gebhart/patrepeval huggingface dataset:
Critical Role of Multidrug Efflux Pump CmeABC in Bile Resistance and In Vivo Colonization ofCampylobacter jejuni (2003)

CmeABC functions as a multidrug efflux pump contributing to the resistance of Campylobacter to a broad range of antimicrobials. In this study, we examined the role of CmeABC in bile resistance and its contribution to the adaptation of Campylobacter jejuni in the intestinal tract of the chicken, a natural host and a major reservoir for Campylobacter. Inactivation of cmeABC drastically decreased the resistance of Campylobacter to various bile salts. Addition of choleate (2 mM) in culture medium impaired the in vitro growth of the cmeABC mutants but had no effect on the growth of the wild-type strain. Bile concentration varied in the duodenum, jejunum, and cecum of chicken intestine, and the inhibitory effect of the intestinal extracts on the in vitro growth of Campylobacter was well correlated with the total bile concentration in the individual sections of chicken intestine. When inoculated into chickens, the wild-type strain colonized the birds as early as day 2 postinoculation with a density as high as 10(7) CFU/g of feces. In contrast, the cmeABC mutants failed to colonize any of the inoculated chickens throughout the study. The minimum infective dose for the cmeABC mutant was at least 2.6 x 10(4)-fold higher than that of the wild-type strain. Complementation of the cmeABC mutants with a wild-type cmeABC allele in trans fully restored the in vitro growth in bile-containing media and the in vivo colonization to the levels of the wild-type strain. Immunoblotting analysis indicated that CmeABC is expressed and immunogenic in chickens experimentally infected with C. jejuni. Together, these findings provide compelling evidence that CmeABC, by mediating resistance to bile salts in the intestinal tract, is required for successful colonization of C. jejuni in chickens. Inhibition of CmeABC function may not only control antibiotic resistance but also prevent the in vivo colonization of pathogenic Campylobacter.
ChemInform Abstract: Asymmetric Synthesis of Highly Functionalized 8‐Oxabicyclo(3.2.1) octene Derivatives. (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
New closed-form expressions for calculating the magnetic field of thin conductors with azimuthal current direction (2003)

New closed-form expressions are derived and presented to compute the 3D magnetostatic fields of thin finite cylindrical conductors with current flowing in the azimuthal direction. All results are obtained in analytical form and enable one to easily calculate the magnetic field in either regular or singular cases. These closed-form expressions for the thin cylinders are much more convenient for applications than in previous cases.
Contribution of antibody-secreting cells induced in mucosal lymphoid tissues of pigs inoculated with respiratory or enteric strains of coronavirus to immunity against enteric coronavirus challenge. (1994)

Two antigenically related porcine coronaviruses, transmissible gastroenteritis virus (TGEV) which infects primarily the intestinal tract and causes severe diarrhea, and porcine respiratory coronavirus (PRCV) which infects the respiratory tract and causes subclinical or mild respiratory infections, presented a unique opportunity to study the interrelationship of gut-(GALT) and bronchus-associated lymphoid tissues (BALT) and their contribution to protective immunity against TGEV infection. Pigs were inoculated oral-nasally with TGEV or with PRCV at eleven days of age and challenged 24 days later with TGEV. All pigs initially given TGEV developed diarrhea and were completely protected against disease upon challenge. In contrast, pigs given PRCV had no clinical disease and shed virus in nasal secretions only; after challenge, 5 of 12 pigs developed diarrhea. Virus-specific IgG and IgA Ab-secreting cells (ASC) were enumerated by ELISPOT in the mesenteric and bronchial lymph nodes, spleens, and gut lamina propria at challenge and various post challenge days. Before challenge, in pigs exposed to TGEV, IgA-ASC in the duodenum and jejunum constituted the major ASC response. Conversely, PRCV-exposed pigs had mainly IgG-ASC in bronchial lymph nodes, with low ASC responses in the gut. After challenge, numbers of IgG-ASC increased rapidly in the gut lamina propria and mesenteric lymph nodes of only PRCV-primed pigs. Our results suggest that virus-specific IgG-ASC precursors derived in BALT of PRCV-primed pigs may migrate to the gut in response to TGEV challenge and contribute to the partial protection observed. The presence of IgA-ASC in the gut lamina propria of TGEV-primed pigs at the time of challenge correlated with complete protection against TGEV challenge. Thus a dichotomy exists in the BALT and GALT ASC responses; immunization via BALT induced a systemic type of response (IgG-ASC) and provided imperfect protection against an enteric pathogen, whereas immunization via GALT induced IgA-ASC and provided complete protection.
Synthesis and Photophysics of a 1-Pyrenyl Substituted 2‘-Deoxyuridine-5-Carboxamide Nucleoside:  Electron Transfer Products as CIS INDO/S Excited States (2000)

This paper reports results of the synthesis and photophysical study of 5-(N-carboxy-1-aminopyrenyl)-2‘-deoxyuridine (PA-dU) and its spectroscopic model N-acetyl-1-aminopyrene (PA-Ac). Absorbance and emission spectra, emission quantum yields, and emission lifetimes are reported for both compounds in three solvents. The data show that the emission yield quenching of PA-dU relative to PA-Ac varies from 95 to 99% in the solvent series THF, MeCN, and MeOH. In contrast to the monoexponential kinetics for (π,π*)1 emission from PA-Ac, the (π,π*)1 emission from the PA-dU nucleoside decays with two lifetimes in THF and three in MeCN and MeOH. The multiexponential emission decays are likely due to the presence of multiple nucleoside conformers. The average (π,π*)1 lifetimes for PA-dU in THF, MeCN, and MeOH are, respectively, 4.8, 2.7, and 0.55 ns and correspond to lifetime quenching values of 58, 81, and 96%, respectively. The lifetime quenching values for PA-dU in THF and MeCN do not agree with the emission yield quenching values in these solvents of, respectively, 95 and 96%. Thus in these two solvents the emitting states for PA-dU have lower radiative rates than do the emitting states for PA-Ac in the same solvents. However, for PA-dU in MeOH the lifetime quenching percentages of 96% over the 380−440 nm range and 98% over the 405−440 nm range are in good agreement with the emission yield quenching value of 99% in this solvent. Additionally, the emission spectrum of PA-dU in MeOH matches the (π,π*) emission spectrum of PA-Ac in MeOH, while the emission spectra of PA-dU in THF and MeCN do not match the corresponding spectra of PA-Ac. Thus choice of solvent tunes the electronic nature and the radiative rate of the emitting state in PA-dU. Emission quenching in PA-dU is assigned to intramolecular electron transfer (ET), and the 550−600 nm emission region of PA-dU reflects the relaxation dynamics of the pyrene•+/dU•- ET product. Strikingly emission lifetimes in this spectral region in all three solvents are extremely short, ≤100 ps. CIS INDO/S computations of the excited states for the 5-(N-carboxy-1-aminopyrenyl)-1-methyluracil (PA-UMe) model show that two factors are major contributors to the variation in ET product (ET1) energy among the eleven PA-UMe conformers identified. The first is the energy of the uracil LUMO (a redox effect), and the second is the pyrenyl/UMe subunit separation distance (a Coulombic effect). Importantly, the dihedral angle between the bridging carbonyl and the C5−C4 bond in UMe is strongly correlated with the energy of the uracil LUMO (R = 0.94) and thus with the ET1 energy. Finally, quantitative study of the energy of the ET1 state versus pyrenyl/UMe separation distance shows a smooth x-1 increase in ET1 energy as the separation distance increases (R = 0.9994). Additionally, the extrapolated ET1 energy at infinite subunit separation equals the difference between the LUMO and HOMO energies.
Ticket based service access for the mobile user (1997)

Article Ticket based service access for the mobile user Share on Authors: Bhrat Patel Department of Computer Science, University College London, London WC1E 6BT, United Kingdom Department of Computer Science, University College London, London WC1E 6BT, United KingdomView Profile , Jon Crowcroft Department of Computer Science, University College London, London WC1E 6BT, United Kingdom Department of Computer Science, University College London, London WC1E 6BT, United KingdomView Profile Authors Info & Claims MobiCom '97: Proceedings of the 3rd annual ACM/IEEE international conference on Mobile computing and networkingSeptember 1997 Pages 223–233https://doi.org/10.1145/262116.262150Online:26 September 1997Publication History 48citation1,023DownloadsMetricsTotal Citations48Total Downloads1,023Last 12 Months10Last 6 weeks1 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Statistical methods and software for the analysis of highthroughput reverse genetic assays using flow cytometry readouts (2006)

Highthroughput cell-based assays with flow cytometric readout provide a powerful technique for identifying components of biologic pathways and their interactors. Interpretation of these large datasets requires effective computational methods. We present a new approach that includes data pre-processing, visualization, quality assessment, and statistical inference. The software is freely available in the Bioconductor package prada. The method permits analysis of large screens to detect the effects of molecular interventions in cellular systems.
Gastrointestinal stromal tumours in patients with neurofibromatosis type 1: A case report and retrospective review of 72 cases (2012)

In the present study, the features of gastrointestinal stromal tumours ( GIST ) in patients with neurofibromatosis type 1 ( NF1 ) are analysed, and the fundamental differences between NF1 ‐associated GIST and the common types of GIST are illustrated. We report a case of NF1 ‐associated GIST, and discuss the clinical and pathological data of 71 reported cases from the P ub M ed/ MEDLINE database over the past two decades. The clinical characteristics, histopathology, biological behaviour, immunohistochemistry, phenotype and gene mutation status of GIST in NF1 are carefully reviewed. A total of 72 cases (35 females and 37 males; median age: 53 years) was included in this study. More than 80 per cent of lesions were located in the small intestine, most of which were multicentric (63.89 per cent), and the median diameter of the tumours was 4 cm (range: 0.3–20 cm). The positive expression rates for transmembrane type III receptor tyrosine kinase ( KIT) , CD34 , S ‐100, smooth muscle actin, and desmin were 100 per cent, 94.34 per cent, 37.5 per cent, 35.9 per cent and 7.41 per cent, respectively. There were just six cases found with the KIT gene mutation; no cases were found with mutations in the platelet‐derived growth factor receptor‐α ( PDGFRA ) gene. Patients with NF1 have a high risk of developing GIST . NF1 ‐associated GIST are significantly different from common GIST in terms of clinical characteristics, histopathology, biological behaviour, immunohistochemistry and the mutation status of the KIT and PDGFRA genes. In addition, in this research, we indicate that different pathogenetic mechanisms are involved in their evolution, and that i matinib has limited effects on GIST in NF1 patients.
Coordinate expression of Mn-containing superoxide dismutase and Cu,Zn-containing superoxide dismutase in human fibroblasts with trisomy 21 (1985)

The amount of Mn superoxide dismutase (MnSOD) and the activity of Cu,Zn-superoxide dismutase (CuZnSOD) have been studied in human fibroblasts of five subjects with trisomy 21 and five subjects with normal karyotype, using nuclear magnetic relaxation and polarographic methods. In the trisomic fibroblasts we have found a mean molar amount of MnSOD 25.4% lower than in the control, and an amount of CuZnSOD 54.7% higher. A positive significant correlation between the activities of both enzymes has been observed indicating that the two enzymes dismute the O2- cooperatively. However, the increase of MnSOD per unit of CuZnSOD appears significantly lower in the trisomic fibroblasts, an effect that is not due to a diminished inducibility of MnSOD. These findings suggest that the MnSOD and CuZnSOD genes interact to preserve the normal level of total SOD activity.
Spotlight on lorlatinib and its potential in the treatment of NSCLC: the evidence to date (2018)

Abstract: The identification of anaplastic lymphoma kinase ( ALK ), an oncogenetic driver mutation, in lung cancer has paved the way for a new era in the treatment of non-small cell lung cancer (NSCLC). Targeting ALK using tyrosine kinase inhibitors (TKI) has dramatically improved the prognosis of patients with ALK -rearranged NSCLC. However, most patients relapse on ALK-TKI therapy within a few years because of acquired resistance. One mechanism of acquiring resistance is a second mutation on the ALK gene, and the representative mutation is L1996M in the gatekeeper residue. In particular, the solvent-front ALK G1202R mutation is the common cause of resistance against first- and second-generation ALK-TKIs. Another major concern regarding ALK-TKI is metastasis to the central nervous system, commonly observed in patients relapsing after ALK-TKI therapy. The next-generation ALK inhibitor lorlatinib (PF-06463922) has therefore been developed to inhibit resistant ALK mutations, including ALK G1202R, and to penetrate the blood–brain barrier. In a Phase I/II trial, the safety and efficacy of lorlatinib were demonstrated in patients with advanced ALK -positive NSCLC, most of whom had central nervous system metastases and had previous ALK-TKI treatment. In this review, we discuss the structure, pharmacodynamics, and pharmacokinetics of lorlatinib and compare its characteristics with those of other ALK inhibitors. Furthermore, clinical trials for lorlatinib are summarized, and future perspectives in the management of patients with ALK -rearranged NSCLC are discussed. Keywords: non-small cell lung cancer, anaplastic lymphoma kinase, ALK inhibitor, lorlatinib
Predicting antimicrobial susceptibility from the bacterial genome: A new paradigm for one health resistance monitoring (2020)

The laboratory identification of antibacterial resistance is a cornerstone of infectious disease medicine. In vitro antimicrobial susceptibility testing has long been based on the growth response of organisms in pure culture to a defined concentration of antimicrobial agents. By comparing individual isolates to wild-type susceptibility patterns, strains with acquired resistance can be identified. Acquired resistance can also be detected genetically. After many decades of research, the inventory of genes underlying antimicrobial resistance is well known for several pathogenic genera including zoonotic enteric organisms such as Salmonella and Campylobacter and continues to grow substantially for others. With the decline in costs for large scale DNA sequencing, it is now practicable to characterize bacteria using whole genome sequencing, including the carriage of resistance genes in individual microorganisms and those present in complex biological samples. With genomics, we can generate comprehensive, detailed information on the bacterium, the mechanisms of antibiotic resistance, clues to its source, and the nature of mobile DNA elements by which resistance spreads. These developments point to a new paradigm for antimicrobial resistance detection and tracking for both clinical and public health purposes.
Smart body armor inspired by flow in bone (2011)

An understanding of biomaterials' smart properties and how biocomposite materials are manufactured by cells provides not only bio-inspiration for new classes of smart actuators and sensors but also foundational technology for smart materials and their manufacture. In this case study, I examine the unique smart properties of bone, which are evident at multiple length scales and how they provide inspiration for novel classes of mechanoactive materials. I then review potential approaches to engineer and manufacture bioinspired smart materials that can be applied to solve currently intractable problems such as the need for "smart" body armor or decor cum personal safety devices.
Redirection of lipid flux toward phospholipids in yeast increases fatty acid turnover and secretion (2018)

Bio-based production of fatty acids and fatty acid-derived products can enable sustainable substitution of petroleum-derived fuels and chemicals. However, developing new microbial cell factories for producing high levels of fatty acids requires extensive engineering of lipid metabolism, a complex and tightly regulated metabolic network. Here we generated a <i>Saccharomyces cerevisiae</i> platform strain with a simplified lipid metabolism network with high-level production of free fatty acids (FFAs) due to redirected fatty acid metabolism and reduced feedback regulation. Deletion of the main fatty acid activation genes (the first step in β-oxidation), main storage lipid formation genes, and phosphatidate phosphatase genes resulted in a constrained lipid metabolic network in which fatty acid flux was directed to a large extent toward phospholipids. This resulted in simultaneous increases of phospholipids by up to 2.8-fold and of FFAs by up to 40-fold compared with wild-type levels. Further deletion of phospholipase genes <i>PLB1</i> and <i>PLB2</i> resulted in a 46% decrease in FFA levels and 105% increase in phospholipid levels, suggesting that phospholipid hydrolysis plays an important role in FFA production when phospholipid levels are increased. The multiple deletion mutant generated allowed for a study of fatty acid dynamics in lipid metabolism and represents a platform strain with interesting properties that provide insight into the future development of lipid-related cell factories.
Adaptive source representation for distributed video coding (2009)

In the last few years distributed video coding (DVC) has become a new paradigm for video compression where the encoding process needs to be simple. DVC allows for the development of new applications where the computational complexity and the amount of memory inside the video encoder are limited. In this paper, we introduce a new data representation and coding method for DVC systems. The proposed method consists of an adaptive binary representation based on the maximum difference between the source picture and the side information. This adaptive representation provides a reduction of bitrate without any loss of information, while maintaining the low complexity of the encoder. Experimental results show a significant increase in performance over conventional DVC methods.
Oxidative Stress and Aberrant Cell Cycle in Alzheimer’s Disease Lymphocytes: Diagnostic Prospects (2015)

In Alzheimer's disease (AD), molecular changes are observed not only in patients' neurons but also in peripheral cells, such as blood lymphocytes. These include changes in the level of oxidative stress markers, mitochondria impairment, and aberrant cell cycle regulation in AD blood lymphocytes. While the concepts of early causes of AD are currently highly controversial, these findings provide support for the cell cycle hypothesis of AD pathomechanism and emphasize the systemic nature of the disease. Moreover, because of difficulties in studying dynamic processes in the human brain, lymphocytes seem to be useful for readout of AD molecular mechanisms. In addition, lymphocytes as easily accessible human cells have potential diagnostic value. We summarize current perspectives for the development of new therapeutic strategies based on oxidative stress and cell cycle dysregulation in AD, and for diagnostic methodologies involving new markers in AD lymphocytes.
Antimicrobial activity of bacteria from marine sponge Suberea mollis and bioactive metabolites of Vibrio sp. EA348 (2020)

Discovery of potential bioactive metabolites from sponge-associated bacteria have gained attraction in recent years. The current study explores the potential of sponge (<i>Suberea mollis</i>) associated bacteria against bacterial and fungal pathogens. Sponge samples were collected from Red sea in Obhur region, Jeddah, Saudi Arabia. Of 29 isolated bacteria belong to four different classes i.e. <i>Firmicutes</i> (62%), <i>γ-Proteobacteria</i> (21%), α-<i>Proteobacteria</i> (10%) and <i>Actinobacteria</i> (7%). Among them nineteen (65%) bacterial strains showed antagonistic activity against oomycetes and only 3 (10%) bacterial strains were active against human pathogenic bacteria tested. Most bioactive genera include <i>Bacillus</i> (55%), <i>Pseudovibrio</i> (13%) and <i>Ruegeria</i> (10%). Enzyme production (protease, lipase, amylase, cellualse) was identified in 12 (41%) bacterial strains where potential strains belonging to <i>γ-Proteobacteria</i> and <i>Firmicutes</i> groups. Production of antimicrobial metabolites and hydrolysates in these bacteria suggest their potential role in sponge against pathogens. Further bioactive metabolites from selected strain of <i>Vibrio</i> sp. EA348 were identified using LC-MS and GC-MS analyses. We identified many active metabolites including antibiotics such as Amifloxacin and fosfomycin. Plant growth hormones including Indoleacetic acid and Gibberellin A3 and volatile organic compound such as methyl jasmonate were also detected in this strain. Our results highlighted the importance of marine bacteria inhabiting sponges as potential source of antimicrobial compounds and plant growth hormones of pharmaceutical and agricultural significance.
SENSITOMETRY OF CRT FILM (1983)

CRT film sensitometry is very difficult compared with the method with direct photographing film. The authors created a light source simulating the wavelength of the imaging camera's emitting light by means of glass and gelatin filters. Then, using commercial exposure meter, we measured CRT film sensitometry. Problems raised in advance included the matter of antimetrical irregularity due to the difference between exposing time of the imaging camera and that of exposure meter. However, no actual problem was found as long as the experiment was concerned. Conclusively, good result was obtained in measuring CRT film sensitometry with a light source simulating the image camera's light emitting wavelength by means of filters.