gebhart/patrepeval huggingface dataset:
Production, purification and immobilisation of inulinase from Kluyveromyces fragilis (1994)

Abstract Kluyveromyces fragilis (NCIM 3217), Kluyveromyces marxianus (NCIM 3231), Hansenula polymorpha (NCIM 3377), Pichia fermentan (NCIM 3408), Pichia polymorpha (NCIM 3419) and Debaryomyces castellii (NCIM 3446) were grown on an inulin‐based growth medium. Only K. fragilis produced extracellular inulinase with a maximum after 36 h of growth at 25–27°C. Sucrose and fructose were weak inducers of inulinase as compared to inulin whereas with glucose the inulinase level was minimal. An aqueous extract of chicory roots containing 1% fructan was a better carbon source than inulin and peptone was the best nitrogen source for the production of inulinase. The maximum yield of inulinase was about 7 units cm −3 of medium. The invertase to inulinase ratio of 10 in the culture filtrate was reduced to 1·6 on purifying inulinase by ethanol precipitation followed by chromatography on Sephadex G‐200, DEAE‐cellulose and CM‐cellulose columns. Using this purification procedure, inulinase was purified 26‐fold. With inulin as substrate, the shape of the velocity curve was nearer to a sigmoidal pattern whereas with sucrose the curve was hyperbolic. The molecular weight of inulinase was determined as 250 ± 10 kDa. The crude and purified inulinase preparations did not release sucrose or oligosaccharides from inulin, indicating that the enzyme has primarily exo‐inulinase activity. Using the metal‐link chelation method, 40% of inulinase was immobilised on cellulose. Maximum activity of crude, purified and immobilised inulinase preparations was observed at 55°C. The half‐life of immobilised inulinase at 25°C was 5 days.
Enantioselective Total Syntheses of Plectosphaeroic Acids B and C (2013)

Evolution of the synthetic strategy that culminated in the first total syntheses of the structurally unique plectosphaeroic acids B (2) and C (3) is described. The successful enantioselective route to (+)-2 and (+)-3 proceeds in 6 and 11 steps from the known hexahydro-2H-pyrazinopyrrolo[2,3-b]indole-1,4-dione 39, which in turn is available in enantiomerically pure form by chemical synthesis. The central challenge in this synthesis endeavor was uniting the hexahydro-2H-pyrazinopyrrolo[2,3-b]indole-1,4-dione and cinnabarinic acid fragments of these marine alkaloids. Critical for achieving this successful C-N bond formation was the use of an iodocinnabarinic acid diester in which the amino group was masked with two Boc substituents, a Cu(I) carboxylate complex and the weak base KOAc. The highly congested C-N bond generated in this coupling, in conjunction with the delicate nature of the densely functionalized coupling partners, provided a striking testament to the power of modern copper-mediated amination methods. Two approaches, one stereoselective, for introducing the methylthio substituents of (+)-plectosphaeroic acid B were developed. The epitrisulfide ring of (+)-plectosphaeroic acid C was formed by ring expansion of an epidisulfide precursor.
Identification and characterization of adhesive factors of Clostridium difficile involved in adhesion to human colonic enterocyte‐like Caco‐2 and mucus‐secreting HT29 cells in culture (1993)

Summary Experiments reported in this communication showed that the highly toxinogenic Cd 79685, Cd 4784, and Wilkins Clostridium difficile strains and the moderately toxinogenic FD strain grown in the presence of blood adhere to polarized monolayers of two cultured human intestinal cell lines: the human colonic epithelial Caco‐2 cells and the human mucus‐secreting HT29‐MTX cells. Scanning electron microscopy revealed that the bacteria interacted with well‐defined apical microvilli of differentiated Caco‐2 cells and that the bacteria strongly bind to the mucus layer that entirely covers the surface of the HT29‐MTX cells. The binding of C. difficile to Caco‐2 cells developed in parallel with the differentiation features of the Caco‐2 cells, suggesting that the protein(s) which constitute C. difficile‐binding sites are differentiation‐related brush border protein(s). To better define this interaction, we tentatively characterized the mechanism(s) of adhesion of C. difficile with adherence assays. It was shown that heating of C. difficile grown in the presence of blood enhanced the bacterial interaction with the brush border of the enterocyte‐like Caco‐2 cells and the human mucus‐secreting HT29‐MTX cells. A labile surface‐associated component was involved in C. difficile adhesion since washes of C. difficile grown in the presence of blood without heat shock decreased adhesion. After heating, washes of C. difficile grown in the presence of blood did not modify adhesion. Analysis of surface‐associated proteins of C. difficile subjected to different culture conditions was con‐ducted. After growth of C. difficile Cd 79685, Cd 4784, FD and Wilkins strains in the presence of blood and heating, two predominant SDS‐extractable proteins with molecular masses of 12 and 27 kDa were observed and two other proteins with masses of 48 and 31 kDa disappeared. Direct involvement of the 12 and 27 kDa surface‐associated proteins in the adhe‐sion of C. difficile strains was demonstrated by using rat polycolonal antibodies pAb 12 and pAb 27 directed against the 12 and 27kDa proteins. Indeed, adhesion to Caco‐2 cell monoiayers of C. difficiie strains grown in the presence of blood, without or with heat‐shock, was blocked. Taken together, our results suggest that C. difficiie may utilize blood components as adhesins to adhere to human intestinal cultured cells.
Global Changes in Staphylococcus aureus Gene Expression in Human Blood (2011)

Staphylococcus aureus is a leading cause of bloodstream infections worldwide. In the United States, many of these infections are caused by a strain known as USA300. Although progress has been made, our understanding of the S. aureus molecules that promote survival in human blood and ultimately facilitate metastases is incomplete. To that end, we analyzed the USA300 transcriptome during culture in human blood, human serum, and trypticase soy broth (TSB), a standard laboratory culture media. Notably, genes encoding several cytolytic toxins were up-regulated in human blood over time, and hlgA, hlgB, and hlgC (encoding gamma-hemolysin subunits HlgA, HlgB, and HlgC) were among the most highly up-regulated genes at all time points. Compared to culture supernatants from a wild-type USA300 strain (LAC), those derived from an isogenic hlgABC-deletion strain (LACDhlgABC) had significantly reduced capacity to form pores in human neutrophils and ultimately cause neutrophil lysis. Moreover, LACDhlgABC had modestly reduced ability to cause mortality in a mouse bacteremia model. On the other hand, wild-type and LACDhlgABC strains caused virtually identical abscesses in a mouse skin infection model, and bacterial survival and neutrophil lysis after phagocytosis in vitro was similar between these strains. Comparison of the cytolytic capacity of culture supernatants from wild-type and isogenic deletion strains lacking hlgABC, lukS/F-PV (encoding PVL), and/or lukDE revealed functional redundancy among twocomponent leukotoxins in vitro. These findings, along with a requirement of specific growth conditions for leukotoxin expression, may explain the apparent limited contribution of any single two-component leukotoxin to USA300 immune evasion and virulence.
Matrix-assisted laser desorption/ionization mass spectrometry of immobilized duplex DNA probes (1995)

Matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry was used to analyze short DNA duplex probes with one strand immobilized on solid supports (straptavidin-coated magnetic beads or controlled pore glass beads). Only the non-immobilized strand could be detected. Partial denaturation was found when the duplex probes were mixed with 3-hydroxypicolinic acid, ammonium citrate matrix. The strategy has several applications, such as fast DNA sequence analysis and DNA diagnostics.
Linking the Thoughts: Analysis of Argumentation Structures in Scientific Publications (2015)

This paper presents the results of an annotation study focused on the fine-grained analysis of argumentation structures in scientific publications. Our new annotation scheme specifies four types of binary argumentative relations between sentences, resulting in the representation of arguments as small graph structures. We developed an annotation tool that supports the annotation of such graphs and carried out an annotation study with four annotators on 24 scientific articles from the domain of educational research. For calculating the inter-annotator agreement, we adapted existing measures and developed a novel graphbased agreement measure which reflects the semantic similarity of different annotation graphs.
A sound decomposition system based on a deterministic plus residual model (1990)

Based on a deterministic plus residual model, a system is developed that extracts stable sinusoidal components from a musical sound and leaves a residual waveform as a result. The two components can be added to obtain an identity with the original sound. The technique is based on the short-time Fourier transform. From the set of spectra returned by the transform, the prominent peaks are detected at every frame and assigned to a number of frequency trajectories by means of a peak continuation algorithm. The relevance of this algorithm is that it detects the stable sinusoids present in the original sound (the deterministic component). Each trajectory includes an amplitude, frequency, and phase value for every analysis frame. From each trajectory, a time varying sinusoid is generated and the sum of all these sinusoids form the deterministic component. Since the synthesized waveform has preserved amplitude and phase of the original sound, a time domain subtraction succeeds in obtaining a residual waveform free of the detected sinusoidal components.
Mutation profiling of tumor DNA from plasma and tumor tissue of colorectal cancer patients with a novel, high-sensitivity multiplexed mutation detection platform (2014)

The multiplexed SCODA mutation enrichment and detection method can be applied to mutation profiling and quantitation of ctDNA, and is likely to have particular utility in the metastatic setting, including patients undergoing metastatectomy.
Migration and Granulomatous Reaction After Periurethral Injection of Polytef (Teflon) (1984)

Although patients with urinary incontinence have been treated successfully by periurethral injection of polytef paste, this study in continent animals demonstrates migration of polytef particles from the injection site. We injected polytef paste periurethrally into female dogs and male monkeys. Particles were found at 50 to 70 days in pelvic nodes in six of seven animals and lungs in four of seven (the kidneys and brain were not studied); and at 10 1/2 months in pelvic nodes, lungs, and brain in seven of seven; kidneys in four of seven; and spleen in two of seven. X-ray microanalysis confirmed that the particles were polytef. At 10 1/2 months, polytef granulomas were found at all injection sites and some sites of distant migration. Since these granulomas signify chronic foreign-body reaction, we believe that until the long-term effects in humans are known, polytef paste should not be used in children or young adults with normal life expectancy.
Cancer prevention by bovine lactoferrin and underlying mechanisms a review of experimental and clinical studies (2002)

In experimental studies, bovine lactoferrin (bLF) has been found to significantly inhibit colon, esophagus, lung, and bladder carcinogenesis in rats when administered orally in the post-initiation stage. Furthermore, concomitant administration with carcinogens resulted in inhibition of colon carcinogenesis, possibly by suppression of phase I enzymes, such as cytochrome P450 1A2 (CYP1A2), which is preferentially induced by carcinogenic heterocyclic amines. Enhancement of the activities of their phase II counterparts, such as glutathione S-transferase might have also played a critical role in post-initiation suppression in a study of tongue carcinogenesis. Anti-metastatic effects were moreover detected when bLF was given intragastrically to mice bearing highly metastatic colon carcinoma 26 cells (Co 26Lu), with apparent enhancing influence on local and systemic immunity. Marked increase in the number of cytotoxic T and NK cells in the mucosal layer of the small intestine and peripheral blood cells was thus found, this in turn enhancing the production of Interleukin 18 (IL-18) and caspase-1 in the epithelial cells of the small intestine, with possible consequent induction of interferon (IFN)-gamma positive cells. Furthermore, bLF has been found to exert anti-hepatitis C virus (HCV) activity in a preliminary clinical trial in patients with chronic active hepatitis due to this virus, a main causative factor in hepatocellular carcinoma development in Japanese. More extensive clinical trials are now underway in the National Cancer Center Hospital and other institutes to further explore the preventive potential against colon carcinogenesis.
A hyperactive piggyBac transposase for mammalian applications (2011)

DNA transposons have been widely used for transgenesis and insertional mutagenesis in various organisms. Among the transposons active in mammalian cells, the moth-derived transposon piggyBac is most promising with its highly efficient transposition, large cargo capacity, and precise repair of the donor site. Here we report the generation of a hyperactive piggyBac transposase. The active transposition of piggyBac in multiple organisms allowed us to screen a transposase mutant library in yeast for hyperactive mutants and then to test candidates in mouse ES cells. We isolated 18 hyperactive mutants in yeast, among which five were also hyperactive in mammalian cells. By combining all mutations, a total of 7 aa substitutions, into a single reading frame, we generated a unique hyperactive piggyBac transposase with 17-fold and ninefold increases in excision and integration, respectively. We showed its applicability by demonstrating an increased efficiency of generation of transgene-free mouse induced pluripotent stem cells. We also analyzed whether this hyperactive piggyBac transposase affects the genomic integrity of the host cells. The frequency of footprints left by the hyperactive piggyBac transposase was as low as WT transposase (~1%) and we found no evidence that the expression of the transposase affects genomic integrity. This hyperactive piggyBac transposase expands the utility of the piggyBac transposon for applications in mammalian genetics and gene therapy.
Valproic acid, a mood stabilizer and anticonvulsant, protects rat cerebral cortical neurons from spontaneous cell death: a role of histone deacetylase inhibition (2003)

We studied the neuroprotective effects of valproic acid (VPA), a primary mood stabilizer and anticonvulsant, in cultured rat cerebral cortical neurons (CCNs). CCNs underwent spontaneous cell death when their age increased in culture. As shown by mitochondrial activity and calcein-AM assays, treatment of CCNs with VPA starting from day 9 in vitro markedly increased viability and prolonged the life span of the cultures. The neuroprotective action of VPA was time-dependent and occurred at therapeutic levels with a maximal effect at about 0.5 mM. LiCl (1 mM) also protected CCNs from aging-induced, spontaneous cell death but less effectively. VPA-induced neuroprotection in aging CCN cultures was associated with a robust increase in histone H3 acetylation levels and the protective effect was mimicked by treatment with a histone deacetylase inhibitor, trichostatin A, but not by VPA analogs which are inactive in blocking histone deacetylase. Our results suggest a role of histone deacetylase inhibition in mediating the neuroprotective action of VPA.
Polybasic KKR Motif in the Cytoplasmic Tail of Nipah Virus Fusion Protein Modulates Membrane Fusion by Inside-Out Signaling (2007)

The cytoplasmic tails of the envelope proteins from multiple viruses are known to contain determinants that affect their fusogenic capacities. Here we report that specific residues in the cytoplasmic tail of the Nipah virus fusion protein (NiV-F) modulate its fusogenic activity. Truncation of the cytoplasmic tail of NiV-F greatly inhibited cell-cell fusion. Deletion and alanine scan analysis identified a tribasic KKR motif in the membrane-adjacent region as important for modulating cell-cell fusion. The K1A mutation increased fusion 5.5-fold, while the K2A and R3A mutations decreased fusion 3- to 5-fold. These results were corroborated in a reverse-pseudotyped viral entry assay, where receptor-pseudotyped reporter virus was used to infect cells expressing wild-type or mutant NiV envelope glycoproteins. Differential monoclonal antibody binding data indicated that hyper- or hypofusogenic mutations in the KKR motif affected the ectodomain conformation of NiV-F, which in turn resulted in faster or slower six-helix bundle formation, respectively. However, we also present evidence that the hypofusogenic phenotypes of the K2A and R3A mutants were effected via distinct mechanisms. Interestingly, the K2A mutant was also markedly excluded from lipid rafts, where approximately 20% of wild-type F and the other mutants can be found. Finally, we found a strong negative correlation between the relative fusogenic capacities of these cytoplasmic-tail mutants and the avidities of NiV-F and NiV-G interactions (P = 0.007, r(2) = 0.82). In toto, our data suggest that inside-out signaling by specific residues in the cytoplasmic tail of NiV-F can modulate its fusogenicity by multiple distinct mechanisms.
Photoacoustic reconstruction using beamformed RF data: a synthetic aperture imaging approach (2015)

Photoacoustic (PA) imaging is becoming an important tool for various clinical and pre-clinical applications. Acquiring pre-beamformed channel ultrasound data is essential to reconstruct PA images. Accessing these pre-beamformed channel data requires custom hardware to allow parallel beam-forming, and is available for only few research ultrasound platforms. However, post-beamformed radio frequency (RF) data is readily available in real-time and in several clinical and research ultrasound platforms. To broaden the impact of clinical PA imaging, our goal is to devise new PA reconstruction approach based on these post-beamformed RF data. In this paper, we propose to generate PA image by using a single receive focus beamformed RF data. These beamformed RF data are considered as pre-beamformed input data to a synthetic aperture beamforming algorithm, where the focal point per received RF line is a virtual element. The image resolution is determined by the fixed focusing depth as well as the aperture size used in fixed focusing. In addition, the signal-to-noise (SNR) improvement is expected because beamforming is performed twice with different noise distribution. The performance of the proposed method is analyzed through simulation, the practical feasibility is validated experimentally. The results indicate that the post-beamformed RF data has potential to be re-beamformed to a PA image using the proposed synthetic aperture beamformer.
Healing after Arterial Dilatation with Radiofrequency Thermal and Nonthermal Balloon Angioplasty Systems (1993)

Thermal balloon angioplasty has been proposed as a means of reducing acute and delayed reclosure of arteries after percutaneous transluminal balloon angioplasty. A radiofrequency (rf) balloon catheter was used to perform thermal balloon angioplasty on canine arteries in vivo. The histologic appearance of rf-treated sites was compared with that of control sites treated by conventional percutaneous transluminal angioplasty. Acutely, rf-treated sites showed a reduced medial cellularity with preservation of internal elastic lamina except at the transitional zone between thermal injury and normal artery, where localized internal elastic lamina disruption was found. Nonthermal sites showed generalized disruption of internal elastic lamina and normal medial cellularity. Both thermal and nonthermal sites displayed a return of intimal cover commencing at 1 to 2 weeks and completed by 4 weeks. Diffuse myointimal hyperplasia appeared by 2 weeks after injury at breaks in the internal elastic lamina along the nonthermal vessels but was localized to the transitional zone in thermal injury sites. In rf-treated vessels, repopulation of the acellular thermally modified media had commenced by 4 weeks, and by 8 weeks the media was diffusely repopulated by spindle-shaped cells resembling smooth muscle cells lying between and aligned with preserved connective tissue laminae. Overall, the distribution and extent of the proliferative response after rf thermal balloon angioplasty were less than those seen after nonthermal balloon angioplasty. Thermal sites, which underwent reintimalization before medial cells returned, were considerably less prone to the development of myointimal hyperplasia. These results suggest that this modality may have beneficial effects on arterial healing after angioplasty.
Regulation of matrix metalloproteinase-9 and inhibition of tumor invasion by the membrane-anchored glycoprotein RECK (1998)

A human fibroblast cDNA expression library was screened for cDNA clones giving rise to flat colonies when transfected into v-Ki-ras-transformed NIH 3T3 cells. One such gene, RECK, encodes a membrane-anchored glycoprotein of about 110 kDa with multiple epidermal growth factor-like repeats and serine-protease inhibitor-like domains. While RECK mRNA is expressed in various human tissues and untransformed cells, it is undetectable in tumor-derived cell lines and oncogenically transformed cells. Restored expression of RECK in malignant cells resulted in suppression of invasive activity with concomitant decrease in the secretion of matrix metalloproteinase-9 (MMP-9), a key enzyme involved in tumor invasion and metastasis. Moreover, purified RECK protein was found to bind to, and inhibit the proteolytic activity of, MMP-9. Thus, RECK may link oncogenic signals to tumor invasion and metastasis.
Inhibition of vesicular stomatitis viral mRNA synthesis by interferons (1987)

Interferon (IFN) treatment inhibited the replication of vesicular stomatitis virus (VSV) in human GM2767 and mouse JLSV-11 cells. The replication of this virus in either human RD-114 or mouse A402 cells was insensitive to IFN treatment. We analyzed various steps in the VSV life cycle as they occurred under different conditions of IFN treatment to identify the point(s) at which IFN was exerting its inhibitory effect. IFN treatment led to strong inhibition of viral protein synthesis and accumulation of viral RNA in both lines of IFN-sensitive cells. No such effect was observed in the IFN-resistant cells. Using a temperature-sensitive mutant (tsG41) and wild-type VSV that were not undergoing protein synthesis, we determined that the major site of action of IFN against VSV replication in JLSV-11 and GM2767 cells was at the level of primary viral transcription. The accumulation of primary viral transcripts was strongly inhibited in these cells by IFN treatment. This effect was not a consequence of any effect of IFN on virus entry and uncoating. Thus, it appears that IFN exerts a direct effect on the VSV transcriptional process in GM2767 and JLSV-11 cells.