gebhart/patrepeval huggingface dataset:
DNA hairpin loops in solution. Correlation between primary structure, thermostability and reactivity with single-strand-specific nuclease from mung bean (1991)

Hairpin structures formed by seven DNA inverted repeats have been studied by PAGE, UV(CD)-spectroscopy and nuclease cleavage. The hairpins consisted of (CG)3 stems and loops of 2, 3 and 4 residues. Thermal stabilities (Tm) have been determined in low and high ionic strength buffers, where the hairpins were structured in the B- and Z-DNA form respectively. The thermodynamic parameters of hairpin formation have been obtained by a two-state analysis of the hairpin-coil transitions. It is found that, on increasing the number of bases in the loop from 2 to 3 and 4, the Tms of the B-hairpins decrease, whereas the Tms of the same hairpins in the Z-form increase. This confirms previous evidence (1,2) that in a hairpin molecule the size and structure of the loop are modulated by the conformation of the helical stem. Moreover, B-hairpins with loops comprising 2, 3 and 4 bases have been digested with the single-strand-specific nuclease from mung bean. In our experimental conditions (0 degrees C) the nuclease preferentially cleaves the unbonded nucleotides of the loops. However, the rates of loop hydrolysis, which roughly follow a first-order kinetics, markedly depend on the size of the loop. At a ratio of 3 enzyme units/micrograms DNA, the half-lives of hairpins which are expected to form loops of 4, 3 and 2 residues are 90, 145 and 440 minutes respectively. Thermostability and enzymatic digestion data suggest that two-membered loops can be formed in B-hairpins but not in Z-hairpins.
The Role of Galectins in Mouse Development. (1997)

ガレクチンはβ-ガラクトシドに特異的な糖認識分子のファミリーである。分子量が14から36kDaと小さく、細胞内の分布状況も様々であることから、他の動物レクチンとは区別される。現在のところ、このガレクチン遺伝子ファミリーは10種類が同定されている。様々なガレクチンの胚形成における空間的・時間的分布を調べてみると、その発現パターンは絶えず変化しており、発生過程の様々な段階で働いていることが示唆される。胚形成におけるガレクチンの機能を解明するため、我々はガレクチン-1とガレクチン-3遺伝子を欠失させた変異体を作った。ガレクチン-1またはガレクチン-3のどちらかの変異をホモで持つ変異体は、生存も可能で繁殖能力も持っていた。子宮内での着床時に、胚の表面にガレクチン-1とガレクチン-3両方が発現されるが、両ガレクチンの二重変異ホモの胚も着床に成功し、目立った表現型もない。現在、二重変異を起こしたマウスについてより詳細な解析を行っている。
Recent advances in verocytotoxin-producing escherichia coli infections : proceedings of the 2nd International Symposium and Workshop on Verocytotoxin (Shiga-like toxin)-producing Escherichia coli Infections, Bergamo, Italy, 27-30 June 1994 (1994)

Part 1 Public health, epidemiology, food safety, and laboratory diagnosis: summary - public health epidemiology food safety laboratory diagnosis, I.K. Wachsmuth three years PCR screening for VTEC in human stools in Brussels, D. Pierard et al the role of enterohaemorrhagic E. Coli serotypes other than 0157:H7 as causes of disease, P.N. Goldwater and K.A. Bettelheim detection of verocytotoxin-producing escherichia coli in meat in Belgium, D. Pierard et al developments of a clinically useful diagnostic enzymes immunoassay for enterohemorrhagic escherichia coli infection, D.W.K. Acheson et al. Part 2 Toxin structure, function, and mechanisms of interaction with eukaryotic cells: overview of session 2 - toxin structure-function, receptors, cell biology, S.B. Calderwood identification of a candidate gal alpha-4 binding pocket in the B subunit of escherichia coli verotoxin 1, D. Bast et al the role of monocytes in the pathogenesis of the haemolytic uraemic syndrome (HUS), P.A. van Setten et al. Part 3 Virulence factors and mechanisms of pathogenicity of VTEC including mechanisms of mucosal colonization and systemic VT-induced injury: intracellular changes in 'attaching and effacing' adhesion, S. Knutton et al effects of sugars on the adhesion of vero cytotoxin-producing escherichia coli of serogroups 0157 and 0111, Y. Nishikawa et al regulation of shiga-like toxin-II production by the nucleoid-associated DNA-binding protein H-NS, I. Muhldorfer et al. Part 4 Clinical and pathophysiological aspects of the hemolytic uremic syndrome (HUS) including endothelial cell biology, inflammatory mediators, and immunity: a critical review of haemolytic uraemic syndrome pathophysiology, C.M. Taylor verocytotoxin (VT1) induces the expression of heat shock protein 70 (hsp 70) in vero and human endothelial cells, I.D. Chant et al serum and urinary cytokines in childhood haemolytic uremic syndrome and thrombotic thrombocytopenic purpura, D. Karpman et al. (Part Contents).
Light Field Image Coding Using High-Order Intrablock Prediction (2017)

This paper proposes a two-stage high-order intrablock prediction method for light field image coding. This method exploits the spatial redundancy in lenslet light field images by predicting each image block, through a geometric transformation applied to a region of the causal encoded area. Light field images comprise an array of microimages that are related by complex geometric transformations that cannot be efficiently compensated by state-of-the-art image coding techniques, which are usually based on low-order translational prediction models. The two-stage nature of the proposed method allows us to choose the order of the prediction model most suitable for each block, ranging from pure translations to projective or bilinear transformations, optimized according to an appropriate rate-distortion criterion. The proposed higher order intrablock prediction approach was integrated into a high efficiency video coding (HEVC) codec and evaluated for both unfocused and focused light field camera models, using different resolutions and microlens arrays. Experimental results show consistent bitrate savings, which can go up to 12.62%, when compared to a lower order intrablock prediction solution and 49.82% when compared to HEVC still picture coding.
Modular apparatus for electrostatic actuation of common atomic force microscope cantilevers (2015)

Piezoelectric actuation of atomic force microscope (AFM) cantilevers often suffers from spurious mechanical resonances in the loop between the signal driving the cantilever and the actual tip motion. These spurious resonances can reduce the accuracy of AFM measurements and in some cases completely obscure the cantilever response. To address these limitations, we developed a specialized AFM cantilever holder for electrostatic actuation of AFM cantilevers. The holder contains electrical contacts for the AFM cantilever chip, as well as an electrode (or electrodes) that may be precisely positioned with respect to the back of the cantilever. By controlling the voltages on the AFM cantilever and the actuation electrode(s), an electrostatic force is applied directly to the cantilever, providing a near-ideal transfer function from drive signal to tip motion. We demonstrate both static and dynamic actuations, achieved through the application of direct current and alternating current voltage schemes, respectively. As an example application, we explore contact resonance atomic force microscopy, which is a technique for measuring the mechanical properties of surfaces on the sub-micron length scale. Using multiple electrodes, we also show that the torsional resonances of the AFM cantilever may be excited electrostatically, opening the door for advanced dynamic lateral force measurements with improved accuracy and precision.
Hot water drying and briquetting of lignites (2015)

The objective of this research was to characterize the effects of hot-water drying on a Montana lignite and to see if this drying process changes the briquetting ability of the coal.A Savage lignite was hot-water-dried at temperatures between 200C and 300C in a cold-charge autoclave.Hot and cold off-gases of the drying processes were tested for their contents.The dried coals were tested for their moisture content, ash content, gross heating value and ultimate elemental contents.Briquets were made from the raw lignite and the dried coals using 5 different binders in varying concentrations.Water was.included in the briquetting mixture in some trials.All.briquets were tested for compressive strength.The off-gases mainly consisted of CO2 and nitrogen.With increasing drying temperature the dried coals exhibited a higher carbon content, lower oxygen content and a higher heating value than did the raw lignite.The moisture content of the lignite decreased with increasing drying temperature.An increase in the moisture reduction occured at a drying temperature between 240C and 260C.This is a temperature where significant CO2 production has been shown previously to occur.Compressive strength of briquets made without water decreased with increasing lignite drying temperature.Briquets made with water as part of the briquetting mixture showed a compressive strength minimum with respect to drying temperature for briquets made with a lignite dried at 2400C.Binder choice made little difference in briquet strength for briquets made using lignite dried at:300C.Binder choice had a larger impact for briquets made with the raw lignite.Water in the briqueting mixture didn't increase briquet moisture content.
Antibacterial Coatings Based on Chitosan for Pharmaceutical and Biomedical Applications (2018)

The risk of bacterial colonization of abiotic surfaces of biomedical devices poses important challenges for the pharmaceutical and biomaterials science fields. In this scenario, antibacterial coatings have been developed, using a number of different molecules and materials. Among them, chitosan is a non-cytotoxic, biocompatible biopolymer with an inherent antimicrobial activity that has been already used in a wide variety of healthcare and industrial applications. Herein, chitosan-based antibacterial coatings are critically surveyed, with a special emphasis on their production methods, pharmaceutical and biomedical applications, along with their pros and cons, and finally highlighting the key challenges to be faced and future perspectives in this field.
Automatic detection of selective arterial devices for advanced visualization during abdominal aortic aneurysm endovascular repair (2015)

Here we address the automatic segmentation of endovascular devices used in the endovascular repair (EVAR) of abdominal aortic aneurysms (AAA) that deform vascular tissues. Using this approach, the vascular structure is automatically reshaped solving the issue of misregistration observed on 2D/3D image fusion for EVAR guidance. The endovascular devices we considered are the graduated pigtail catheter (PC) used for contrast injection and the stent-graft delivery device (DD). The segmentation of the DD was enhanced using an asymmetric Frangi filter. The segmented geometries were then analysed using their specific features to remove artefacts. The radiopaque markers of the PC were enhanced using a fusion of Hessian and newly introduced gradient norm shift filters. Extensive experiments were performed using a database of images taken during 28 AAA-EVAR interventions. This dataset was divided into two parts: the first half was used to optimize parameters and the second to compile performances using optimal values obtained. The radiopaque markers of the PC were detected with a sensitivity of 88.3% and a positive predictive value (PPV) of 96%. The PC can therefore be positioned with a majority of its markers localized while the artefacts were all located inside the vessel lumen. The major parts of the DD, the dilatator tip and the pusher surfaces, were detected accurately with a sensitivity of 85.9% and a PPV of 88.7%. The less visible part of the DD, the stent enclosed within the sheath, was segmented with a sensitivity of 63.4% because the radiopacity of this region is low and uneven. The centreline of the DD in this stent region was alternatively traced within a 0.74 mm mean error. The automatic segmentation of endovascular devices during EVAR is feasible and accurate; it could be useful to perform elastic registration of the vascular lumen during endovascular repair.
Multi-Pulse Based Code Excited Linear Predictive Speech Coder with Fine Granularity Scalability for Tonal Language (2010)

The flexible bit-rate speech coder plays an important role in the modern speech communication. The MP-CELP speech coder which is a candidate of the MPEG4 natural speech coder supports a flexible and wide bit-rate range. However, a fine scalability had not been included. To support finer scalability of the coding rate, it had been studied in this study. Approach: In this study, based on the MP-CELP speech coding with HPDR technique, Fine Granularity Scalability was introduced by adjusting the amount of transmitted fixed excitation information. The FGS feature aim at changing the bit rate of the conventional coding more finely and more smoothly. Results: Through performance analysis and computer simulation, the quality of scalability of the MP-CELP coding was presented with an improvement from conventional scalable MP-CELP. The HPDR technique is also applied to the MP-CELP to use for tonal language, meanwhile it can support the core coding rate of 4.2, 5.5, 7.5 kbps and additional scaled bit rates. Conclusion: The core coder with high pitch delay resolution technique and adaptive codebook for tonal speech quality improvement has been conducted and the FGS brings about further efficient scalability.
Stereospecific and Nonstereospecific Effects of (+)- and (—)-Morphine: Evidence for a New Class of Receptors? (1977)

The unnatural (+) enantiomer of morphine had minimal activity in three opiate assays in vitro: the rat brain homogenate binding assay, the electrically stimulated guinea pig ileum assay, and the inhibition of adenylate cyclase in neuroblastoma X glioma hybrid cell homogenates. When (+)-morphine was microinfected into the periaqueductal gray (a site known to mediate morphine analgesia) of drug-naive rats, there was only minimal analgesia, but the hyperresponsivity usually observed after microinfection of (-)-morphine occurred. Also, when (+)-morphine was microinfected into the midbrain reticular formation of drug-naive rats, rotation similar to that following microinjection of (-)-morphine occurred. These behaviors were not blocked by naloxone. Significantly, they typically occur in precipitated abstinence in morphine-dependent rats. These observations suggest that there are at least two classes of receptors, one stereospecific and blocked by naloxone and the other only weakly stereospecific and not blocked by naloxone, and that precipitated abstinence may be due, in part, to a selective blockade of receptors of the former class but not of the latter.
Chemical tailoring of gelatin to adjust its chemical and physical properties for functional bioprinting (2013)

Double chemical functionalization of gelatin by methacrylation and acetylation of free amino groups enables control over both the viscous behavior of its solutions and the mechanical properties of the resulting hydrogels after photochemical crosslinking. The degree of methacrylation is controlled by the molar excess of methacrylic anhydride applied. Tenfold molar excess leads to highly methacrylated gelatin (GM<sub>10</sub>), resulting in solutions with low viscosities within the inkjet-printable range (10 wt%: 3.3 ± 0.5 mPa s, 37 °C) and crosslinked hydrogels with high storage moduli G' (10 wt%: 15.2 ± 6.4 kPa). Twofold excess of methacrylic anhydride leads to less methacrylated gelatin (GM<sub>2</sub>) proper for preparation of soft hydrogels (10 wt%: G' = 9.8 ± 4.6 mPa s) but its solutions are highly viscous (10 wt%: 14.2 ± 1.1 mPa s, 37 °C) and thus prone to clogging printing nozzles. Here we show that additional introduction of acetyl functionalities into GM<sub>2</sub> results in a significant decrease in solution viscosity (10 wt%: 2.9 ± 0.2 mPa s, 37 °C) and prevention of physical gel formation. In such a manner twofold functionalized gelatin can be inkjet-printed while the degree of chemical crosslinking remains low and the resulting gels are soft. Thus, by adjustable twofold modification of gelatin, i.e. inserting photochemically reactive and inert groups, a versatile bioink for inkjet bioprinting is created, which allows for addressing ECM based hydrogel matrices with a broad range of physical properties. Moreover, bioinks are proven to be cytocompatible and proper for inkjet printing of viable mammalian cells.
Convertible Glenoid Components Facilitate Revisions to Reverse Shoulder Arthroplasty Easier: Retrospective Review of 13 Cases (2018)

Removal of a cemented glenoid component often leads to massive glenoid bone loss, which makes it difficult to implant a new glenoid baseplate. The purpose of this study was to demonstrate the feasibility of revisions with a completely convertible system and to report clinical and radiographic results of a retrospective review of 13 cases. Between 2003 and 2011, 104 primary total shoulder arthroplasties (TSAs) were performed with an uncemented glenoid component in our group. Of these patients, 13 (average age, 64 years) were revised to reverse shoulder arthroplasty (RSA) using a modular convertible platform system and were included in this study. Average follow-up after revision was 22 months. Outcome measures included pain, range of motion, Constant-Murley scores, Simple Shoulder Tests, and subjective shoulder values. Active flexion increased significantly from a mean of 93° (range, 30°-120°) to 138° (range, 95°-170°) (P = 0.021), and active external rotation increased significantly from 8° (range, -20°-15°) to 25° (range, -10°-60°). Mean pain scores significantly improved from 4.2 to 13.3 points. The mean Constant Scores improved from 21 (range, 18-32) to 63 (range, 43-90). Subjectively, 12 patients rated their shoulder as better or much better than preoperatively. This retrospective study shows that a complete convertible system facilitates conversion of TSAs to RSAs with excellent pain relief and a significant improvement in shoulder function.
Inverse metamorphic zonation in very low-grade Tibetan zone series of SE Zanskar and its tectonic consequences (NW India, Himalaya) (1993)

The metamorphism of the carbonate rocks of the SE Zanskar Tibetan zone has been studied by `'illite crystallinity'' and calcite-dolomite thermometry. The epizonal Zangla unit overlies the anchizonal Chumik unit. This discontinuous inverse zonation demonstrates a late to post-metamorphic thrust of the first unit over the second. The studied area underwent a complex tectonic history: - The tectonic units were stacked from the NE to the SW, generating recumbent folds, NE dipping thrusts and the regional metamorphism. The compressive movements were active under lower temperature conditions, resulting in late thrusts that disturbed the metamorphic zonation. The discontinuous inverse metamorphic zonation dates from this phase. - A NE vergent backfolding phase occurred at lower temperature conditions. It caused the uplift of more metamorphic levels. - A late extensional phase is revealed by the presence of NE dipping low angle normal faults, and a major high angle fault, the Sarchu fault. The low angle normal faults locally run along earlier thrusts (composite tectonic contacts). Their throw has been sufficient to reset a normal stratigraphic superposition (young layers overlying old ones), but insufficient to erase the inverse metamorphic relationship. However, the combined action of backfolding and normal faulting can locally lessen, or even cancel, the inverse metamorphic superposition. After deduction of the normal fault translation, the vertical component of the original thrust displacement through stratigraphy is 400 m, which is a value far too low to explain the temperature difference between the two units. The horizontal component of displacement is therefore far more important than the vertical one. The regional distribution of metamorphism within the Zangla unit points out to an anchizonal front and an epizonal inner part. This fact is in agreement with nappe tectonics.
Activation of synoviolin promoter in rheumatoid synovial cells by a novel transcription complex of interleukin enhancer binding factor 3 and GA binding protein α (2008)

Our findings indicate that ILF-3, which has been known to regulate IL-2 expression in T cells, up-regulates synoviolin expression with GABPalpha in rheumatoid synovial cells. ILF-3 might be a target for RA treatment through its effect on IL-2 in T cells and synoviolin in rheumatoid synovial cells.
Basis of cerulenin resistance of two strains of Candida albicans (1995)

The basis of cerulenin resistance of Candida albicans strains 4918-2 and 4918-10 has been investigated. Parasexual genetic analyses established that cerulenin resistance to concentrations of at least 5 micrograms ml-1 is dominant in both strains. The results also showed that strain 4918-2 is heterozygous for resistance, while the change from resistance to sensitivity of strain 4918-10 is reversible. Experiments to define the mechanism(s) responsible for resistance focused on cerulenin uptake and fatty-acid synthase activity. Cerulenin uptake by strains 4918-2 and 4918-10 was 24% of that of the wild-type (strain 4918). Uptake was restored in UV-induced cerulenin-sensitive segregants of strains 4918-2 and 4918-10, and varied from 63% to 200% of parental values. Fatty-acid synthase from strains 4918-2 and 4918-10 was resistant to cerulenin as judged by differences in the inactivation of the enzyme by the agent. However, inactivation kinetics of fatty-acid synthase of cerulenin-sensitive segregants did not revert to the parental inactivation profile. Further investigation showed that nine out of ten segregants were resistant to cerulenin at concentrations between 1 and 4 micrograms ml-1 while strain 4918 was sensitive to cerulenin at all concentrations tested. Thus, the results suggest that alteration of fatty-acid synthase and changes in permeability contribute to total cerulenin resistance of each strain.
CCD mosaic technique for large-field digital mammography (1996)

The authors present a novel technique for large-field digital mammography. The instrument uses a mosaic of electronic digital imaging [charge coupled device (CCD)] arrays, novel area scanning, and a radiation exposure and scatter reducing mechanism. The imaging arrays are mounted on a carrier platform in a checker-board pattern mosaic. To fill in the gaps between array-active areas the platform Is repositioned three times and four X-ray exposures are made. The multiple image areas are then recombined by a digital computer to produce a composite image of the entire region. To reduce X-ray scatter and exposure, a lead aperture plate is interposed between X-ray source and patient. The aperture plate has a mosaic of square holes in alignment with the imaging array pattern and the plate is repositioned in synchronism with the carrier platform. The authors discuss proof-of-concept testing demonstrating technical feasibility of their approach. The instrument should be suitable for incorporation into standard mammography units. Unique features of the new technique are: large field coverage (18x24 cm); high spatial resolution (14-17 lp/mm); scatter rejection; and excellent contrast characteristics and lesion detectability under clinical conditions.