gebhart/patrepeval huggingface dataset:
Degradation ofn-Hexadecane and Its Metabolites byPseudomonas aeruginosaunder Microaerobic and Anaerobic Denitrifying Conditions (2000)

A strategy for sequential hydrocarbon bioremediation is proposed. The initial O(2)-requiring transformation is effected by aerobic resting cells, thus avoiding a high oxygen demand. The oxygenated metabolites can then be degraded even under anaerobic conditions when supplemented with a highly water-soluble alternative electron acceptor, such as nitrate. To develop the new strategy, some phenomena were studied by examining Pseudomonas aeruginosa fermentation. The effects of dissolved oxygen (DO) concentration on n-hexadecane biodegradation were investigated first. Under microaerobic conditions, the denitrification rate decreased as the DO concentration decreased, implying that the O(2)-requiring reactions were rate limiting. The effects of different nitrate and nitrite concentrations were examined next. When cultivated aerobically in tryptic soy broth supplemented with 0 to 0.35 g of NO(2)(-)-N per liter, cells grew in all systems, but the lag phase was longer in the presence of higher nitrite concentrations. However, under anaerobic denitrifying conditions, even 0.1 g of NO(2)(-)-N per liter totally inhibited cell growth. Growth was also inhibited by high nitrate concentrations (>1 g of NO(3)(-)-N per liter). Cells were found to be more sensitive to nitrate or nitrite inhibition under denitrifying conditions than under aerobic conditions. Sequential hexadecane biodegradation by P. aeruginosa was then investigated. The initial fermentation was aerobic for cell growth and hydrocarbon oxidation to oxygenated metabolites, as confirmed by increasing dissolved total organic carbon (TOC) concentrations. The culture was then supplemented with nitrate and purged with nitrogen (N(2)). Nitrate was consumed rapidly initially. The live cell concentration, however, also decreased. The aqueous-phase TOC level decreased by about 40% during the initial active period but remained high after this period. Additional experiments confirmed that only about one-half of the derived TOC was readily consumable under anaerobic denitrifying conditions.
The Red Cell Membrane (1976)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
MICs and MBCs of clarithromycin against Mycobacterium avium within human macrophages (1993)

The inhibitory and bactericidal activities of clarithromycin were determined quantitatively against the intracellular populations of five Mycobacterium avium strains growing in monocyte-derived human macrophages. The MICs were 1.0 microgram/ml, and the MBCs ranged from 16.0 to 64.0 micrograms/ml; these values were similar to the MICs and MBCs found in broth cultures at pH 7.4 and were substantially lower than those found in broth cultures at pHs 6.8 and 5.0. Since the intracellular environment has a neutral or even an acidic pH, relatively low MICs and MBCs found in macrophage cultures can be associated with the fact that the drug concentrations in macrophages are substantially higher than those in the medium in which these cells are cultivated. Pretreatment of the macrophages 2 days prior to infection decreased the MICs twofold in comparison with results of experiments in which the drug was added to already infected macrophages.
Participation of one isozyme of cytosolic glycerophosphate dehydrogenase in the adipose conversion of 3T3 cells. (1979)

Growing surface cultures of 3T3 cells possess a low level of glycerophosphate dehydrogenase, an important enzyme in triglyceride synthesis. When 3T3-C2, a subline that does not undergo appreciable adipose conversion, reaches confluence, the level of the enzyme does not increase. In 3T3-F442A, a subline that undergoes the conversion with high frequency, the specific activity of the enzyme increases about 600-fold. The enzyme of the adipose 3T3 cells is different from that of non-adipose 3T3 cells in its thermal stability and its affinity for dihydroxyacetone phosphate. The enzyme of the adipose cells probably corresponds to the stable "adult" form of the enzyme, as described previously, and the enzyme of non-adipose 3T3 cells is probably the unstable "embryonic" form. For this reason, the change in the enzyme that takes place during the adipose conversion is greater than would be indicated simply by the total increase in specific activity. If, as seems likely, the two forms of glycerophosphate dehydrogenase are the products of independent genes, the adipose conversion may activate a hitherto silent gene for the stable enzyme.
Adenosine receptor agonists differentially regulate IL-10, TNF-alpha, and nitric oxide production in RAW 264.7 macrophages and in endotoxemic mice (1996)

Adenosine released into the extracellular space by immunologic and nonimmunologic stimuli has been shown to regulate various immune functions. In this study we report that i.p. pretreatment of mice with CGS-21680 HCl (CGS), a selective agonist of A2 adenosine receptors, at 0.2 to 2 mg/kg caused an augmentation of plasma IL-10 levels induced by i.p. injection of LPS, but decreased plasma levels of LPS-induced TNF-alpha. 2-Chloro-N6-cyclopentyladenosine (CCPA), an agonist of A1 adenosine receptors, at 0.5 mg/kg diminished LPS-induced plasma TNF-alpha concentrations, but enhanced LPS-induced IL-10 levels only at the highest dose used (2 mg/kg). The specific A3 adenosine receptor agonist 1-deoxy-1-[6-[[(3-iodophenyl)methyl]amino]-9H-purin-9-yl]-N-methyl-beta- D-ribofuranuronamide, at 0.2 and 0.5 mg/kg potentiated LPS-stimulated IL-10 production and inhibited LPS-induced TNF-alpha production. LPS-induced plasma nitrite and nitrate levels (the breakdown products of nitric oxide (NO)) were suppressed by CGS and CCPA. In the RAW 264.7 macrophage cell line, pretreatment of the cells with both CGS and CCPA inhibited LPS-induced IL-10, TNF-alpha, and NO production, each in a concentration-dependent manner. The inhibitory effect of these drugs on cytokine and NO production was associated with improved mitochondrial respiration. Neither CGS nor CCPA affected the LPS-induced nuclear translocation of transcription factor nuclear factor-kappaB in these cells. These results demonstrate that adenosine receptor stimulation differentially modulates the LPS-induced production of IL-10, TNF-alpha, and NO in vitro and in vivo. The increase in LPS-induced IL-10 production and suppression of LPS-induced TNF-alpha and NO production caused by adenosine receptor activation may explain some of the immunomodulatory actions of adenosine released in excess during inflammatory and/or ischemic insult.
Mechanisms of Bcl-2 protein function. (1998)

The Bcl-2 protein blocks a distal step in an evolutionarily conserved pathway for programmed cell death and apoptosis. The gene encoding this protein was first discovered because of its involvement in the t(14;18) chromosomal translocations commonly found in B-cell lymphomas. Overexpression of Bcl-2 also occurs in many other types of human cancers, and prevents cell death induced by nearly all anticancer drugs and radiation. Since the discovery of Bcl-2 over ten years ago, several cellular and viral homologs have been identified, some of which suppress cell death and others which promote apoptosis. Many of these proteins can interact with each other through a complex network of homo- and heterodimers. Though functionally important, dimerization events still do not explain in a broader sense how these proteins actually control cell life and death. Recent findings that Bcl-2 can function both as an ion channel and as an adapter or docking protein however are beginning to provide insights into the molecular mechanisms through which these proteins regulate the programmed cell death pathway in normalcy and disease.
Evolution of Morphology, Modulus, and Conductivity in Polymer Electrolytes Prepared via Polymerization-Induced Phase Separation (2015)

Polymer electrolytes are alternatives to liquid electrolytes traditionally used in electrochemical devices such as lithium-ion batteries and fuel cells. In particular, block polymer electrolytes are promising candidates because they self-assemble into well-defined microstructures, in which orthogonal properties can be integrated into a single material (e.g., high modulus in domain A, fast ion transport in domain B). However, the performance of block polymer electrolytes often falls short, due to the lack of long-range continuity of both domains and relatively low strength. We recently reported a simple, one-pot synthetic strategy to prepare polymer electrolytes with the highest reported combination of modulus and ionic conductivity, attributes enabled by a co-continuous, cross-linked network morphology. In this work we aim to understand the mechanism by which this nanoscale morphology is formed by performing a series of in situ, time-resolved experiments—small-angle X-ray scattering, conductivity, rheology, and reaction kinetics—to monitor the electrolyte as it transitions from a macroscopically homogeneous liquid to a microphase-separated solid. The results suggest that the chain connectivity of the diblock gives rise to isotropic concentration fluctuations that increase in amplitude and coherence such that the network morphology is ultimately produced. The kinetic trapping of this network morphology by chemical cross-linking prior to the ordering transition is shown to be critically important to the resulting advantageous bulk electrolyte properties.
Sacral Neuromodulation in Patients With Fecal Incontinence: A Single-Center Study (2004)

Sacral neuromodulation is a feasible treatment option for fecal incontinence in patients with structurally intact sphincters.
Localization of Distinct Peyer's Patch Dendritic Cell Subsets and Their Recruitment by Chemokines Macrophage Inflammatory Protein (Mip)-3α, Mip-3β, and Secondary Lymphoid Organ Chemokine (2000)

We describe the anatomical localization of three distinct dendritic cell (DC) subsets in the murine Peyer's patch (PP) and explore the role of chemokines in their recruitment. By two-color in situ immunofluorescence, CD11b(+) myeloid DCs were determined to be present in the subepithelial dome (SED) region, whereas CD8alpha(+) lymphoid DCs are present in the T cell-rich interfollicular region (IFR). DCs that lack expression of CD8alpha or CD11b (double negative) are present in both the SED and IFR. By in situ hybridization, macrophage inflammatory protein (MIP)-3alpha mRNA was dramatically expressed only by the follicle-associated epithelium overlying the SED, while its receptor, CCR6, was concentrated in the SED. In contrast, CCR7 was expressed predominantly in the IFR. Consistent with these findings, reverse transcriptase polymerase chain reaction analysis and in vitro chemotaxis assays using freshly isolated DCs revealed that CCR6 was functionally expressed only by DC subsets present in the SED, while all subsets expressed functional CCR7. Moreover, none of the splenic DC subsets migrated toward MIP-3alpha. These data support a distinct role for MIP-3alpha/CCR6 in recruitment of CD11b(+) DCs toward the mucosal surfaces and for MIP-3beta/CCR7 in attraction of CD8alpha(+) DCs to the T cell regions. Finally, we demonstrated that all DC subsets expressed an immature phenotype when freshly isolated and maintained expression of subset markers upon maturation in vitro. In contrast, CCR7 expression by myeloid PP DCs was enhanced with maturation in vitro. In addition, this subset disappeared from the SED and appeared in the IFR after microbial stimulation in vivo, suggesting that immature myeloid SED DCs capture antigens and migrate to IFR to initiate T cell responses after mucosal microbial infections.
Analysis of cytomorphologically abnormal cervical scrapes for the presence of 27 mucosotropic human papillomavirus genotypes, using polymerase chain reaction (1994)

The aim of this study was to investigate the distribution of 27 mucosotropic human papillomavirus (HPV) genotypes (HPV 6, 11, 13, 16, 18, 30, 31, 32, 33, 35, 39, 40, 42, 43, 44, 45, 51, 52, 53, 54, 55, 56, 57, 58, 59, 61 and 66) in cytomorphologically abnormal cervical scrapes (Pap IIIa-Pap IV; n = 1,373) using the polymerase chain reaction (PCR) method on crude cell suspensions. The scrapes were analyzed for the presence of HPV DNA by HPV general-primer-mediated PCR (GP-PCR), which allows the detection of a broad spectrum of HPV types at the subpicogram level. Subsequently, 2 HPV typing procedures based on either type-specific PCR (for HPV 6, 11, 16, 18, 31 and 33) or characterization of GP-PCR products by hybridization (for HPV 13, 30, 32, 35, 39, 40, 43, 44, 45, 51, 52, 53, 54, 55, 56, 57, 58, 59, 61 and 66) were applied. Increasing total HPV prevalence was found with increasing severity of dysplasia from 71% in Pap IIIa to 100% in Pap IV scrapes (carcinoma in situ). The scrapes which were positive by type-specific PCR included 47% cases of Pap IIIa, 71% cases of Pap IIIb and 90% cases of Pap IV. Moreover, 12% of Pap IIIa scrapes, 6% of Pap IIIb scrapes and 8% of Pap IV scrapes revealed positivity for one or more of the remaining HPV types, as determined by successive hybridizations of the GP-PCR products. Taking the typing data together, we noted that the level of HPV heterogeneity decreased from 22 different HPV types (HPV 6, 11, 16, 18, 31, 33, 35, 39, 40, 42, 43, 44, 45, 51, 52, 54, 55, 56, 58, 59, 61 and 66) detected in the group of Pap IIIa scrapes to 13 (HPV 6, 11, 16, 18, 31, 33, 35, 45, 51, 52, 58, 59 and 61) and 10 HPV genotypes (HPV 6, 16, 18, 31, 33, 45, 51, 52, 54 and 58) in the Pap IIIb and Pap IV classes, respectively. An increasing prevalence rate from Pap IIIa to Pap IV was found for HPV 16, 18, 31, 33, 45 and 54. The prevalence rate of identified HPV genotypes increased from 59% in Pap IIIa to 98% in Pap IV, indicating that almost all high-risk HPV genotypes related to cervical cancer in The Netherlands have been characterized.
Polyketide biosynthesis: a millennium review (2001)

The first page of this article is displayed as the abstract.
Complement factor H mutations and gene polymorphisms in haemolytic uraemic syndrome: the C-257T, the A2089G and the G2881T polymorphisms are strongly associated with the disease (2003)

Mutations in complement factor H (HF1) gene have been reported in non-Shiga toxin-associated and diarrhoea-negative haemolytic uraemic syndrome (D-HUS). We analysed the complete HF1 in 101 patients with HUS, in 32 with thrombotic thrombocytopenic purpura (TTP) and in 106 controls to evaluate the frequency of HF1 mutations, the clinical outcome in mutation and non-mutation carriers and the role of HF1 polymorphisms in the predisposition to HUS. We found 17 HF1 mutations (16 heterozygous, one homozygous) in 33 HUS patients. Thirteen mutations were located in exons XXII and XXIII. No TTP patient carried HF1 mutations. The disease manifested earlier and the mortality rate was higher in mutation carriers than in non-carriers. Kidney transplants invariably failed for disease recurrences in patients with HF1 mutations, while in non-mutated patients half of the grafts were functioning after 1 year. Three HF1 polymorphic variants were strongly associated with D-HUS: -257T (promoter region), 2089G (exonXIV, silent) and 2881T (963Asp, SCR16). The association was stronger in patients without HF1 mutations. Two or three disease-associated variants led to a higher risk of HUS than a single one. Analysis of available relatives of mutated patients revealed a penetrance of 50%. In 5/9 families the proband inherited the mutation from one parent and two disease-associated variants from the other, while unaffected carriers inherited the protective variants. In conclusion HF1 mutations are frequent in patients with D-HUS (24%). Common polymorphisms of HF1 may contribute to D-HUS manifestation in subjects with and without HF1 mutations.
The Impact of Hospital-Wide Use of a Tapered-Cuff Endotracheal Tube on the Incidence of Ventilator-Associated Pneumonia (2013)

BACKGROUND: Aspiration of colonized oropharyngeal secretions is a major factor in the pathogenesis of ventilator-associated pneumonia (VAP). A tapered-cuff endotracheal tube (ETT) has been demonstrated to reduce aspiration around the cuff. Whether these properties are efficacious in reducing VAP is not known. METHODS: This 2-period, investigator-initiated observational study was designed to assess the efficacy of a tapered-cuff ETT to reduce the VAP rate. All intubated, mechanically ventilated patients over the age of 18 were included. During the baseline period a standard, barrel-shaped-cuff ETT (Mallinckrodt Hi-Lo) was used. All ETTs throughout the hospital were then replaced with a tapered-cuff ETT (TaperGuard). The primary outcome variable was the incidence of VAP per 1,000 ventilator days. RESULTS: We included 2,849 subjects, encompassing 15,250 ventilator days. The mean ± SD monthly VAP rate was 3.29 ± 1.79/1,000 ventilator days in the standard-cuff group and 2.77 ± 2.00/1,000 ventilator days in the tapered-cuff group ( P = .65). While adherence to the VAP prevention bundle was high throughout the study, bundle adherence was significantly higher during the standard-cuff period (96.5 ± 2.7%) than in the tapered-cuff period (90.3 ± 3.5%, P = .01). CONCLUSIONS: In the setting of a VAP rate very near the average of ICUs in the United States, and where there was high adherence to a VAP prevention bundle, the use of a tapered-cuff ETT was not associated with a reduction in the VAP rate.
.beta.(Leu121-Lys122) segment of fibrinogen is in a region essential for plasminogen binding by fibrin fragment E (1984)

It was shown previously that two sequentially nonidentical regions of human fibrin(ogen), present in fragments D and E, carry specific plasminogen-binding sites [V aradi , A., & Patthy , L. (1983) Biochemistry 22, 2440-2446]. Comparison of the affinity of a variety of fragment E species for immobilized Lys-plasminogen revealed that fragment E3e [(alpha 20/24-78, beta 54-122, gamma 1-53)2] possesses a strong plasminogen-binding site, whereas fragment E3t [(alpha 20/24-78, beta 54-120, gamma 1-53)2] has 30-fold lower affinity for the affinant . Since the two fragments differ only in the beta ( Leu121 - Lys122 ) segment, this suggests that residues beta ( Leu121 - Lys122 ), present in the triple-helical connector region of fibrin(ogen), are essential for plasminogen binding by fragment E. Reduction and alkylation of fragment E3e lead to the destruction of the plasminogen-binding site, indicating that none of the separated, alkylated polypeptide chains of the fragment are able to bind to plasminogen and probably the coiled-coil superstructure of the connector region is necessary for the maintenance of the plasminogen-binding site of fragment E.
Sequences of 3' end of genome and of 5' end of open reading frame 1a of lactate dehydrogenase-elevating virus and common junction motifs between 5' leader and bodies of seven subgenomic mRNAs (1993)

The sequences of the 3'-terminal 3.7 kb of the genome and of a 1.7 kb 5' end cDNA clone of one isolate of lactate dehydrogenase-elevating virus (LDV) are reported. The 3' end sequence encodes six major independent open reading frames (ORFs 2 to 7), which are overlapping by between one and 130 nucleotides. Each ORF is expressed at the 5' end of one of six 3'-coterminal subgenomic mRNAs (mRNAs 2 to 7, respectively; 3.5 to 0.8 kb). The smallest mRNA, mRNA 7, encodes the nucleocapsid protein, VP1; mRNA 6 probably encodes the non-glycosylated envelope protein, VP2; and mRNAs 2 to 5 encode proteins of 26.0K, 21.5K, 19.2K and 22.4K, respectively, each possessing several potential N-glycosylation sites and membrane-spanning segments. About 72% of the LDV genome segment carrying ORFs 2 to 7 exhibits about 50% or higher nucleotide identity with the corresponding genome segment of swine infertility and respiratory syndrome (Lelystad) virus (LV), whereas only limited similarity is observed in discontinuous regions of the same corresponding genome segments of LDV and equine arteritis virus (EAV). EAV and LV belong to the same new group of positive-strand RNA viruses as LDV. One additional subgenomic mRNA of about 4 kb is produced in LDV- but not in EAV- or LV-infected cells. The 5' end of this mRNA (1-1) carries a continuous coding sequence. The N-terminal 80 amino acids of the predicted product exhibit about 50% identity with segments in the ORF 1b proteins of both EAV and LV. These segments are located 117 to 150 amino acids upstream of the C termini of the ORF 1b proteins of these viruses. The 5' end cDNA clone contains part of a 5' leader associated with all seven subgenomic mRNAs and the 5' end of ORF 1a. The junctions between the 5' leader and the bodies of all seven subgenomic mRNAs have been determined. Only a single junction sequence was detected for each mRNA. Linkage occurs between a 5' UAUAACC 3' sequence at the 3' end of the leader and only partially identical segments specified downstream in the genome preceding ORFs 2 to 7. The generated junctions differ for different subgenomic mRNAs but possess the consensus sequence 5' U(A/G)(U/A)AACC 3'. In mRNA 7, the UA in positions 1 and 2 are derived from the leader, but a G in position 2 in mRNAs 1-1, 3 and 4 and an A in position 3 in mRNA 6 seem to be specified by the 3' genomic sequences.(ABSTRACT TRUNCATED AT 400 WORDS)
Chronic Administration of Cannabidiol to Healthy Volunteers and Epileptic Patients (1980)

In phase 1 of the study, 3 mg/kg daily of cannabidiol (CBD) was given for 30 days to 8 health human volunteers. Another 8 volunteers received the same number of identical capsules containing glucose as placebo in a double-blind setting. Neurological and physical examinations, blood and urine analysis, ECG and EEG were performed at weekly intervals. In phase 2 of the study, 15 patients suffering from secondary generalized epilepsy with temporal focus were randomly divided into two groups. Each patient received, in a double-blind procedure, 200-300 mg daily of CBD or placebo. The drugs were administered for along as 4 1/2 months. Clinical and laboratory examinations, EEG and ECG were performed at 15- or 30-day intervals. Throughout the experiment the patients continued to take the antiepileptic drugs prescribed before the experiment, although these drugs no longer controlled the signs of the disease. All patients and volunteers tolerated CBD very well and no signs of toxicity or serious side effects were detected on examination. 4 of the 8 CBD subjects remained almost free of convulsive crises throughout the experiment and 3 other patients demonstrated partial improvement in their clinical condition. CBD was ineffective in 1 patient. The clinical condition of 7 placebo patients remained unchanged whereas the condition of 1 patient clearly improved. The potential use of CBD as an antiepileptic drug and its possible potentiating effect on other antiepileptic drugs are discussed.
Heterodyne detection of the complete electric field of femtosecond four-wave mixing signals (1998)

A novel optimized heterodyne method that recovers the complete electric field of any four-wave mixing signal at its point of origin is demonstrated. A tracer pulse is sent along the signal path and characterized at the sample by frequency-resolved optical gating. Spectral interferometry is used to determine the phase difference between the tracer and a reference pulse, the absorptive change in tracer phase in the sample, and the reference-signal phase difference. Together, these measurements allow calculation of the signal phase at the sample. The phase of three pulse-scattering signals from solutions of the infrared dye IR 144 in methanol determines the absolute signal-emission time within 0.5 fs.