gebhart/patrepeval huggingface dataset:
Genetic analysis of the <i>rfb</i> region of <i>Shigella flexneri</i> encoding the Y serotype O‐antigen specificity (1991)

The gene cluster (rfb region) which determines the biosynthesis of the Shigella flexneri O-antigen of the Y serotype specificity was cloned from a S. flexneri serotype 2a strain. Two plasmids, pPM2212 and pPM2213, which conferred O-antigen biosynthesis were generated from separate cosmid clones by deletion with Clal. These plasmids expressed O-antigen in Escherichia coli K12 like that of the parental strain, as assessed by reactions to antisera in colony and Western immunoblots, sensitivity to bacteriophage Sf6, and by silver staining of lipopolysaccharides separated by sodium dodecyl sulphate/polyacrylamide gel electrophoresis. These plasmids also mediated O-antigen expression in an E. coli K12 rfb-delete background, indicating that all the necessary genes have been cloned. A detailed restriction map of the region has been constructed and analysis of various subclones has allowed the limits of the coding region for O-antigen biosynthesis to be defined to a maximum of 11 kb. Expression of these plasmids demonstrates a novel phenotype associated with control of lipopolysaccharide chain length. The gene(s) responsible maps adjacent to, but separate from, those associated with the biosynthesis of the O-antigen unit. Analysis of plasmid-encoded proteins in minicells and maxicells has facilitated the construction of a physical map. Finally, plasmid pPM-2212 was used to probe a collection of S. flexneri serotypes by Southern hybridization. With the exception of serotype 6, which appears to be unrelated, a similar pattern was found in all serotypes.
The influence of the soil matrix on nitrogen mineralisation and nitrification. II. The pore system as a framework for mapping the organisation of the soil matrix (1998)

Large numbers of small undisturbed soil volumes (1·7 cm3 ) were collected from the surface layer of a 2 m by 3 m field plot on a red earth near Wagga Wagga, New South Wales. The hypothesis tested was that an analysis of relationships between the volume of different pore size classes and various soil properties, measured on these soil volumes, can provide an understanding of soil organisation within the framework of the pore system. Three discrete findings were presented in confirmation of the hypothesis. (1) A non-uniform distribution of organic N through the pore system was indicated by the data analysis. Soil organic N tended to be concentrated in pores &lt;0·6 µm and in pores 10-30 µm, but not in the intermediate pore size class (pores 0·6-10 µm). Concentrations of organic N in pores &lt;0·6 µm are probably because of physical protection from microbial decomposition, but concentrations of organic N in pores 10-30 µm are probably because these pores are infrequently water-filled, and this limits bacterial activity more severely than in the pores 0·6-10 µm. Currently available assays for potentially mineralisable N cannot account for the effect of substrate location within the pore system, and a characterisation of the soil for the distribution of N in pores may enhance their utility. Soil disturbance is likely to alter organic matter distribution through the pore system and alter mineralisation dynamics. (2) Observations of pore size distributions before and after wetting suggested that soils which were high in organic matter and clay tended to have a greater volume of pores 0 ·6-30 µm which are unstable to drying and rewetting. It is proposed that these unstable pores 0 ·6-30 µm had been produced by the movement and alignment of clay particles during the growth of microbial colonies. (3) The volume of pores &lt;0·6 µm had a relatively strong negative correlation with pH and a relatively strong positive correlation with Mn2+ . A mechanism based on redox chemistry principles was proposed to explain these relationships. It was suggested that the volume of pores &lt;0·6 µm is related to the potential anaerobicity of the soil volume. In anaerobic conditions, the terminal electron acceptor for organic C oxidation may be MnO2 instead of O2, and in these circumstances, considerably more H+ would be consumed than in aerobic conditions. It is suggested that this alkaline effect extends into regions of the matrix where N mineralisation and nitrification are occurring, and stimulates these processes. The greater nitrification which may result from such a chain of events may, over time, effect greater acidification in those soil volumes which have greater microporosity.
Strategies to Prolong the Intravaginal Residence Time of Drug Delivery Systems (2009)

The vagina has been studied as a favorable site for local and systemic delivery of drugs for female-related conditions. There are a large number of vaginal medications on the market and most of them require frequent application due to their short vaginal residence time. A prolonged vaginal residence time of formulations is therefore a key parameter for improved therapeutic efficacy. Promising approaches to prolong the residence time base on mucoadhesion, in- situ sol-gel transition and mechanical fixation. Mucoadhesive drug delivery systems can be tailored to adhere to the vaginal tissue. In-situ gelling systems offer the advantage of increased viscosity in vaginal cavity and consequently reduce outflow from the vagina. Mechanical fixation needs specially shaped drug delivery systems and reduce the frequency of administration significantly. Within this review an overview on these different strategies and systems is provided. Furthermore, the techniques to evaluate the potential of these systems for prolonged vaginal residence time are described.
Mutational Analysis of <i>Bacillus subtilis</i> Glutamine Phosphoribosylpyrophosphate Amidotransferase Propeptide Processing (1999)

Glutamine phosphoribosylpyrophosphate amidotransferase from Bacillus subtilis is a member of an N-terminal nucleophile hydrolase enzyme superfamily, several of which undergo autocatalytic propeptide processing to generate the mature active enzyme. A series of mutations was analyzed to determine whether amino acid residues required for catalysis are also used for propeptide processing. Propeptide cleavage was strongly inhibited by replacement of the cysteine nucleophile and two residues of an oxyanion hole that are required for glutaminase function. However, significant propeptide processing was retained in a deletion mutant with multiple defects in catalysis that was devoid of enzyme activity. Intermolecular processing of noncleaved mutant enzyme subunits by active wild-type enzyme subunits was not detected in hetero-oligomers obtained from a coexpression experiment. While direct in vitro evidence for autocatalytic propeptide cleavage was not obtained, the results indicate that some but not all of the amino acid residues that have a role in catalysis are also needed for propeptide processing.
GRAPE AND PROJECT MILKYWAY (2005)

We overview the GRAPE (GRAvity piPE) project. The goal of the GRAPE project is to accelerate the astrophysical N-body simulations. Since almost all computing time is spent for the evaluation of the gravitational force between particles, we can greatly accelerate many N-body simulations by developing a specialized hardware for the force calculation. In 1989, the first such hardware, GRAPE-1, was completed, with the peak speed of 120 Mflops. In 2003, GRAPE-6 was completed, with the peak speed of 64 Tflops, which is nearly 106 times faster than GRAPE-l and was the fastest computer at that time. In this paper, we review the basic concept of the GRAPE hardwares, the history of the GRAPE project, and two ongoing projects, GRAPE-DR and Project Milkyway.
Myostatin maps to porcine chromosome 15 by linkage and physical analyses (1998)

Myostatin belongs to the transforming growth factor-beta superfamily, and is expressed specifically in developing and mature skeletal muscle. Myostatin appears to act as a negative regulator of muscle development, since mice with targeted disruption of this gene display a large increase in muscle mass. In this study, the porcine myostatin gene was mapped to chromosome 15q2.3 by fluorescence in situ hybridization. Myostatin was also positioned within the chromosome 15 linkage group using both a polymorphism located in the second intron and an associated microsatellite. The development of highly polymorphic markers associated with myostatin will support population studies to identify alleles of this gene that affects muscle mass and/or fat deposition in swine.
Nonalcoholic Fatty Liver Disease and Hepatocellular Carcinoma: A Weighty Connection (2010)

Hepatocellular carcinoma (HCC) is a common and deadly malignancy that is increasing in incidence in developed countries. The emergence of hepatitis C virus (HCV) accounts for about half of this increase in HCC, although the etiology of HCC in 15%-50% of new HCC cases remains unclear. The most common form of chronic liver disease in developed countries is nonalcoholic fatty liver disease (NAFLD), which encompasses a broad spectrum of histopathology. The prevalence of NAFLD, including the more aggressive nonalcoholic steatohepatitis (NASH), is increasing with the growing epidemics of diabetes and obesity. NASH can progress to cirrhosis and its related complications. Growing evidence suggests that NASH accounts for a large proportion of idiopathic or cryptogenic cirrhosis, which is associated with the typical risk factors for NASH. HCC is a rare, although important complication of NAFLD. Diabetes and obesity have been established as independent risk factors for the development of HCC. New evidence also suggests that hepatic iron deposition increases the risk of HCC in NASH-derived cirrhosis. Multiple case reports and case reviews of HCC in the setting of NASH support the associations of diabetes and obesity with the risk of HCC, as well as suggest age and advanced fibrosis as significant risks. Insulin resistance and its subsequent inflammatory cascade that is associated with the development of NASH appear to play a significant role in the carcinogenesis of HCC. The complications of NASH, including cirrhosis and HCC, are expected to increase with the growing epidemic of diabetes and obesity.
Treatment of COVID-19 (2020)

There is no specific antiviral treatment recommended for COVID-19 yet and no vaccine is currently available. The treatment is mainly symptomatic. Oxygen therapy and mechanical ventilation constitute the major intervention for patients with severe infection causing respiratory failure. Ongoing trials also show reassuring results with the use of convalescent plasma therapy, but it is still not recommended as a treatment modality and continues to be in testing phase. This article deals with few of the drugs and vaccines in clinical trials showing promising outcomes as of first week of May, 2020.
Interfacial interactions and properties of filled polymers. II: Dispersion of filler particles (1989)

Abstract The specific interaction characteristics and the inherent agglomeration of variously surface coated rutile pigments have been assessed, respectively, by inverse gas chromatographic and powder rheological methods. Standardized methods were used to disperse the pigments in polyethylene and chlorinated polyethylene. Measurements were made of energy requirements for dispersion and of the quality of dispersion attained. It was found that in the non‐polar polyethylene matrix, dispersion processes depended on the strength of pigment agglomerates, but not on the specific interaction potential of the solids. Conversely, in the acidic chlorinated polyethylene, acid/base interactions influenced dispersion but the process was independent of inherent pigment agglomeration.
Design and Analysis of Approximate Compressors for Multiplication (2014)

Inexact (or approximate) computing is an attractive paradigm for digital processing at nanometric scales. Inexact computing is particularly interesting for computer arithmetic designs. This paper deals with the analysis and design of two new approximate 4-2 compressors for utilization in a multiplier. These designs rely on different features of compression, such that imprecision in computation (as measured by the error rate and the so-called normalized error distance) can meet with respect to circuit-based figures of merit of a design (number of transistors, delay and power consumption). Four different schemes for utilizing the proposed approximate compressors are proposed and analyzed for a Dadda multiplier. Extensive simulation results are provided and an application of the approximate multipliers to image processing is presented. The results show that the proposed designs accomplish significant reductions in power dissipation, delay and transistor count compared to an exact design; moreover, two of the proposed multiplier designs provide excellent capabilities for image multiplication with respect to average normalized error distance and peak signal-to-noise ratio (more than 50 dB for the considered image examples).
Natural extracellular nanovesicles and photodynamic molecules: is there a future for drug delivery? (2017)

Photodynamic molecules represent an alternative approach for cancer therapy for their property (i) to be photo-reactive; (ii) to be not-toxic for target cells in absence of light; (iii) to accumulate specifically into tumour tissues; (iv) to be activable by a light beam only at the tumour site and (v) to exert cytotoxic activity against tumour cells. However, to date their clinical use is limited by the side effects elicited by systemic administration. Extracellular vesicles are endogenous nanosized-carriers that have been recently introduced as a natural delivery system for therapeutic molecules. We have recently shown the ability of human exosomes to deliver photodynamic molecules. Therefore, this review focussed on extracellular vesicles as a novel strategy for the delivery of photodynamic molecules at cancer sites. This completely new approach may enhance the delivery and decrease the toxicity of photodynamic molecules, therefore, represent the future for photodynamic therapy for cancer treatment.
Bisphosphonates and Time to Osteonecrosis Development (2009)

Bisphosphonate-associated osteonecrosis of the jaw (BONJ) is a complication of long-term bisphosphonate (BP) use. Given the beneficial effects of BP on bone quality in patients with cancer or osteoporosis, it is of great importance to understand the risk as it relates to time to event or cumulative dose until the onset of disease. Because there is no information on the lowest toxic dose from clinical trials, here we report on a review of 71 case series published since 2003. We calculated the weighted mean time to event, as well as the minimum reported time and dose for zoledronate, pamidronate, and oral bisphosphonates. The mean time to BONJ after zoledronate treatment was calculated at 1.8 years and the minimum was 10 months; after pamidronate, the mean time was 2.8 years and the minimum was 1.5 years; and after oral BP therapy, the mean time was 4.6 years and the minimum was 3 years. Zoledronic acid seems to be the most potent among the nitrogen-containing BPs. Factors that seem to affect BONJ and time to event were invasive dental procedures and other comorbid factors such as advanced age, rheumatoid arthritis, diabetes, use of corticosteroids, vitamin D deficiency, and more. Understanding the pathophysiology of the disease requires further research.
Human monocyte inflammatory mediator gene expression is selectively regulated by adherence substrates. (1989)

During the process of extravasation, monocytes transiently adhere to capillary endothelium and subsequently with a variety of extracellular matrix components. These early interactions are likely to serve as modifiers of transcriptional activity and serve to prime monocytes for rapid synthesis of mediators. We have previously reported that adherence to plastic rapidly induced or down-regulated steady-state mRNA levels of a number of monocyte inflammatory mediator genes. We now report that adherence to surfaces pretreated with fibronectin resulted in TNF-alpha and CSF-1 mRNA levels approximating adherence to plastic, whereas adherence to fibronectin, fibronectin/anti-fibronectin complexes, or collagen resulted in markedly decreased levels of CSF-1 induction and lysozyme down-regulation. In contrast, monocyte adherence to collagen induced the highest sustained levels of TNF-alpha expression. PMA, but not the chemotactic factor FMLP, stimulated non-adherent monocytes to express c-fos and TNF-alpha and down-regulate lysozyme mRNA. Although all donors responded to adherence, several failed to produce CSF-1 mRNA after PMA stimulation in the non-adherent state. These data demonstrate that monocyte mediator expression may be more dependent on the selectivity of signals induced by adherence to different substrates than the initial chemotactic response.
Reaction of O6-alkylguanine-DNA alkyltransferase with O6-methylguanine analogs: evidence that the oxygen of O6-methylguanine is protonated by the protein to effect methyl transfer (1992)

The DNA repair protein O6-alkylguanine-DNA alkyltransferase (AGT) repairs the promutagenic O6-methylguanine lesion by transferring the methyl group to a cysteine residue on the protein. A mechanism in which AGT activates the guanyl moiety as a leaving group by protonation of a heteroatom on guanine was probed by reacting AGT with analogues of O6-methylguanine in which the heteroatoms were changed. The initial rates of reaction were measured at various substrate concentrations in 50 mM Hepes, 1 mM EDTA, 1 mM DTT, and 10% glycerol, pH 7.8 at 37 degrees C. The kinact (h-1) and Kin (mM) were determined for O6-methylguanine (1.66 +/- 0.19, 1.51 +/- 0.32), 6-methoxypurine (1.07 +/- 0.25, 10.6 +/- 4.2), S6-methyl-6-thioguanine (0.63 +/- 0.04, 1.17 +/- 0.18), 6-methylthiopurine (no reaction), Se6-methyl-6-selenoguanine (1.76 +/- 0.28, 10.6 +/- 5.0), 6-methylselenopurine (2.51 +/- 0.62, 15.7 +/- 6.3), O6-methyl-1-deazaguanine (1.71 +/- 0.34, 14.8 +/- 4.4), O6-methyl-3-deazaguanine (1.90 +/- 0.24, 2.54 +/- 0.59), and O6-methyl-7-deazaguanine (1.97 +/- 0.26, 2.56 +/- 0.72). These results indicate that replacement of the nitrogens does not affect the kinact parameter but the Kin is increased upon removal of the exocyclic amino group and the nitrogen at the 1-position. Replacement of the oxygen with sulfur decreases the kinact, and replacement with selenium increases the Kin. The results are consistent with a mechanism in which O6-methylguanine binds to the active site of AGT with hydrogen bonds to the oxygen, the exocyclic amino group, and the nitrogen at the 1-position of the substrate.(ABSTRACT TRUNCATED AT 250 WORDS)
Synthesis and Characterization of a Biomimetic Formulation of Clofazimine Hydrochloride Microcrystals for Parenteral Administration (2018)

Clofazimine (CFZ) is a broad spectrum antimycobacterial agent recommended by the World Health Organization as a first line treatment for leprosy and second line treatment for multidrug resistant tuberculosis. Oral administration of CFZ leads to a red skin pigmentation side effect. Since CFZ is a weakly basic, red phenazine dye, the skin pigmentation side effect results from lipophilic partitioning of the circulating, free base (neutral) form of CFZ into the skin. Here, we developed a stable and biocompatible formulation of CFZ-HCl microcrystals that mimics the predominant form of the drug that bioaccumulates in macrophages, following long term oral CFZ administration. In mice, intravenous injection of these biomimetic CFZ-HCl microcrystals led to visible drug accumulation in macrophages of the reticuloendothelial system with minimal skin accumulation or pigmentation. In fact, no skin pigmentation was observed when the total amount of CFZ-HCl administered was equivalent to the total oral dose leading to maximal skin pigmentation. Thus, parenteral (injected or inhaled) biomimetic formulations of CFZ-HCl could be instrumental to avoid the pigmentation side effect of oral CFZ therapy.
On the Interpretability of Machine Learning Models and Experimental Feature Selection in Case of Multicollinear Data (2020)

In the field of machine learning, a considerable amount of research is involved in the interpretability of models and their decisions. The interpretability contradicts the model quality. Random Forests are among the best quality technologies of machine learning, but their operation is of “black box” character. Among the quantifiable approaches to the model interpretation, there are measures of association of predictors and response. In case of the Random Forests, this approach usually consists of calculating the model’s feature importances. Known methods, including the built-in one, are less suitable in settings with strong multicollinearity of features. Therefore, we propose an experimental approach to the feature selection task, a greedy forward feature selection method with least-trees-used criterion. It yields a set of most informative features that can be used in a machine learning (ML) training process with similar prediction quality as the original feature set. We verify the results of the proposed method on two known datasets, one with small feature multicollinearity and another with large feature multicollinearity. The proposed method also allows for a domain expert help with selecting among equally important features, which is known as the human-in-the-loop approach.
High-Speed Voltage Control Spintronics Memory (VoCSM) Having Broad Design Windows (2018)

Voltage Control Spintronics Memory (VoCSM) is a magnetic memory combining the spin Hall effect and Voltage Controlled Magnetic Anisotropy (VCMA). It has the potential to make MRAM work faster. In this paper, we described memory design of a write window and a read window of high-speed VoCSM from experimental data. The design windows of both writing and reading are large enough for gigabit memory.
A new system for the reduction of 4-hydroxymandelic acids (1997)

Nous decrivons un nouveau systeme de reduction des acides 4-hydroxymandeliques, relativement aise a mettre en oeuvre avec des reactifs disponibles, peu couteux et non polluants pour l'environnement. La reduction de ces acides constitue une voie importante de synthese des acides (4-hydroxyphenyl)acetiques. Ce nouveau systeme de reduction est constitue de bisulfite de sodium ou de dithionite de sodium en quantite catalytique, et d'acide formique en leger exces.
Electric phase delays in tunable acousto-optic filters applying extended transducers (2012)

The paper examines operation of wide angle tunable acousto-optic filters applying multiple transducers. The analysis was carried out for a tellurium dioxide device with a large transducer consisting of 7 identical sections connected in series. It was found that the sections of the transducer generated acoustic waves with a phase shift. This shift was caused by time delay when a driving electric signal propagated over the sections. The phase shift between adjacent sections was dependent on frequency of a driving electric signal, while a total phase delay between side sections of the transducer depended on a number of connected sections. Experimental investigation of the filter was performed at the driving frequencies 100-240 MHz. The measured total time delay between side sections of the transducer was equal to 1.6 ns, while the delay between adjacent sections was limited to 0.23 ns. It was proved that presence of the phase shifts influenced on spectral transmission characteristics of the tunable acousto-optic filter and also on relative intensity of side lobes.