem) or vehicle (Veh) treatment in sham and Hem mice. The results indicate that plasma Prl levels increased significantly in Mcp-treated mice (sham-Veh 249.9 +/- 5.3, Hem-Veh 229.9 +/- 7.6, Hem-Mcp 596.9 +/- 73.1 ng/ml, one-way ANOVA, P < 0.05 vs. Veh). To determine whether Mcp produces its salutary effects directly or indirectly via increased Prl secretion, splenocyte proliferation and splenocyte interleukin (IL)-2 and IL-3 release from untreated sham or Hem mice were determined in the presence of increasing concentrations of mouse Prl or Mcp. The addition of Mcp had no effect on splenocyte immune functions in vitro. However, the addition of Prl restored the hemorrhage-induced depressed splenocyte proliferation as well as splenocyte IL-2 and IL-3 release in vitro in a dose-dependent manner. Thus the beneficial effects of Mcp on immune functions after Hem appear to be mediated by Prl. Because Mcp increases plasma levels of the immunoenhancing hormone Prl, this agent should be considered a useful adjunct for the treatment of immunodepression in trauma victims.
Deep Convolutional Neural Networks for Automatic Detection of Orbital Blowout Fractures (2019)

Orbital blow out fracture is a common disease in emergency department and a delay or failure in diagnosis can lead to permanent visual changes. This study aims to evaluate the ability of an automatic orbital blowout fractures detection system based on computed tomography (CT) data.Orbital CT scans of adult orbital blowout fractures patients and normal cases were obtained from Shanghai Ninth People's Hospital between January and March 2017. The region of fractures was annotated using 3D Slicer. The Inception V3 convolutional neural networks were constructed utilizing the Python programming language with PyTorch as the framework to extract high dimension features from each slice in a CT scan. These extracted features are processed through a XGBoost model to make the final differentiation of fracture cases and nonfracture ones. Accuracy, receiver operating characteristics, and area under the curve were evaluated.This study used 94 CT scans diagnosed with orbital blowout fractures and 94 healthy control cases. The automatic detection system showed accuracy of 92% in single-image classification and 87% in patient level detection. The area under the receiver operating characteristic curve was 0.9574.Using a deep learning-based automatic detection system of orbital blowout fracture can accurately detect and classify orbital blowout fractures from CT scans. The convolutional neural networks model combined with an accurate annotation system could achieve good performance in a small dataset. Further studies with large and multicenter data are required to refine this technology for possible clinical applications.