gebhart/patrepeval huggingface dataset:
Characterisation of the <i>E. coli</i> and <i>Salmonella qseC</i> and <i>qseE</i> mutants reveals a metabolic rather than adrenergic receptor role (2022)

Catecholamine stress hormones (norepinephrine, epinephrine, and dopamine) are signals that have been shown to be used as environmental cues, which affect the growth and virulence of normal microbiota as well as pathogenic bacteria. It has been reported that Escherichia coli and Salmonella use the two-component system proteins QseC and QseE to recognise catecholamines and so act as bacterial adrenergic receptors. In this study, we mutated the E. coli O157:H7 and Salmonella enterica serovar Typhimurium genes encoding QseC and QseE and found that this did not block stress hormone responsiveness in either species. Motility, biofilm formation, and analysis of virulence of the mutants using two infection models were similar to the wild-type strains. The main differences in phenotypes of the qseC and qseE mutants were responses to changes in temperature and growth in different media particularly with respect to salt, carbon, and nitrogen salt sources. In this physiological respect, it was also found that the phenotypes of the qseC and qseE mutants differed between E. coli and Salmonella. These findings collectively suggest that QseC and QseE are not essential for E. coli and Salmonella to respond to stress hormones and that the proteins may be playing a role in regulating metabolism.
Position of Pro and Ser near Glu<sup>7.32</sup>in the Extracellular Loop 3 of Mammalian and Nonmammalian Gonadotropin-Releasing Hormone (GnRH) Receptors Is a Critical Determinant for Differential Ligand Selectivity for Mammalian GnRH and Chicken GnRH-II (2003)

A Glu/Asp7.32 residue in the extracellular loop 3 of the mammalian GnRH receptor (GnRHR) is known to interact with Arg8 of mammalian GnRH (mGnRH), which may confer preferential ligand selectivity for mGnRH than for chicken GnRH-II (cGnRH-II). However, some nonmammalian GnRHRs also have the Glu/Asp residue at the same position, yet respond better to cGnRH-II than mGnRH. Amino acids flanking Glu/Asp7.32 are differentially arranged such that mammalian and nonmammalian GnRHRs have an S-E/D-P motif and P-X-S/Y motif, respectively. We presumed the position of Ser7.31 or Pro7.33 of rat GnRHR as a potential determinant for ligand selectivity. Either placing Pro before Glu7.32 or placing Ser after Glu7.32 significantly decreased the sensitivity and/or efficacy for mGnRH, but slightly increased that for cGnRH-II in several mutant receptors. Among them, those with a PEV, PES, or SES motif exhibited a marked decrease in sensitivity for mGnRH such that cGnRH-II had a higher potency than mGnRH, showing a reversed preferential ligand selectivity. Chimeric mGnRHs in which positions 5, 7, and/or 8 were replaced by those of cGnRH-II revealed a greater ability to activate these mutant receptors than mGnRH, whereas they were less potent to activate wild-type rat GnRHR than mGnRH. Interestingly, a mutant bullfrog type I receptor with the SEP motif exhibited an increased sensitivity for mGnRH but a decreased sensitivity for cGnRH-II. These results indicate that the position of Pro and Ser near Glu7.32 in the extracellular loop 3 is critical for the differential ligand selectivity between mammalian and nonmammalian GnRHRs.
Ir vibrational CD in model deoxyoligonucleotides: Observation of the B → Z phase transition and extended coupled oscillator intensity calcuations (1989)

The first observation of ir vibrational CD (VCD) in small model DNA molecules is reported. The VCD signals in the 1550-1750-cm-1 spectral region, which originate from coupling of carbonyl stretching modes of the nucleic acid bases, are found to be sensitive to the handedness of the polymer helix. The formalism to calculate VCD intensities of polymers is developed from the exciton model derived earlier by Tinoco [(1963) Radiation Res. 20, 133; (1960) J. Chem. Phys. 33, 1332; (1964) J. Am. Chem. Soc. 86, 297] and Schellman and co-workers [(1975) Biopolymers 14, 173; (1969) J. Phys. Chem. 73, 28]. The resulting equations, which are a direct extension of the dimeric case known as the "coupled oscillator," are used in model calculations of the helical polymers.
Glucagon-Like Peptide-1 Induces Cell Proliferation and Pancreatic-Duodenum Homeobox-1 Expression and Increases Endocrine Cell Mass in the Pancreas of Old, Glucose-Intolerant Rats (2000)

Glucose homeostasis in mammals is maintained by insulin secretion from the beta-cells of the islets of Langerhans. Type 2 diabetes results either from primary beta-cell failure alone and/or a failure to secrete enough insulin to overcome insulin resistance. Here, we show that continuous infusion of glucagon-like peptide-1 (7-36) (GLP-1; an insulinotropic agent), to young and old animals, had effects on the beta-cell of the pancreas other than simply on the insulin secretory apparatus. Our previous studies on a rodent model of glucose intolerance, the aging Wistar rat, show that a plateau in islet size, insulin content, and beta-cell mass is reached at 13 months, despite a continuing increase in body weight. Continuous sc infusion of GLP-1 (1.5 pM/kg x min), over 5 days, resulted in normal glucose tolerance. Our current results in both young and old rats demonstrate that treatment caused an up-regulation of pancreatic-duodenum homeobox-1 (PDX-1) expression in islets and total pancreas, induced pancreatic cell proliferation, and beta-cell neogenesis. The effects on levels of PDX-1 messenger RNA were abrogated by simultaneous infusion of Exendin (9-39), a specific antagonist of GLP-1. PDX-1 protein levels increased 4-fold in whole pancreata and 6-fold in islets in response to treatment. Beta-cell mass increased to 7.2 +/- 0.58 from 4.88 +/- 0.38 mg, treated vs. control, respectively, P < 0.02. Total pancreatic insulin content also increased from 0.55 +/- 0.02 to 1.32 +/- 0.11 microg/mg total pancreatic protein. Therefore, GLP-1 would seem to be a unique therapy that can stimulate pancreatic cell proliferation and beta-cell differentiation in the pancreas of rodents.
Transtrochanteric Anterior Rotational Osteotomy for Osteonecrosis of the Femoral Head in Patients 20 Years or Younger (2009)

Level 4 (Therapeutic Study).
Hemosuccus pancreaticus successful treatment by double balloon-assisted coil embolization for active bleeding from the main trunk of the superior mesenteric artery (2018)

We report a case of a 63-year-old man with hemosuccus pancreaticus due to large pseudoaneurysm originating from the main trunk of the superior mesenteric artery (SMA). The patient was treated successfully with the double balloon-assisted coil embolization technique combined with proximal and distal balloon inflation in the short segment of the SMA. This technique preserved the pancreaticoduodenal arterial arcade and the supply to the distal part of the SMA by embolizing SMA in a short segment.
Application Technology on Ceramics for Structural Components of High-Temperature Machines (1989)

Fine ceramics offer excellent strength and durability characteristics at elevated temperatures, however brittle materials exhibit catastrophic failure without any plastic deformation. In consideration of these characteristics, we discussed the structural design concepts which must be established to assure the best use of ceramics for high-temperature machines requiring high reliability. Based on the ceramic-oriented structural design concepts, a ceramic/metal hybrid structure of the 1st stage ceramic stator vanes in industrial gas turbines was developed. In this hybrid stator vane, components exposed to high temperature and a corrosive environment were made of ceramics. Metal was used as the strength member. Moreover, a thermal shock testing method for ceramic to evaluate thermal shock resistance, which is an extremely important factor in ceramic component use was proposed.
Are non-lactose-fermenting Escherichia coli important diarrhoeal pathogens in children and adults? (2023)

In our study two pathotypes (EAEC, EIEC) were predominant among NLF <i>E. coli</i> and these were not only important aetiological agents in children, but also in adults. Our study also sheds light on the epidemiology of EIEC, which is one of the most neglected DEC pathotypes, as hardly any microbiological laboratories process NLF <i>E. coli</i> for EIEC.
Audio-Tactile and Peripersonal Space Processing Around the Trunk in Human Parietal and Temporal Cortex: An Intracranial EEG Study (2018)

Interactions with the environment happen within one's peripersonal space (PPS)-the space surrounding the body. Studies in monkeys and humans have highlighted a multisensory distributed cortical network representing the PPS. However, knowledge about the temporal dynamics of PPS processing around the trunk is lacking. Here, we recorded intracranial electroencephalography (iEEG) in humans while administering tactile stimulation (T), approaching auditory stimuli (A), and the 2 combined (AT). To map PPS, tactile stimulation was delivered when the sound was far, intermediate, or close to the body. The 19% of the electrodes showed AT multisensory integration. Among those, 30% showed a PPS effect, a modulation of the response as a function of the distance between the sound and body. AT multisensory integration and PPS effects had similar spatiotemporal characteristics, with an early response (~50 ms) in the insular cortex, and later responses (~200 ms) in precentral and postcentral gyri. Superior temporal cortex showed a different response pattern with AT multisensory integration at ~100 ms without a PPS effect. These results, represent the first iEEG delineation of PPS processing in humans and show that PPS and multisensory integration happen at similar neural sites and time periods, suggesting that PPS representation is based on a spatial modulation of multisensory integration.
Novel hydroxyectoines based formulations are suitable for preserving viability of <i>Limosilactobacillus fermentum</i>, <i>Levilactobacillus brevis</i> SP-48 and <i>Bifidobacterium lactis</i> HN019 during freeze-drying and storage, and in simulated gastrointestinal fluids (2023)

This study aimed at evaluating the influence of compatible solutes such as ectoine and hydroxyectoine (HOE), on bacterial cell viability during freeze-drying and storage (at 4 °C and 25 °C), in comparison to the well-established use of trehalose. Three strains, namely Limosilactobacillus fermentum, Levilactobacillus brevis SP-48, and Bifidobacterium lactis HN019 were used as models demonstrating that the highest survival rate during freeze drying was observed for cells protected with HOE. Although trehalose was more effective during lyophilization, interestingly the combination of trehalose and HOE most efficiently preserved long-term cell viability (viability loss < 0.5 log units after 6 months of storage). Finally, the ability of HOE to contribute to strain resistance in simulated gastrointestinal juices was evaluated and the latter protected all the strains tested more efficiently than all the other solutes, in particular the viability was improved from 58%, 87.5%, and 94% when cells were dried with saline solution to 88%, 98.3%, and 98% when lyophilized with HOE for L. fermentum, L. brevis, and B. lactis, respectively. In conclusion, the addition of HOE to trehalose improves the stability of probiotics during storage and enhances the survivability in simulated gastrointestinal tract conditions.
The Synthetic Bacterial Lipopeptide Pam3CSK4 Modulates Respiratory Syncytial Virus Infection Independent of TLR Activation (2010)

Respiratory syncytial virus (RSV) is an important cause of acute respiratory disease in infants, immunocompromised subjects and the elderly. However, it is unclear why most primary RSV infections are associated with relatively mild symptoms, whereas some result in severe lower respiratory tract infections and bronchiolitis. Since RSV hospitalization has been associated with respiratory bacterial co-infections, we have tested if bacterial Toll-like receptor (TLR) agonists influence RSV-A2-GFP infection in human primary cells or cell lines. The synthetic bacterial lipopeptide Pam3-Cys-Ser-Lys4 (Pam3CSK4), the prototype ligand for the heterodimeric TLR1/TLR2 complex, enhanced RSV infection in primary epithelial, myeloid and lymphoid cells. Surprisingly, enhancement was optimal when lipopeptides and virus were added simultaneously, whereas addition of Pam3CSK4 immediately after infection had no effect. We have identified two structurally related lipopeptides without TLR-signaling capacity that also modulate RSV infection, whereas Pam3CSK4-reminiscent TLR1/2 agonists did not, and conclude that modulation of infection is independent of TLR activation. A similar TLR-independent enhancement of infection could also be demonstrated for wild-type RSV strains, and for HIV-1, measles virus and human metapneumovirus. We show that the effect of Pam3CSK4 is primarily mediated by enhanced binding of RSV to its target cells. The N-palmitoylated cysteine and the cationic lysines were identified as pivotal for enhanced virus binding. Surprisingly, we observed inhibition of RSV infection in immortalized epithelial cell lines, which was shown to be related to interactions between Pam3CSK4 and negatively charged glycosaminoglycans on these cells, which are known targets for binding of laboratory-adapted but not wild-type RSV. These data suggest a potential role for bacterial lipopeptides in enhanced binding of RSV and other viruses to their target cells, thus affecting viral entry or spread independent of TLR signaling. Moreover, our results also suggest a potential application for these synthetic lipopeptides as adjuvants for live-attenuated viral vaccines.
The third parameter in reactive barrier films (2005)

Abstract The lag time of a barrier film can be dramatically increased by the addition of sacrificial scavengers that consume solute before crossing the barrier. This increase in lag time is independent of the scavengers' reaction rate. This reaction rate does affect the amount of solute that crosses the membrane before steady state, a premature leakage that may render the barrier unsuitable regardless of its putative lag time and permeability. A third parameter is needed to characterize the barrier's transient behavior. Guided by experiments, we offer two candidate parameters for quantifying these changes. Correlations of these parameters are determined numerically and compared with experimental results. © 2005 American Institute of Chemical Engineers AIChE J, 51: 456–463, 2005
Exploring the Biosynthetic Potential of TsrM, a B<sub>12</sub>‐dependent Radical SAM Methyltransferase Catalyzing Non‐radical Reactions (2022)

B<sub>12</sub> -dependent radical SAM enzymes are an emerging enzyme family with approximately 200,000 proteins. These enzymes have been shown to catalyze chemically challenging reactions such as methyl transfer to sp2- and sp3-hybridized carbon atoms. However, to date we have little information regarding their complex mechanisms and their biosynthetic potential. Here we show, using X-ray absorption spectroscopy, mutagenesis and synthetic probes that the vitamin B<sub>12</sub> -dependent radical SAM enzyme TsrM catalyzes not only C- but also N-methyl transfer reactions further expanding its synthetic versatility. We also demonstrate that TsrM has the unique ability to directly transfer a methyl group to the benzyl core of tryptophan, including the least reactive position C4. Collectively, our study supports that TsrM catalyzes non-radical reactions and establishes the usefulness of radical SAM enzymes for novel biosynthetic schemes including serial alkylation reactions at particularly inert C-H bonds.
Electronic Structure of CdSe Nanoparticles Adsorbed on Au Electrodes by an Organic Linker: Fermi Level Pinning of the HOMO (2009)

Assemblies of CdSe nanoparticles (NPs) on a dithiol-coated Au electrode were created, and their electronic energetics were quantified. This report describes the energy level alignment of the filled and unfilled electronic states of CdSe nanoparticles with respect to the Au Fermi level. Using cyclic voltammetry, it was possible to measure the energy of the filled states of the CdSe NPs with respect to the Au substrate relative to a Ag/AgNO3 electrode, and by using photoemission spectroscopy, it was possible to independently measure both the filled state energies (via single photon photoemission) and those of the unfilled states (via two photon photoemission) with respect to the vacuum level. Comparison of these two different measures shows good agreement with the IUPAC-accepted value of the absolute electrode potential. In contrast to the common model of energy level alignment, the experimental findings show that the CdSe filled states become ‘pinned’ to the Fermi level of the Au electrode, even for moderately small NP sizes.
Boosting dopamine to lift depression? (2016)

The brain reward circuit that is dysfunctional in depression can be targeted pharmacologically.
Error propagation in protocol stacks (2002)

Error control is frequently performed at multiple levels of a protocol stack. To better understand the overall performance of an entire stack from the error control perspective, we consider an idealized model consisting of two layers. The lower layer transmits cells directly over a noisy radio channel, modeled as a Gilbert channel. These cells consist of a header (H) that is distinct from the payload (P). A cell is correctly received if and only if both H and P are correct. When cell errors occur, the lower layer attempts to recover the erroneous cells through a selective repeat ARQ protocol. The higher layer protocol entity, called a connection-fragment, is composed of L cells and is successful when all its L cells are correctly received. During a prolonged outage, a large number of consecutive cells may be in error. Perceiving a lack of activity, the higher layer entity resets the connection-fragment after some time. For example, such a run of errors may indicate a loss of sync and induce a reset. We assume that the connection is reset once H+1 header errors have occurred in a row. After some time, the connection-fragment is re-established and all cells, including those that were correctly received in the prematurely aborted previous connection-fragment attempt, are retransmitted. We study the time needed to complete a connection, including packet retransmissions at the lower layer and possible reinitialization of the connection at the higher layer.
Effect of phospholipid on substrate phosphorylation by a catalytic fragment of protein kinase C. (1987)

Limited tryptic digestion of protein kinase C purified from mouse brain generated a 36-kDa fragment which no longer required Ca2+ and phospholipid for activity or bound phorbol ester. Under appropriate conditions, the isolated fragment was stable for several months at 4 degrees C or upon freezing and storage at -70 degrees C. Kinetic characteristics of the fragment were similar to those for the intact protein kinase. Although the fragment did not require phospholipid for activity, anionic phospholipids affected the extent of its activity in a pH-, substrate-, and substrate concentration-dependent manner. This effect appeared to be due to complex formation between the phospholipid and substrate. The catalytic fragment thus permits detection of a second point of interaction of phospholipid with the protein kinase C system in addition to the already described phospholipid regulatory domain.
Motion Compensated Dynamic MRI Reconstruction With Local Affine Optical Flow Estimation (2019)

This paper proposes a novel framework to reconstruct dynamic magnetic resonance imaging (DMRI) with motion compensation (MC). Specifically, by combining the intensity-based optical flow constraint with the traditional compressed sensing scheme, we are able to jointly reconstruct the DMRI sequences and estimate the interframe motion vectors. Then, the DMRI reconstruction can be refined through MC with the estimated motion field. By employing the coarse-to-fine multi-scale resolution strategy, we are able to update the motion field in different spatial scales. The estimated motion vectors need to be interpolated to the finest resolution scale to compensate the DMRI reconstruction. Moreover, the proposed framework is capable of handling a wide class of prior information (regularizations) for DMRI reconstruction, such as sparsity, low rank, and total variation. The formulated optimization problem is solved by a primal-dual algorithm with linesearch due to its efficiency when dealing with non-differentiable problems. Experiments on various DMRI datasets validate the reconstruction quality improvement using the proposed scheme in comparison to several state-of-the-art algorithms.
Abstract 5435: Molecular subclasses of human hepatocellular carcinoma predict sensitivity to fibroblast growth factor receptor inhibition (2014)

Abstract Background: A recent gene expression classification of hepatocellular carcinoma (HCC) includes two poor survival subclasses, termed S1 and S2. S1 cells are more locally invasive, while S2 cells express E-cadherin and secrete AFP. As the expression of fibroblast growth factor receptors (FGFRs) differs between the S1 and S2 gene signatures, this study investigated whether molecular subclasses of HCC could predict sensitivity to FGFR inhibition. Methods: The effects of AZD4547 and BGJ398, two small molecule inhibitors of FGFR1-4, were assessed in four S1 and five S2 human HCC cell lines. Western blotting was performed for FGFR1-4 and phosphorylated p42/44 as a marker of MAPK signaling. Small interfering RNA (siRNA) transfection was used to assess the effects of individual FGFR knockdown. Results: Cell proliferation was inhibited at least two-fold more in S2 than in S1 cell lines at all doses tested above 1 uM of BGJ398 and AZD4547 (p&amp;lt;0.002). BGJ398 also decreased MAPK signaling in S2 but not in S1 cell lines. In xenografts from the S2 cell line HuH-7, BGJ398 reduced tumor volume by 70% over 14 days and this effect was associated with decreased MAPK signaling and a 36% decline in the number of Ki67 positive cells. BGJ398 had no effect on xenografts from the S1 cell line SK-Hep. All cell lines expressed FGFR1 and FGFR2, but only S2 cell lines expressed FGFR3 and FGFR4. FGFR4 siRNA decreased proliferation by 59 ± 12% in all five S2 cell lines (p&amp;lt;0.00001), a significantly greater decrease than seen with knockdown of FGFR1, FGFR2 or FGFR3. FGFR4 knockdown also decreased MAPK signaling in S2 cell lines. Conclusions: The S2 molecular subclass of HCC is sensitive to FGFR inhibition. FGFR4-MAPK signaling plays an important role in driving proliferation of S2 cells. This classification system may help identify those patients who are most likely to benefit from inhibition of the FGFR pathway. Citation Format: Benjamin Schmidt, Lan Wei, Danielle K. DePeralta, Yujin Hoshida, Michael Lanuti, Kenneth K. Tanabe, Bryan C. Fuchs. Molecular subclasses of human hepatocellular carcinoma predict sensitivity to fibroblast growth factor receptor inhibition. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5435. doi:10.1158/1538-7445.AM2014-5435