gebhart/patrepeval huggingface dataset:
Correlation of β-Lactamase Production and Colistin Resistance among Enterobacteriaceae Isolates from a Global Surveillance Program (2015)

The increasing use of carbapenems for treating multidrug-resistant (MDR) Gram-negative bacterial infections has contributed to the global dissemination of carbapenem-resistant Enterobacteriaceae (CRE). Serine and metallo-β-lactamases (MBLs) that hydrolyze carbapenems have become prevalent and endemic in some countries, necessitating the use of older classes of agents, such as colistin. A total of 19,719 isolates of Enterobacteriaceae (excluding Proteeae and Serratia spp., which have innate resistance to colistin) were collected from infected patients during 2012 and 2013 in a global surveillance program and tested for antimicrobial susceptibility using CLSI methods. Isolates of CRE were characterized for carbapenemases and extended-spectrum β-lactamases (ESBLs) by PCR and sequencing. Using EUCAST breakpoints, the rate of colistin susceptibility was 98.4% overall, but it was reduced to 88.0% among 482 carbapenemase-positive isolates. Colistin susceptibility was higher among MBL-positive isolates (92.6%) than those positive for a KPC (87.9%) or OXA-48 (84.2%). Of the agents tested, only tigecycline (MIC90, 2 to 4 μg/ml) and aztreonam-avibactam (MIC90, 0.5 to 1 μg/ml) consistently tested with low MIC values against colistin-resistant, ESBL-positive, and carbapenemase-positive isolates. Among the 309 (1.6%) colistin-resistant isolates from 10 species collected in 38 countries, 58 carried a carbapenemase that included KPCs (38 isolates), MBLs (6 isolates), and OXA-48 (12 isolates). These isolates were distributed globally (16 countries), and 95% were Klebsiella pneumoniae. Thirty-nine (67.2%) isolates carried additional ESBL variants of CTX-M, SHV, and VEB. This sample of Enterobacteriaceae demonstrated a low prevalence of colistin resistance overall. However, the wide geographic dispersion of colistin resistance within diverse genus and species groups and the higher incidence observed among carbapenemase-producing MDR pathogens are concerning.
FLC or not FLC: the other side of vernalization (2008)

Vernalization is the promotion of the competence for flowering by long periods of low temperatures such as those typically experienced during winters. In Arabidopsis, the vernalization response is, to a large extent, mediated by the repression of the floral repressor FLC, and the stable epigenetic silencing of FLC after cold treatments is essential for vernalization. In addition to FLC, other vernalization targets exist in Arabidopsis. In grasses, vernalization seems to be entirely independent of FLC. Here, the current understanding of FLC-independent branches of the vernalization pathway in Arabidopsis and vernalization without FLC in grasses is discussed. This review focuses on the role of AGL19, AGL24, and the MAF genes in Arabidopsis. Interestingly, vernalization acts through related molecular machineries on distinct targets. In particular, protein complexes similar to Drosophila Polycomb Repressive Complex 2 play a prominent role in establishing an epigenetic cellular memory for cold-regulated expression states of AGL19 and FLC. Finally, the similar network topology of the apparently independently evolved vernalization pathways of grasses and Arabidopsis is discussed.
Generic tools for conditionally altering protein abundance and phenotypes on demand (2014)

Conditional gene expression and modulating protein stability under physiological conditions are important tools in biomedical research. They led to a thorough understanding of the roles of many proteins in living organisms. Current protocols allow for manipulating levels of DNA, mRNA, and of functional proteins. Modulating concentrations of proteins of interest, their post-translational processing, and their targeted depletion or accumulation are based on a variety of underlying molecular modes of action. Several available tools allow a direct as well as rapid and reversible variation right on the spot, i.e., on the level of the active form of a gene product. The methods and protocols discussed here include inducible and tissue-specific promoter systems as well as portable degrons derived from instable donor sequences. These are either constitutively active or dormant so that they can be triggered by exogenous or developmental cues. Many of the described techniques here directly influencing the protein stability are established in yeast, cell culture and in vitro systems only, whereas the indirectly working promoter-based tools are also commonly used in higher eukaryotes. Our major goal is to link current concepts of conditionally modulating a protein of interest's activity and/or abundance and approaches for generating cell and tissue types on demand in living, multicellular organisms with special emphasis on plants.
Increased shedding of soluble fragments of P‐cadherin in nipple aspirate fluids from women with breast cancer (2008)

Breast cancer, a worldwide disease with increasing incidence, develops from ductal/lobular epithelium. Nipple aspirate fluid (NAF), secreted from the breast ducts and lobules, can be analyzed to assess breast metabolic activity. P-cadherin is frequently over-expressed in high-grade invasive breast carcinomas and has been reported to be an enhancer of migration and invasion of breast cancer cells, being correlated with tumor aggressiveness. The present study analyzed the soluble fragment of P-cadherin in milk, NAF and matched plasma samples of healthy subjects and in women with precancer conditions and breast cancer. Soluble P-cadherin was detected in all plasma and milk samples, and in about 31.3% of NAF samples. The lowest levels of soluble P-cadherin were found in plasma, with no significant difference among NoCancer, PreCancer and Cancer patients. The highest concentration of soluble P-cadherin was detected in milk collected during the first trimester of lactation, significantly with respect to all NAF samples. There were significantly higher levels of soluble P-cadherin in NAF from Cancer patients than those in women with NoCancer and PreCancer (P < 0.0001). Although no significant difference was found between in situ and invasive breast cancer, soluble P-cadherin levels were found at high concentrations in c-erbB-2-positive tumors, showing a positive correlation with disease stage grouping and tumor grade, and an inverse relationship with estrogen/progesterone receptor status. High levels of the soluble fragment of P-cadherin in Cancer NAF suggest its possible release via proteolytic processing, favoring cancer cell detachment from breast duct, and suggesting that measuring soluble P-cadherin in NAF may improve the identification of women with increased breast cancer risk.
Synthesis, crystal structures, electronic structure and magnetic behaviour of the trithiatriazapentalenyl radical, C2S3N3 (2001)

A novel synthesis of the title compound, C2S3N3 (1) is reported. X- and K-band EPR spectra on dilute solutions of 1 indicate delocalisation of the unpaired spin density over both heterocyclic rings in agreement with DFT calculations. An XRPD study indicates that it crystallises in two morphologies with both phases formed during vacuum sublimation. The XRPD studies indicate that on cooling below 230 K, only the triclinic phase (P) becomes detectable, whereas on warming above 320 K, just the monoclinic phase (P21/c) becomes observed. The crystal structure of the monoclinic phase has been examined by variable temperature single crystal X-ray diffraction in the region 300–225 K and reveals a regular π-stacked structure. A crystal structure of the triclinic phase is reported at 150 K and exhibits a dimeric π-stacked motif. Susceptibility measurements show that the monoclinic phase is paramagnetic whereas the triclinic phase is diamagnetic. This radical exhibits thermal hysteresis with a wide range of bistability; EPR and magnetic susceptibility measurements indicate Tc↓ = 234 K, and Tc↑ = 317 K. The magnetic behaviour of the monoclinic phase is consistent with strong antiferromagnetic exchange interactions between open shell doublet states (J = −320 K) along the π-stacking direction, although significant inter-stack interactions are required to model the data adequately. In contrast the dimeric phase is essentially diamagnetic, with the residual paramagnetism indicating a very large singlet–triplet separation (|2J| > 2000 K). The magnetic exchange interactions in both phases are probed through a series of DFT calculations using the broken-symmetry approach. These confirm the presence of strong magnetic exchange interactions along the π-stacking direction in the high temperature phase (2J = −182 K), but with additional interstack interactions which are an order of magnitude smaller. Calculations on the triclinic phase indicate that it is best considered as a dimer with an open-shell singlet state with a very large singlet–triplet separation (2J = −2657 K). The magnitude of J for both phases from theory and experiment are in good agreement. The origin of the thermal hysteresis is attributed to the presence of two energetically similar structures which have a low energy barrier to interconversion. The thermodynamic parameters associated with the interconversion process have been probed by DSC studies. It confirms the first order nature of the transition with Tc↓ = 232.3 K (ΔH↓ = 1.41 kJ mol−1, ΔS↓ = 6.0 J mol−1 K−1) and Tc↑ = 320.5 K (ΔH↑ = 1.86 kJ mol−1, ΔS↑ = 5.8 J mol−1 K−1).
Treatment of a chronic allodynia-like response in spinally injured rats: effects of systemically administered excitatory amino acid receptor antagonists (1996)

A chronic allodynia-like response to mechanical stimulation was observed in rats after severe spinal cord ischemia. This allodynia-like response was not relieved by most conventional analgesics used for treating chronic neuropathic pain. The present experiments evaluated the effects of systemically administered excitatory amino acid receptor antagonists, including the non-competitive N-methyl-D-aspartate (NMDA) receptor/channel blockers MK-801 and dextromethorphan, the competitive NMDA receptor antagonist CGS 19755 and a competitive antagonist of the alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic acid (AMPA) receptor NBQX, on the chronic allodynia-like response in spinally injured rats. Systemic MK-801, dextromethorphan and CGS 19755 dose-dependently relieved the mechanical allodynia-like response. Systemic MK-801 and CGS 19755, but not dextromethorphan, also induced severe motor impairment at analgesic doses. All three NMDA antagonists increased spontaneous motor activity. Systemic NBQX reduced muscle tone and caused sedation. The mechanical allodynia was only relieved by NBQX at a sedative dose. It is concluded that systemic NMDA, but not AMPA, receptor antagonists may have an analgesic effect upon the chronic allodynia-like response. However, the analgesic effect of all NMDA antagonists was associated with side effects. Dextromethorphan, which is clinically tolerated and produced less side effects, may be useful for treating chronic pain associated with central nervous system injury.
Effect of Carbon Dioxide and pH on Susceptibility of Bacteroides fragilis Group to Erythromycin (1981)

We examined the effects of pH and incubation in a CO(2)-containing atmosphere on the activity of erythromycin against 81 strains of the Bacteroides fragilis group. A striking reduction in erythromycin activity was noted when the pH decreased below 7.0 and when the organisms were incubated with CO(2).
Negative‐Refraction Metamaterials (2005)

Contributors. Preface. 1. Negative-Refractive-Index Transmission-Line Metamaterials (A. Iyer & G. Eleftheriades). 2. Passive Microwave Devices and Antennas Using Negative-Refractive-Index Transmission-Line Metamaterials (G. Eleftheriades). 3. Super Resolving Negative-Refractive-Index Transmission-Line Lenses (A. Grbic & G. Eleftheriades). 4. Gaussian Beam Interactions with DNG Metamaterials (R. Ziolkowski). 5. Negative Index Lenses (D. Schurig & D. Smith). 6. Planar Anisotropic Resonance-Cone Metamaterials (K. balmain & A. Luttgen). 7. Negative Refraction and Subwavelength Imaging in Photonic Crystals (C. Luo & J. Joannopoulos). 8. Plasmonic Nanowire Metamaterials (A. Sarychev & V. Shalaev). 9. An Overview of Salient Properties of Planar Guided-Wave Structures with Double-Negative (DNG) and Single-Negative (SNG) Layers (A Alu and N. Engheta). 10. Dispersion Engineering: The Use of Abnormal Velocities and Negative Index of Refraction to Control the Dispersive Effects (M. Mojahedi & G. Eleftheriades). Index.
The anti‐migraine 5‐HT1B/1D agonist rizatriptan inhibits neurogenic dural vasodilation in anaesthetized guinea‐pigs (2001)

These studies investigated the pharmacology of neurogenic dural vasodilation in anaesthetized guinea-pigs. Following introduction of a closed cranial window the meningeal (dural) blood vessels were visualized using intravital microscopy and the diameter constantly measured using a video dimension analyser. Dural blood vessels were constricted with endothelin-1 (3 microg kg(-1), i.v.) prior to dilation of the dural blood vessels with calcitonin gene-related peptide (CGRP; 1 microg kg(-1), i.v.) or local electrical stimulation (up to 300 microA) of the dura mater. In guinea-pigs pre-treated with the CGRP receptor antagonist CGRP((8-37)) (0.3 mg kg(-1), i.v.) the dilator response to electrical stimulation was inhibited by 85% indicating an important role of CGRP in neurogenic dural vasodilation in this species. Neurogenic dural vasodilation was also blocked by the 5-HT(1B/1D) agonist rizatriptan (100 microg kg(-1)) with estimated plasma levels commensurate with concentrations required for anti-migraine efficacy in patients. Rizatriptan did not reverse the dural dilation evoked by CGRP indicating an action on presynaptic receptors located on trigeminal sensory fibres innervating dural blood vessels. In addition, neurogenic dural vasodilation was also blocked by the selective 5-HT(1D) agonist PNU-142633 (100 microg kg(-1)) but not by the 5-HT(1F) agonist LY334370 (3 mg kg(-1)) suggesting that rizatriptan blocks neurogenic vasodilation via an action on 5-HT(1D) receptors located on perivascular trigeminal nerves to inhibit CGRP release. This mechanism may underlie one of the anti-migraine actions of the triptan class exemplified by rizatriptan and suggests that the guinea-pig is an appropriate species in which to investigate the pharmacology of neurogenic dural vasodilation.
The Effects of Age on Inflammatory and Coagulation-Fibrinolysis Response in Patients Hospitalized for Pneumonia (2010)

Modest age-related increases in coagulation response occur during hospitalization for CAP; however these differences do not explain the large differences in mortality. Despite clinical recovery, immune resolution may be delayed in older adults at discharge.
Experimental Infection of Hamsters with Campylobacter jejuni (1985)

Campylobacter jejuni is a major cause of diarrhea and enterocolitis in humans and animals. A mammalian model has been developed for studying pathogenesis of the disease in hamsters by colonizing the ileum and cecum with C. jejuni via either oral intubation after purgation or direct surgical inoculation into the cecum. This colonization resulted in production of disease including diarrhea and intestinal lesions that resembles enterocolitis due to C. jejuni in humans and domestic animals. The mucosal lesions observed grossly at autopsy included erythema of the ileum and cecum and distention of the cecum with fluid. The cecal mucosa was edematous. Epithelial lesions observed by light microscopy included focal edema, occasional hyperplasia, diffuse hyperemia, and infiltration of the lamina propria with leukocytes. C. jejuni-like bacteria penetrated the epithelium and were observed within the lamina propria of infected animals but not in uninfected controls.
Cyclische Imidsäureester aus Nitrilen und Aminoalkoholen (1974)

Abstract Durch Umsetzung der Nitrile 1 und 6 mit den Aminoalkoholen 2 und 3 in Gegenwart von katalytisch wirkenden Metallsalzen wurden die 2‐Oxazoline 4 und 7 sowie die 4 H ‐5,6‐Dihydro‐ 1,3‐oxazine 5 und 8 erhalten. Analog dargestellte 2‐Aminoalkyl‐2‐oxazoline 13 und 15 wurden bei 190–230°C zu den 2‐Alkenyl‐2‐oxazolinen 14 gespalten.
원저 : 육계,부자의 약침과 경구투여가 2형 당뇨 모델 생쥐의 혈당강하에 미치는 영향 (2010)

Objectives: This study was designed to evaluate the antidiabetes effects of Cinnamomum cassia and Aconitum carmichaeli in type II diabetes mellitus model mice. Methods: The experimental animals were divided into 3 groups and treated for 50 days as follows: control group, pharmacopuncture group and extract administration group. The effects of Cinnamomum cassia and Aconitum carmichaeli were observed by measuring body weight, blood glucose, insulin, insulin immunoreactivity of the pancreas and subpopulation of splenocytes. Results: Cinnamomum cassia sample groups were reduced a little body weight than control group. Glucose level of extract administration group lowered than control and pharmacopuncture group. Insulin immunoreactivity of Aconitum carmichaeli extract group appeared more effective than control and pharmacopuncture group. Conclusions: `This study shows that Cinnamomum cassia and Aconitum carmichaeli have a distinct antidiabetes effect in type II diabetes mellitus model.
Identification of ezrin as an 81-kDa tyrosine-phosphorylated protein in T cells (1992)

We have used APT affinity purification to isolate tyrosine-phosphorylated proteins from MRL lpr/lpr (lpr) mouse T cells. One such protein is pp81 ezrin, previously identified as a tyrosine-phosphorylated protein in epidermal growth factor-stimulated A431 carcinoma cells. Biochemical analyses in A431 and gastric parietal cells have revealed ezrin to be a cytoskeleton-associated cytosolic protein. In Jurkat T cells, however, using similar methods we have shown ezrin to be a cytosolic protein with no measurable cytoskeletal association. We also observed no increases in ezrin tyrosine phosphorylation in TCR-stimulated Jurkat T cells, unless the cells were pretreated with protein tyrosine phosphatase inhibitors, suggesting that T cell ezrin tyrosine phosphorylation is tightly controlled by protein tyrosine phosphatases. The fraction of tyrosine phosphorylated ezrin in lpr T cells was 5 to 10 times that observed in Jurkat T cells, which along with constitutive TCR-zeta phosphorylation and pp60fyn overexpression, is a feature of the lpr defect.
Elevated mRNA levels of DNA methyltransferase‐1 as an independent prognostic factor in primary nonsmall cell lung cancer (2006)

Elevated mRNA expression of DNMT1 may be an independent prognostic factor in NSCLC and CpG island hypermethylation in NSCLC may be maintained by a complex interaction of several factors rather than by a simple transcriptional up-regulation of DNMT1.
Missense mutation of the erythropoietin receptor is a rare event in human erythroid malignancies (1996)

Human erythroid malignancies (polycythemia vera [PV] and erythroleukemia) are associated with erythropoietin (Epo)-independent growth and differentiation. Missense or nonsense mutations in the Epo receptor (Epo-R) have been recently described in experimental erythroleukemia in mice and in cases of erythrocytosis in humans. To search for a similar genetic alteration in erythroleukemia and PV, we entirely sequenced the exons of the Epo-R gene as well as the intron-exon junctions in these disorders using polymerase chain reaction. In 1 of 10 cases of erythroleukemia, a single allele mutation was found in the 8th Epo-R gene exon that changed asparagine 487 into a serine. No Epo-r gene mutation was found in 12 PV cases studied, but the same mutation (N487S) was found in 1 patient with polycythemia that did not fulfill the criteria of PV (polycythemia of unknown origin). We did not detect this mutation after sequencing part of the 8th exon of the Epo-R gene from 21 other patients with polycythemia of unknown origin and 51 normal controls. The Epo-R mutation was also found in Epstein-Barr virus-derived cell lines from both cases, suggesting that it is not related to the malignant clone. Therefore, this mutation does not appear to be somatic, although no familial cases were found. The biologic effect of this mutation was subsequently studied. Erythroid progenitors from the polycythemic patient normally responded to Epo, whereas those from the erythroleukemic patient were Epo-independent due to autocrine stimulation by Epo. The normal and the mutated Epo-R were transfected into the murine Ba/F3 cell line. Both types of cells displayed the same response to Epo for proliferation, differentiation, and inhibition of apoptosis. Although this mutation may destroy a consensus binding site for Grb2, no obvious differences either in the pattern of Epo-induced tyrosine phosphorylated proteins or in the binding of Grb2 to the Epo-R were observed. In conclusion, a somatic Epo-R missense mutation does not appear to be a molecular mechanism involved in the abnormal growth of human erythroleukemia and PV. However, the Epo-R mutation (N487S) that we describe is located in the same tyrosine sequence beginning at AA 485 as the one previously observed (P488S) in as case of polycythemia (Sokol et al, Exp Hematol 22:447, 1994). These results suggest that this phosphopeptide sequence may play an important role in Epo signalling.
A history-based macro by example system (1992)

Many tasks performed using computer interfaces are very repetitive. While programmers can write macros or procedures to automate these repetitive tasks, this requires special skills. Demonstrational systems make macro building accessible to all users, but most provide either no visual representation of the macro or only a textual representation. We have developed a history-based visual representation of commands in a graphical user interface. This representation supports the definition of macros by example in several novel ways. At any time, a user can open a history window, review the commands executed in a session, select operations to encapsulate into a macro, and choose objects and their attributes as arguments. The system has facilities to generalize the macro automatically, save it for future use, and edit it.
Optically Active Cyclic Hexapeptides with Covalently Attached Pyrene Probes:  Selective Alkaline Earth Metal Ion Recognition Using Excimer Emission (2002)

[structure: see text] The synthesis of two optically active pyrene-modified cyclic hexapetides and their selectivity toward the complexation of alkaline earth metal ions are reported. Complexation was studied by optical and chiroptical methods. The cyclic peptides are forming 2:1 sandwich complexes with the metal ions.
Cloning of Baeyer‐Villiger monooxygenases from Comamonas , Xanthobacter and Rhodococcus using polymerase chain reaction with highly degenerate primers (2003)

To clone novel type 1 Baeyer-Villiger monooxygenase (BVMO) genes, we isolated or collected 25 bacterial strains able to grow on alicyclic compounds. Twelve of the bacterial strains yielded polymerase chain reaction (PCR) fragments with highly degenerate primers based on the sequences of known and putative BVMOs. All these fragments were found to encode peptides homologous to published BVMO sequences. The complete BVMO genes and flanking DNA were cloned from a Comamonas, a Xanthobacter and a Rhodococcus strain using the PCR fragments as probes. BVMO genes cloned from the first two strains could be expressed to high levels in Escherichia coli using standard expression vectors, and the recombinants converted cyclopentanone and cyclohexanone to the corresponding lactones. The Rhodococcus BVMO, a putative steroid monooxygenase, could be expressed after modification of the N-terminal sequence. However, recombinants expressing this protein did not show activity towards progesterone. An esterase homologue located directly upstream of the Xanthobacter BVMO gene and a dehydrogenase homologue encoded directly downstream of the Comamonas sp. NCIMB 9872 BVMO gene were also expressed in E. coli and shown to specify lactone hydrolase and cyclohexanol dehydrogenase activity respectively.