gebhart/patrepeval huggingface dataset:
Solution structure of the ɛ‐aminohexanoic acid complex of human plasminogen kringle 1 (1994)

The solution structure of the human plasminogen kringle 1 domain complexed to the antifibrinolytic drug 6-aminohexanoic acid (epsilon Ahx) was obtained on the basis of 1H-NMR spectroscopic data and dynamical simulated annealing calculations. Two sets of structures were derived starting from (a) random coil conformations and (b) the (mutated) crystallographic structure of the homologous prothrombin kringle 1. The two sets display essentially the same backbone folding (pairwise root-mean-square deviation, 0.15 nm) indicating that, regardless of the initial structure, the data is sufficient to locate a conformation corresponding to an essentially unique energy minimum. The conformations of residues connected to prolines were localized to energetically preferred regions of the Ramachandran map. The Pro30 peptide bond is proposed to be cis. The ligand-binding site of the kringle 1 is a shallow cavity composed of Pro33, Phe36, Trp62, Tyr64, Tyr72 and Tyr74. Doubly charged anionic and cationic centers configured by the side chains of Asp55 and Asp57, and Arg34 and Arg71, respectively, contribute to anchoring the zwitterionic epsilon Ahx molecule at the binding site. The ligand exhibits closer contacts with the kringle anionic centers (approximately 0.35 nm average O...H distance between the Asp55/Asp57 carboxylate and ligand amino groups) than with the cationic ones (approximately 0.52 nm closest O...H distances between the ligand carboxylate and the Arg34/Arg71 guanidino groups). The epsilon Ahx hydrocarbon chain rests flanked by Pro33, Tyr64, Tyr72 and Tyr74 on one side and Phe36 on the other. Dipolar (Overhauser) connectivities indicate that the ligand aliphatic moiety establishes close contacts with the Phe36 and Trp62 aromatic rings. The computed structure suggests that the epsilon Ahx molecule adopts a kinked conformation when complexed to kringle 1, effectively shortening its dipole length to approximately 0.65 nm.
Predicting How Polyphenol Antioxidants Prevent DNA Damage by Binding to Iron (2008)

Prevention of oxidative DNA damage due to hydroxyl radical is important for the prevention and treatment of disease. Because of their widely recognized antioxidant ability, 12 polyphenolic compounds were assayed by gel electrophoresis to directly quantify the inhibition of DNA damage by polyphenols with Fe(2+) and H2O2. All of the polyphenol compounds have IC50 values ranging from 1-59 microM and inhibit 100% of DNA damage at 50-500 microM concentrations. Gel electrophoresis results with iron(II)EDTA and UV-vis spectroscopy experiments confirm that binding of the polyphenol to iron is essential for antioxidant activity. Furthermore, antioxidant potency of polyphenol compounds correlates to the pKa of the first phenolic hydrogen, representing the first predictive model of antioxidant potency based on metal-binding. Understanding this iron-coordination mechanism for polyphenol antioxidant activity will aid in the design of more-potent antioxidants to treat and prevent diseases caused by oxidative stress, and help develop structure-activity relationships for these compounds.
Angiotensin I‐Converting Enzyme And Metabolism Of The Haematological Peptide N‐Acetyl‐Seryl‐Aspartyl‐Lysyl‐Proline (2001)

1. Angiotensin I-converting enzyme (ACE) has two homologous active N- and C-terminal domains and displays activity towards a broad range of substrates. The tetrapeptide N-acetyl-seryl-aspartyl-lysyl-proline (AcSDKP) has been shown to be hydrolysed in vitro by ACE and to be a preferential substrate for its N-terminal active site. This peptide reversibly prevents the recruitment of pluripotent haematopoietic stem cells and normal early progenitors into the S-phase. 2. Angiotensin I-converting enzyme inhibitors, given as a single dose to normal subjects or during long-term treatment in hypertensive patients, result in plasma AcSDKP levels five- to six-fold higher and urine concentrations 40-fold higher than those of control subjects and/or patients. Thus, AcSDKP is a natural peptide hydrolysed by the N-terminal domain of ACE in vivo. In addition, ACE may be implicated in the process of haematopoietic stem cell regulation by permanently degrading this natural circulating inhibitor of cell entry into the S-phase. 3. Besides hydrolysis by ACE, the second very effective mechanism by which AcSDKP is cleared from plasma is glomerular filtration. Because of its high sensitivity and specificity, the measurement of AcSDKP in plasma and urine provides a valuable tool in screening specific inhibitors of the N-terminal domain of ACE and in monitoring ACE inhibition during chronic treatment. 4. The long-term consequences of AcSDKP accumulation are not known. During chronic ACE inhibition in rats, AcSDKP levels slightly increase in organs with high ACE content (kidneys, lungs). To significantly increase its concentration in target haematopoietic organs (the extracellular fraction of bone marrow), AcSDKP has to be infused on top of a captopril-based treatment. 5. A selective inhibitor of the N-domain of ACE in vitro and in vivo has been identified recently. The phosphinic peptide RXP 407 does not interfere with blood pressure regulation, but does increase, dose dependently, plasma concentrations of AcSDKP in mice, in contrast with lisinopril, which affects the metabolism of both AcSDKP and angiotensin I. N-Terminal-selective ACE inhibitors may be used to selectively control AcSDKP metabolism in target haematopoietic organs. This new therapeutic strategy may be of value for protecting haematopoietic cells from the toxicity of cancer chemotherapy.
Real-world treatment patterns among patients with advanced gastric cancer in South Korea. (2014)

152 Background: This study explored treatment patterns, and cancer-related resource use of patients with metastatic and unresectable gastric cancer (MGC) in South Korea. Methods: Charts of patients ≥ 18 years old were reviewed by 30 physicians to collect de-identified data on MGC or gastroesophageal junction adenocarcinoma [diagnosis on or after January 1, 2009]. Patients received platinum/fluoropyrimidine first-line therapy followed by second-line therapy or best supportive care, had no other primary cancer, and did not participate in a clinical trial following MGC diagnosis. Patient characteristics and treatment patterns were summarized using descriptive statistics. Results: Of 198 patients, 74% were male; 78% were diagnosed with MGC after age 55 (mean=61 yrs); 47% were current or former smokers and 48% reported light to moderate alcohol consumption. The majority of tumors were located in the antrum/pyloris (52%); metastatic sites most often occurred in the peritoneum (54%), lymph nodes (48%), and liver (39%). At diagnosis, the mean Charlson comorbidity index was 0.4 (std dev=0.6). The most common comorbidities were chronic gastritis (23%) and cardiovascular disease (19%). Most patients (80%) received second-line treatment (ECOG scores: 0 -10%, 1 -66%, 2 -22%); 20% received best supportive care only. Single-agent fluoropyrimidine was reported for 22% of patients receiving second-line treatment; 20% were treated with irinotecan with a fluoropyrimidine or platinum agent. Second-line treatment was chosen mainly according to national guidelines (81%) and physician experience (35%). The most common symptoms during second-line treatment were nausea/vomiting (45%) and pain (11%), with antiemetics (45%), analgesics (37%) and nutritional support (11%) most often used as supportive care. Two-thirds of inpatient hospitalizations (30% of second-line patients had ≥ one) were for chemotherapy infusion. Outpatient hospitalization (16%) and visits to the oncologist (38%) were common among second-line patients. Conclusions: Most patients received second-line treatment, though regimens varied. Understanding MGC patient characteristics and treatment patterns in Korea will help address unmet needs.
Conditionally immortalized intestinal epithelial cells: novel approach for study of differentiated enterocytes (1993)

Clonal cell lines have been established from primary fetal rat intestinal epithelial cells by stable transfection with plasmids containing either the simian virus 40 (SV40) large T-antigen gene under the control of the heavy metal inducible metallothionein promoter (pMTWt) or the thermolabile SV40 T-antigen gene under the control of the SV40 early promoter (pZipSVtsa58). pMTWt-transfected cells produced sufficient T-antigen to allow them to proliferate both when the metallothionein promoter was induced and uninduced. No differences were observed in the pattern of intestinal epithelial markers expressed when the cells were cultured in the presence or absence of inducing agent (zinc). In contrast, fetal rat intestinal epithelial cells transfected with pZipSVtsa58 were immortalized conditionally; cells proliferated at 32 degrees C but ceased to proliferate between 48 and 72 h of culture at 39 degrees C. Four of these cell lines were characterized in detail; they showed microvilli and tight junctions as well as dome formation and expressed functional and biochemical markers of intestinal epithelial cells, including keratins 8, 19, and 21, aminopeptidase N, and dipeptidyl peptidase IV. One cell line, 2/4/A1, expressed in addition a low level of lactase and sucrase-isomaltase. The amount and/or activity of some of these markers changed during the switch from the proliferative to the nonproliferative state (switch from culture at 32 to 39 degrees C), resulting in a more differentiated phenotype and mimicking similar changes taking place during intestinal epithelial cell differentiation in vivo.
Rhetorical relations for information retrieval (2012)

Typically, every part in most coherent text has some plausible reason for its presence, some function that it performs to the overall semantics of the text. Rhetorical relations, e.g. contrast, cause, explanation, describe how the parts of a text are linked to each other. Knowledge about this so-called discourse structure has been applied successfully to several natural language processing tasks. This work studies the use of rhetorical relations for Information Retrieval (IR): Is there a correlation between certain rhetorical relations and retrieval performance? Can knowledge about a document's rhetorical relations be useful to IR? We present a language model modification that considers rhetorical relations when estimating the relevance of a document to a query. Empirical evaluation of different versions of our model on TREC settings shows that certain rhetorical relations can benefit retrieval effectiveness notably (>10% in mean average precision over a state-of-the-art baseline).
Excision of specific DNA-sequences from integrated retroviral vectors via site-specific recombination (1995)

Vectors for gene transfer and gene therapy were developed which combine the advantages of the integrase and recombinase systems. This was achieved by inserting two loxP sites for specific DNA excision into an MESV based retroviral vector. We show that this 'retroviral lox system' allows the infection of cells and the expression of transferred genes. In addition, we constructed an efficient retrovirus-based expression system for a modified Cre recombinase. Functional tests for DNA excision from integrated retroviral lox vectors were performed by the use of a negative selectable marker gene (thymidine kinase). Cre expression in cells infected with retroviral lox vectors and subsequent BrdU selection for cells in which site-specific recombination has occurred results in large numbers of independent cell clones. These results were confirmed by detailed molecular analysis. In addition we developed retroviral suicide vectors in which the enhancer/promoter elements of both LTRs were replaced by lox sequences. We show that lox-sequences located in the LTRs of retroviral vectors are stable during retroviral replication. Potential applications of this system would be the establishment of revertants of retrovirus-infected cells by controlled excision of nearly the complete proviral DNA.
T7 RNA polymerase produces 5′ end heterogeneity during in vitro transcription from certain templates (1998)

The use of T7 RNA polymerase to prepare large quantities of RNA of a particular sequence has greatly facilitated the study of both the structure and function of RNA. Generally, it has been believed that the products of this technique are highly homogeneous in sequence, with only a few noted exceptions. We have carefully examined the transcriptional products of several tRNAs that vary in their 5' end sequence and found that, for those molecules that begin with multiple, consecutive guanosines, the transcriptional products are far from homogenous. Although a template beginning with GCG showed no detectable 5' end heterogeneity, two tRNA templates designed to have either four or five consecutive guanosines at their 5' ends had more than 30% of their total transcriptional products extended by at least one untemplated nucleotide at their 5' end. By simply reducing the number of consecutive guanosines, the heterogeneity was reduced significantly. The presence of this 5' end heterogeneity in combination with the 3' end heterogeneity common to T7 transcriptions results in a mixture of RNA molecules even after rigorous size purification.
High-performance 1200-nm InGaAs and 1300-nm InGaAsN quantum-well lasers by metalorganic chemical vapor deposition (2003)

We present the characteristics of high-performance strain-compensated MOCVD-grown 1200-nm InGaAs and 1300-nm InGaAsN quantum-well (QW) lasers using AsH <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> and U-Dimethylhydrazine as the group V precursors. The design of the InGaAsN QW active region utilizes an In-content of approximately 40%, which requires only approximately 0.5% N-content to realize emission wavelengths up to 1315-nm. Threshold current densities of only 65-90 A/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> were realized for InGaAs QW lasers, with emission wavelength of 1170-1233 nm. Room-temperature threshold and transparency current densities of 210 and 75-80 A/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , respectively, have been realized for InGaAsN QW lasers with emission wavelength of 1300-nm. Despite the utilization of the highly-strained InGaAsN QW, double-QW lasers have been realized with excellent lasing performance.
Transfection of mammalian cells by the methods of receptor mediated gene transfer and particle bombardment. (1999)

The efficacy of currently developed methods for gene transfer into mammalian cells depends primarily on the transfection technique, and also on the type of targeted cells. Considering the importance of gene transfer in the creation of gene therapies, our study was aimed at the assessment of transfection capacity of receptor mediated gene transfer method (RMGT), and method of particle bombardment (helios gene gun system--HGG) in different normal and malignant mammalian cells ex vivo. In addition, the HGG was also assessed for its ability to transfect tumor cells of subcutaneous (s.c.) tumors in C57Bl/6 mice in vivo. Using RMGT an average ex vivo transfection rate of 35.7%, and 20.4% was achieved in malignant melanoma B-16, and human breast adenocarcinoma MCF7, respectively. However, in normal fibroblast L929 cells the transfection by RMGT succeeded only in 2.1% of the cells. On the other hand, the transfection efficacy of HGG was comparable in both malignant cell lines resulting in an average gene transfer to 9.6% of B-16 and 10.5% of MCF7 cells, while only 3.9% of normal fibroblasts were successfully transfected. Application of HGG for an in vivo gene transfer into s.c. B-16 melanoma tumors in C57Bl/6 mice resulted in a successful but limited transfection of the epithelium as well as of the superficially sited tumor cells. Taking into consideration both methods, RMGT is more appropriate for ex vivo transfection of cells, under the condition that target cells express a specific receptor for the molecule attached to the carrier. On the other hand, HGG is not complicated to use, no requirements for specific structures on target cells are necessary (potentially usable in different cells), and it has applicability in direct in vivo transfection processes.
Real-Time Object Segmentation of the Disparity Map Using Projection-Based Region Merging (2007)

Robots have been mostly used in industrial environment, but modern developments of household robot-cleaner suggest the necessity of household robots as becoming in reality. Most industrial robots have been used for factory automation that perform simple and iterative tasks at high speed, whereas household robots need various interfaces with a man while moving in indoor environment like a household robot-cleaner does. Robots activate in indoor environment using various sensors such as vision, laser, ultrasonic sensor, or voice sensor to detect indoor circumstance. Especially robot's routing plan and collision avoidance need three-dimensional information of robot's surrounding environment. This can be obtained by using a stereo vision camera which provides a general and huge amount of 3-D information. But this computation is too big to solve in real-time with the existing microprocessor when using a stereo vision camera for capturing 3-D image information. High-level computer vision tasks, such as robot navigation and collision avoidance, require 3-D depth information of the surrounding environment at video rate. Current generalpurpose microprocessors are too slow to perform stereo vision at video rate. For example, it takes several seconds to execute a medium-sized stereo vision algorithm for a single pair of images using one 1 GHz general-purpose microprocessor. To overcome this limitation, designers in the last decade have built reprogrammable chips called FPGA(Field-Programmable Gate Arrays) hardware systems to accelerate the performance of the vision systems. These devices consist of programmable logic gates and routing which can be re-configured to implement practically any hardware function. Hardware implementations allow one to apply the parallelism that is common in image processing and vision algorithms, and to build systems to perform specific calculations quickly compared to software implementations. A number of methods of finding depth information in video-rate have been reported. Among others, multi-baseline stereo theory is developed and the video-rate stereo machine has the capability of generating a dense depth map of 256x240 pixels at the frame rate of 30 frames/sec in [1-2]. An algorithm proposed from parallel relaxation algorithm for disparity computation [3] results reduction of error rate and enhancement of computational complexity
Action of secretin on pancreatic enzyme secretion in man. Studies on pure pancreatic juice. (1984)

The action of pure, natural secretin on the pancreatic secretion of enzymes was investigated in six patients with external transduodenal drainage of the main pancreatic duct performed after biliary tract surgery. Secretin infused for five successive 50 minute periods at increasing doses of 0.03, 0.1, 0.3, 0.9 and 2.7 clinical units (CU)/kg/h, produce a dose dependent increase in protein and lipase output. A weak but significant (p less than 0.02) increase of enzyme output above the fasting level was already observed with the lowest dose. The maximal output of protein and lipase, observed with the highest dose of secretin infused, corresponded to about 50% of that induced by maximal doses of cerulein (100 ng/kg/h) plus secretin (1 CU/kg/h). As far as bicarbonate is concerned, the lowest dose of secretin (0.03 CU/kg/h) significantly (p less than 0.001) stimulated bicarbonate output. The dose of 0.9 CU/kg/h of secretin evoked a bicarbonate output of 526 +/- 49 micromol/min; trebling the dose of secretin did not significantly increase the output of bicarbonate above this value. Increasing doses of secretin induced a dose related increase in calcium output. There was a close parallel between calcium and protein outputs, suggesting that the increase in calcium output reflected primarily an increase in the enzyme-associated fraction of pancreatic juice calcium. It is concluded that secretin stimulates pancreatic enzyme secretion in man probably by a direct action on the acinar cells.
The effects of passive humidifier dead space on respiratory variables in paralyzed and spontaneously breathing patients. (2000)

Clinicians should be aware that each type of passive humidifier has inherent dead space characteristics. Passive humidifiers with high dead space may negatively impact the respiratory function of spontaneously breathing patients or carbon dioxide retention in paralyzed patients. When choosing a passive humidifier, the device with the smallest dead space, but which meets the desired moisture output requirements, should be selected.
Inhibitors of the proteasome pathway interfere with induction of nitric oxide synthase in macrophages by blocking activation of transcription factor NF-kappa B. (1996)

The objective of this study was to elucidate the role of the proteasome pathway or multicatalytic proteinase complex in the induction of immunologic nitric oxide (NO) synthase (iNOS) in rat alveolar macrophages activated by lipopolysaccharide. Macrophages were incubated in the presence of lipopolysaccharide plus test agent for up to 24 hr. Culture media were analyzed for accumulation of stable oxidation products of NO (NO2- + N03-, designated as NOX-), cellular RNA was extracted for determination of iNOS mRNA levels by Northern blot analysis, and nuclear extracts were prepared for determination of NF-kappa B by electrophoretic mobility-shift assay. Inhibitors of calpain (alpha-N-acetyl-Leu-Leu-norleucinal; N-benzyloxycarbonyl-Leu-leucinal) and the proteasome (N-benzyloxycarbonyl-Ile-Glu-(O-t-Bu)-Ala-leucinal) markedly inhibited or abolished the induction of iNOS in macrophages. The proteinase inhibitors interfered with lipopolysaccharide-induced NOX- production by macrophages, and this effect was accompanied by comparable interference with the appearance of both iNOS mRNA and NF-kappa B. Calpain inhibitors elicited effects at concentrations of 1-100 microM, whereas the proteasome inhibitor was 1000-fold more potent, producing significant inhibitory effects at 1 nM. The present findings indicate that the proteasome pathway is essential for lipopolysaccharide-induced expression of the iNOS gene in rat alveolar macrophages. Furthermore, the data support the view that the proteasome pathway is directly involved in promoting the activation of NF-kappa B and that the induction of iNOS by lipopolysaccharide involves the transcriptional action of NF-kappaB.
Malic Enzyme of Escherichia coli (1969)

Abstract The TPN+-specific malic enzyme from Escherichia coli has been purified from malate-grown cells. An approximately 100-fold purified preparation is activated by NH4+ and K+ ions. The enzyme is inhibited by acetyl coenzyme A, oxalacetate, TPNH, and DPNH in an allosteric manner. Glycine at concentration ranges above 0.5 m has been shown to activate the enzyme as well as to desensitize it reversibly to the effect of various inhibitors, including DPNH. From teleological arguments it has been concluded that the complex activity controls of malic enzyme are necessitated in bacteria because of the absence of rigid compartmentation controls available to higher organisms.