gebhart/patrepeval huggingface dataset:
An unusual mechanism for resistance to the antibiotic coumermycin A1. (1991)

Bacterial DNA gyrases are type II topoisomerases made up of two A subunits and two B subunits. Coumarins are carbohydrate-containing antibiotics that inhibit topoisomerases II by competing with ATP for binding to the enzymes. High resistance to coumarins is produced in bacterial species by mutations in gyrB, the gene encoding subunit B. We have found an unusual mechanism of resistance to coumarins in Escherichia coli. This mechanism is exhibited by cells containing the wild-type gyrB, or its 5' half, in high copy number. Since homologous mutant gyrB (coumermycin resistant) truncated genes did not confer drug resistance at all under the same conditions, we propose that this mechanism of resistance is due to drug sequestration by the overproduced wild-type GyrB polypeptides. A corollary of this is that the amino half of GyrB is required and sufficient to fashion the ATP-binding domain of DNA gyrase, a conclusion that was further supported by mapping three independent coumarin-resistant mutations at Arg-136 of GyrB. Just upstream of this residue there is a glycine-rich sequence highly conserved in all topoisomerases II, which seems to be a good candidate for the actual ATP-binding site.
Antimicrobial Activity of Peptidomimetics against Multidrug-Resistant Escherichia coli: A Comparative Study of Different Backbones (2012)

Novel remedies in the battle against multidrug-resistant bacterial strains are urgently needed, and one obvious approach involves antimicrobial peptides and mimics hereof. The impact of α- and β-peptoid as well as β(3)-amino acid modifications on the activity profile against β-lactamase-producing Escherichia coli was assessed by testing an array comprising different types of cationic peptidomimetics obtained by a general monomer-based solid-phase synthesis protocol. Most of the peptidomimetics possessed high to moderate activity toward multidrug-resistant E. coli as opposed to the corresponding inactive peptides. Nevertheless, differences in hemolytic activities indicate that a careful choice of backbone design constitutes a significant parameter in the search for effective cationic antimicrobial peptidomimetics targeting specific bacteria.
Under-Agarose Chemotaxis of <i>Dictyostelium discoideum</i> (2006)

In the vegetative state, Dictyostelium amoebae are chemotactic toward pterins released by bacteria, whereas during multicellular development, they become chemotactic to endogenously produced cAMP. A variety of assays have been used to visualize and quantify chemotactic movement. Under-agarose chemotaxis provides a simple and flexible assay that permits high-resolution imaging and quantification of the motility behavior of individual cells and populations by both transmitted light and fluorescence microscopy. The assay requires cells to deform a solid but flexible matrix; therefore, it also provides a way to measure defects in the ability of mutant cells to move in these restrictive conditions.
A Case of Congenital Smooth Muscle Hamartoma with Pseudo-Darier Sign (2014)

症例は生後 8 カ 月の男児。生後 2 週頃，右側胸部の褐色斑に母親が気付いた。生後 3 週頃，タオルや手で擦ることで皮疹が隆起することが数回あった。生後 1 カ 月過ぎから発毛を認め，それ以降は刺激による皮疹の隆起はなくなった。初診時には，表面に多毛を伴う 7×6 cm の不整形で境界やや不明瞭な淡褐色の局面を認めた。病理組織では，真皮全層にわたり好酸性に染まる平滑筋線維の集塊が多数見られ，大部分は毛包と無関係に増生していた。免疫染色では desmin，actin 陽性，vimentin，c-kit 陰性であった。 臨床所見と初診以前の症状，病理所見をあわせて平滑筋母斑と診断した。症状は経過とともに軽減することが多いことから，本例も特に加療は行わず経過観察中である。平滑筋母斑の報告は少なく，経過の報告も少数であるため，本例でも今後経過観察をしていく必要があると考える。
TCPs: Privileged Scaffolds for Identifying Potent LSD1 Inhibitors for Cancer Therapy (2016)

Since the first lysine-specific demethylase (KDM), lysine-specific demethylase 1 (LSD1), was characterized in 2004, several families of KDMs have been identified. LSD1 can specifically demethylate H3K4me1/2, H3K9me1/2 as well as some nonhistone substrates. It has been demonstrated to be an oncogene as well as a drug target. Hence, tens of small-molecule LSD1 inhibitors have been designed, synthesized and applied for cancer treatment. However, the two LSD1 inhibitors that have been advanced into early phase clinical trials are trans-2-phenylcyclopropylamine (TCP) derivatives, which indicate that TCP is a druggable scaffold for LSD1 inhibitor. Here, we review the design, synthesis and properties of reported TCP-based LSD1 inhibitors as well as their biological roles.
Association of a melanocortin 4 receptor (MC4R) polymorphism with performance traits in Lithuanian White pigs (2006)

The melanocortin 4 receptor is expressed in virtually all brain regions of mammals and plays an important role in energy homeostasis. Polymorphisms in this gene may thus be related to growth and obesity. In pigs, a non-synonymous polymorphic site was described (Asp298Asn) and demonstrated to affect cAMP production and to alter adenylyl cyclase signalling. Association studies revealed significant linkage of this mutation with production trait in pigs. In this study, 207 Lithuanian White pigs were genotyped at the MC4R locus and analysed on relationships between genotype and breeding values for several performance traits. The observed allele and genotype frequencies did not deviate significantly from Hardy-Weinberg equilibrium (wildtype allele 0.59; mutant allele 0.41) and are comparable with those described in other Large White populations. The mutant Asn298 allele of the MC4R gene was significantly associated with increased test daily gain, higher lean meat percentage and lower backfat thickness. There was a trend towards an improved feed conversion ratio (p = 0.065) in animals with the mutant allele whereas no significant effect was found on lifetime daily gain. These results indicate that the MC4R polymorphism should be integrated in selection programmes in the Lithuanian White to improve carcass composition.
Polyhedral Formulations and Loop Elimination Constraints for Distribution Network Expansion Planning (2013)

Distribution network expansion planning (DNEP) aims at minimizing the capital and operational cost of the expansion plan; the plan entails choosing conductor types and line construction routes together with substation installation and reinforcement that allow serving the demand while satisfying the physical and technical constraints of the expanded network. Two findings are reported in this paper. First, DNEP can be exactly formulated as a disjunctive conic program, in two equivalent formulations; both formulations admit a tight polyhedral approximation and can be solved for the globally optimal solution using software for mixed-integer linear programming (MILP). Second, the DNEP solution can be computed more efficiently when the linear relaxations of the MILP formulations are strengthened using loop elimination constraints. Numerical results on practical DNEP problems reveal that combining the parallel equivalent-circuit polyhedral formulation with the spanning tree loop elimination constraints yields MILP planning solutions with a tight relative optimality gap and within reasonable computing time. In addition, the results are at least of the same quality if not better than those reported in the recent literature.
Computational investigation of the effect of loading conditions on traumatic mandibular fracture (2019)

The mandible is the most common site of craniofacial fractures due to trauma. In forensic analysis, it is important to have tools that help investigating the amount, direction and location of impact force the causes of mandibular fractures. Finite element analysis can provide a powerful tool in such investigations. Finite element models were developed to computationally investigate the relationship between the direction/location of impact load and the potential location of the mandibular fracture. A 2000N impact force was applied on four different patterns on the mandible surface: lateral, bilateral, axial and transverse. The maximum stresses and strain, which indicate the location fractures, were found to occur either on the condyles or on the site of force application due to induced bending moment. Condyles were found to be the most vulnerable sites irrespective of the force direction. Our models suggested that symphysis fractures were associated with a direct transverse impact to this site or with a bilateral loads on the body. It was also suggested that body and ramus fractures were either associated with a direct impact force to these regions or due to impact load at the symphysis. This study demonstrated the usefulness of finite element analysis in the investigation of the relationship between the direction of impact force and mandibular fracture locations which could be utilized in post-trauma forensic analysis.
Acadesine and myocardial protection. Studies of time of administration and dose-response relations in the rat. (1992)

Acadesine improves the ability of the heart to recover from ischemia and reperfusion when administered before ischemia or with cardioplegia. The mechanism underlying the protection remains to be resolved.
A Deep-Learning-Based Sea Search and Rescue Algorithm by UAV Remote Sensing (2018)

With the promotion of economic globalization, the demand for air travel and maritime travel in all countries has increased significantly. However, the accompanying rate of accidents at sea is increasing rapidly year by year. After the accident, the survival rate of people is closely related to the speed of rescue. Artificial eyesight and radar electronic search and rescue (SAR) are limited due to inaccuracy and limited resources. The rapid development of unmanned aerial vehicle (UAV) technology in recent years has made it possible to obtain stable, high-resolution images from airborne cameras. In this paper, a method of SAR using images captured by UAVs is proposed. The detection of victim is divided into two steps. First, in order to improve the system's real-time, the possible position of a victim may be located from the image through a simple feature to avoid exhaustive search. This step is called hypothesis generation (HG). Then, the pre-trained convolutional neural network (CNN) is used to test the HG region to ensure the accuracy of the system. This step is called hypothesis verification (HV). The result shows that taking advantage of pre-processing + CNN has better comprehensive performance in SAR at sea.
Mass spectrometry - a sensitive probe of molecular geometry (1978)

The unimolecular rearrangement chemistry of molecular ~ons encountered in mass spectrometers is ideally suited for stereoanalytical purposes. This follows from the spatial dependency of the bond making stage of the rearrangement. Examples are noted which demonstrate how such rearrangements may be utilized to assign configuration with and without deuterium labelling even when only one stereoisomer is available. These rearrangements may occur from molecular ions generated by electron impact or field ionization. Chemical ionization and ion cyclotron resonance mass spectrometry are known to be sensitive to stereoisomerism but have yet to be developed as stereoanalytical devices. Simple cleavage reactions of molecular ions may reveal Stereoisomerie information when two diastereemers give rise to identical product ions. In the latter case appearance potential differences and product intensities differences mirror the enthalpic differences of the precursor neutral diastereomers. These thermochemical effects could be utilized to assign configuration tb stereoisomers.
Apoptosis and Inflammation: Role of Adipokines in Inflammatory Bowel Disease (2010)

Leptin and APN maintain the inhibition of anti-CD3-stimulated LPL-T apoptosis by enhancing Bcl-2 and Bcl-xL overexpression and promoting STAT3 phosphorylation while suppressing SOCS3.
Microglial/macrophage GRK2 determines duration of peripheral IL-1β-induced hyperalgesia: Contribution of spinal cord CX3CR1, p38 and IL-1 signaling (2010)

Chronic pain associated with inflammation is a major clinical problem, but the underlying mechanisms are incompletely understood. Recently, we reported that GRK2(+/-) mice with a approximately 50% reduction of GRK2 develop prolonged hyperalgesia following a single intraplantar injection of the pro-inflammatory cytokine interleukin-1beta (IL-1beta). Here we show that spinal microglia/macrophage GRK2 is reduced during chronic inflammation-induced hyperalgesia. Next, we applied CRE-Lox technology to create mice with low GRK2 in microglia/macrophages/granulocytes (LysM-GRK2(f/+)), or sensory neurons or astrocytes. Only mice deficient in microglial/macrophage/granulocyte GRK2 display prolonged IL-1beta-induced hyperalgesia that lasts up to 8days. Two days after intraplantar IL-1beta, increased microglial/macrophage activity occurs in the lumbar but not thoracic spinal cord of GRK2-deficient mice. Intrathecal pre-treatment with minocycline, an inhibitor of microglia/macrophage activation, accelerates resolution of hyperalgesia independent of genotype and prevents transition to chronic hyperalgesia in GRK2(+/-) mice. Ongoing hyperalgesia in GRK2(+/-) mice is reversed by minocycline administration at days 1 and 2 after IL-1beta injection. Similarly, IL-1beta-induced hyperalgesia in LysM-GRK2(f/+) mice is attenuated by intrathecal administration of anti-CX3CR1 to abrogate fractalkine signaling, the p38 inhibitor SB239063 and the IL-1 antagonist IL-1ra. These data establish that chronic inflammatory hyperalgesia is associated with reduced GRK2 in microglia/macrophages and that low GRK2 in these cells is sufficient to markedly prolong hyperalgesia after a single intraplantar injection of IL-1beta. Ongoing hyperalgesia is maintained by spinal microglial/macrophage activity, fractalkine signaling, p38 activation and IL-1 signaling. We propose that chronic inflammation decreases spinal microglial/macrophage GRK2, which prevents silencing of microglia/macrophage activity and thereby contributes to prolonged hyperalgesia.
Effects of the gap junction blocker glycyrrhetinic acid on gastrointestinal smooth muscle cells (2004)

In the tunica muscularis of the gastrointestinal (GI) tract, gap junctions form low-resistance pathways between pacemaker cells known as interstitial cells of Cajal (ICCs) and between ICC and smooth muscle cells. Coupling via these junctions facilitates electrical slow-wave propagation and responses of smooth muscle to enteric motor nerves. Glycyrrhetinic acid (GA) has been shown to uncouple gap junctions, but previous studies have shown apparent nonspecific effects of GA in a variety of tissues. We tested the effects of GA using isometric force measurements, intracellular microelectrode recordings, the patch-clamp technique, and the spread of Lucifer yellow within cultured ICC networks. In murine small intestinal muscles, beta-GA (10 muM) decreased phasic contractions and depolarized resting membrane potential. Preincubation of GA inhibited the spread of Lucifer yellow, increased input resistance, and decreased cell capacitance in ICC networks, suggesting that GA uncoupled ICCs. In patch-clamp experiments of isolated jejunal myocytes, GA significantly decreased L-type Ca(2+) current in a dose-dependent manner without affecting the voltage dependence of this current. The IC(50) for Ca(2+) currents was 1.9 muM, which is lower than the concentrations used to block gap junctions. GA also significantly increased large-conductance Ca(2+)-activated K(+) currents but decreased net delayed rectifier K(+) currents, including 4-aminopyridine and tetraethylammonium-resistant currents. In conclusion, the reduction of phasic contractile activity of GI muscles by GA is likely a consequence of its inhibitory effects on gap junctions and voltage-dependent Ca(2+) currents. Membrane depolarization may be a consequence of uncoupling effects of GA on gap junctions between ICCs and smooth muscles and inhibition of K(+) conductances in smooth muscle cells.
Evidence-based Risk Stratification for Sport Medicine Procedures During the COVID-19 Pandemic (2020)

Orthopaedic practices have been markedly affected by the emergence of the COVID-19 pandemic. Despite the ban on elective procedures, it is impossible to define the medical urgency of a case solely on whether a case is on an elective surgery schedule. Orthopaedic surgical procedures should consider COVID-19-associated risks and an assimilation of all available disease dependent, disease independent, and logistical information that is tailored to each patient, institution, and region. Using an evidence-based risk stratification of clinical urgency, we provide a framework for prioritization of orthopaedic sport medicine procedures that encompasses such factors. This can be used to facilitate the risk-benefit assessment of the timing and setting of a procedure during the COVID-19 pandemic.
Heterogeneous formation of nitryl chloride and its role as a nocturnal NOx reservoir species during CalNex‐LA 2010 (2013)

Abstract The nocturnal conversion of dinitrogen pentoxide (N 2 O 5 ) to nitryl chloride (ClNO 2 ) on chloride‐containing aerosol can be a regionally important NO x (= NO + NO 2 ) recycling and halogen activation pathway that affects oxidant photochemistry the following day. Here we present a comprehensive measurement data set acquired at Pasadena, California, during the CalNex‐LA campaign 2010 that included measurements of odd nitrogen and its major components (NO y = NO x + NO 3 + 2N 2 O 5 + ClNO 2 + HNO 3 + HONO + peroxyacyl, alkyl, and aerosol nitrates) and aerosol size distribution and composition. Nitryl chloride was present during every night of the study (median mixing ratio at sunrise 800 pptv) and was usually a more significant nocturnal NO x and odd oxygen (O x = O 3 + NO 2 + 3N 2 O 5 + ClNO 2 ) reservoir species than N 2 O 5 (whose concentrations were calculated from its equilibrium with NO 2 and NO 3 ). At sunrise, ClNO 2 accounted for 21% of NO z (=NO y − NO x ), 4% of NO y , and 2.5% of O x , respectively (median values). Kinetic parameters for the N 2 O 5 to ClNO 2 conversion were estimated by relating ClNO 2 concentrations to their time‐integrated heterogeneous production from N 2 O 5 and were highly variable between nights. Production of ClNO 2 required conversion of N 2 O 5 on submicron aerosol with average yield (φ) and N 2 O 5 reactive uptake probability (γ) of γφ = 0.008 (maximum 0.04), scaled with submicron aerosol chloride content, and was suppressed by aerosol organic matter and liquid water content. Not all of the observed variability of ClNO 2 production efficiency could be rationalized using current literature parameterizations.
Dyna Planning using a Feature Based Generative Model (2018)

Dyna-style reinforcement learning is a powerful approach for problems where not much real data is available. The main idea is to supplement real trajectories, or sequences of sampled states over time, with simulated ones sampled from a learned model of the environment. However, in large state spaces, the problem of learning a good generative model of the environment has been open so far. We propose to use deep belief networks to learn an environment model for use in Dyna. We present our approach and validate it empirically on problems where the state observations consist of images. Our results demonstrate that using deep belief networks, which are full generative models, significantly outperforms the use of linear expectation models, proposed in Sutton et al. (2008)
Efficient Oxidative Dechlorination and Aromatic Ring Cleavage of Chlorinated Phenols Catalyzed by Iron Sulfophthalocyanine (1995)

An efficient method has been developed for the catalytic oxidation of pollutants that are not easily degraded. The products of the hydrogen peroxide (H(2)O(2)) oxidation of 2,4,6,-trichlorophenol (TCP) catalyzed by the iron complex 2,9,16,23-tetrasulfophthalocyanine (FePcS) were observed to be chloromaleic, chlorofumaric, maleic, and fumaric acids from dechlorination and aromatic cycle cleavage, as well as additional products that resulted from oxidative coupling. Quantitative analysis of the TCP oxidation reaction revealed that up to two chloride ions were released per TCP molecule. This chemical system, consisting of an environmentally safe oxidant (H(2)O(2)) and an easily accessible catalyst (FePcS), can perform several key steps in the oxidative mineralization of TCP, a paradigm of recalcitrant pollutants.
STUDY OF SIFT DESCRIPTORS FOR IMAGE MATCHING BASED LOCALIZATION IN URBAN STREET VIEW CONTEXT (2010)

In this paper we evaluate the quality of vote-based retrieval using SIFT descriptors in a database of street view photography, a challeging context where the fraction of mismatched descriptors tends to be very high. This work is part of the iTowns project, for which high resolution street views of Paris have been taken. The goal is to retrieve the views of a urban scene given a query picture. We have carried out experiments for several techniques of image matching, including a post-processing step to check the geometric consistency of the results. We have shown that the efficiency of SIFT based matching depends largely on the image database content, and that the post-processing step is essential to the retrieval performances. 1
Mechanism of acetylcholine release: possible involvement of presynaptic muscarinic receptors in regulation of acetylcholine release and protein phosphorylation. (1979)

Acetylcholine (AcCho) release from purely cholinergic Torpedo synaptosomes was evoked by K+ depolarization in the presence of Ca2+. Activation of muscarinic receptors, present in the synaptosomal fraction, by the agonist oxotremorine resulted in the inhibition of AcCho liberation. This inhibition was abolished by the muscarinic antagonist atropine, which by itself has no effect. These findings suggest that the muscarinic receptor, present in the electric organ of Torpedo is presynaptic and that its physiological function is to regulate AcCho release by negative feedback. The mechanism of presynaptic muscarinic inhibition was investigated by examining the effect of muscarinic ligands on synaptosomal 45Ca2+ uptake and on the level of phosphorylation of specific synaptosomal proteins. Ca2+-dependent K+ depolarization-induced synaptosomal AcCho release was accompanied by 45Ca2+ uptake and by a marked increase in the phosphorylation of a specific synaptosomal protein (band alpha) of approximately 100,000 daltons. Activation of the muscarinic receptor by the agonist oxotremorine had no detectable effect on synaptosomal 45Ca2+ uptake but resulted in the concomitant inhibition of AcCho release and of phosphorylation of band alpha. The muscarinic antagonist atropine abolished the inhibitory effect of oxotremorine both on AcCho liberation and on phosphorylation of band alpha. These findings suggest that phosphorylation of band alpha may be involved in regulation of the presynaptic processes that underly AcCho release and that activation of the muscarinic receptor by agonists may inhibit AcCho release by blocking the phosphorylation of band alpha.
trans-Bis(2-aminoanilinium-κN2)bis(oxalato-κ2O,O′)copper(II) (2003)

The title compound, [Cu(C2O4)2(C6H9N2)2], crystallizes in the space group P21/c, with the Cu atom located at a centre of symmetry. It is a neutral coordination complex in which the metal exhibits a tetragonally elongated octahedral trans-CuO4N2 coordination environment. Extensive intermolecular hydrogen bonding between the oxalate anions and the ammonium cations determines the molecular packing in the crystal.
Interactions between dietary boron and thiamine affect lipid metabolism (1991)

Standard mfERGs recorded from normal eyes and filtered 10-100 Hz contain less noise, higher SNR, and less intersubject variability than those filtered at 10-300 Hz. This underlies the finding that the 10-100 Hz filter setting identifies more retinal dysfunction than the 10-300 Hz setting.