gebhart/patrepeval huggingface dataset:
Large-Scale Phylogenomics of the <i>Lactobacillus casei</i> Group Highlights Taxonomic Inconsistencies and Reveals Novel Clade-Associated Features (2017)

Although the genotypic and phenotypic properties of the <i>Lactobacillus casei</i> group have been studied extensively, the taxonomic structure has been the subject of debate for a long time. Here, we performed a large-scale comparative analysis by using 183 publicly available genomes supplemented with a <i>Lactobacillus</i> strain isolated from the human upper respiratory tract. On the basis of this analysis, we identified inconsistencies in the taxonomy and reclassified all of the genomes according to their most closely related type strains. This led to the identification of a catalase-encoding gene in all 10 <i>L. casei sensu stricto</i> strains, making it the first described catalase-positive species in the <i>Lactobacillus</i> genus. Moreover, we found that 6 of 10 <i>L. casei</i> genomes contained a SecA2/SecY2 gene cluster with two putative glycosylated surface adhesin proteins. Altogether, our results highlight current inconsistencies in the taxonomy of the <i>L. casei</i> group and reveal new clade-associated functional features. <b>IMPORTANCE</b> The closely related species of the <i>Lactobacillus casei</i> group are extensively studied because of their applications in food fermentations and as probiotics. Our results show that many strains in this group are incorrectly classified and that reclassifying them to their most closely related species type strain improves the functional predictive power of their taxonomy. In addition, our findings may spark increased interest in the <i>L. casei</i> species. We find that after reclassification, only 10 genomes remain classified as <i>L. casei</i>. These strains show some interesting properties. First, they all appear to be catalase positive. This suggests that they have increased oxidative stress resistance. Second, we isolated an <i>L. casei</i> strain from the human upper respiratory tract and discovered that it and multiple other <i>L. casei</i> strains harbor one or even two large, glycosylated putative surface adhesins. This might inspire further exploration of this species as a potential probiotic organism.
Interleaved dc-dc Converters for Photovoltaic Modules (2007)

In the present paper, an application of interleaved dc-dc converter in photovoltaic (PV) modular system has been presented. In the multi-string technology, several PV strings are interfaced with their own dc-dc converter to a common dc-ac inverter. Enlargements are easily achieved since a new string with dc-dc converter can be plugged into the existing platform. This paper proposes a simple method to connect various PV modules in order to improve power quality. Thanks to the proposed digital control method, the PV interleaving becomes simple and efficient in terms of dynamic performances, steady-state condition and well regulated output voltage.
The place of bronchoscopic photodynamic therapy in advanced unresectable lung cancer: experience of 100 cases1 (1999)

(1) PDT is effective in palliation of inoperable advanced lung cancer. (2) Subset of patients with a better performance status have added survival benefit.
Critical Roles for Lipomannan and Lipoarabinomannan in Cell Wall Integrity of Mycobacteria and Pathogenesis of Tuberculosis (2013)

Lipomannan (LM) and lipoarabinomannan (LAM) are mycobacterial glycolipids containing a long mannose polymer. While they are implicated in immune modulations, the significance of LM and LAM as structural components of the mycobacterial cell wall remains unknown. We have previously reported that a branch-forming mannosyltransferase plays a critical role in controlling the sizes of LM and LAM and that deletion or overexpression of this enzyme results in gross changes in LM/LAM structures. Here, we show that such changes in LM/LAM structures have a significant impact on the cell wall integrity of mycobacteria. In Mycobacterium smegmatis, structural defects in LM and LAM resulted in loss of acid-fast staining, increased sensitivity to β-lactam antibiotics, and faster killing by THP-1 macrophages. Furthermore, equivalent Mycobacterium tuberculosis mutants became more sensitive to β-lactams, and one mutant showed attenuated virulence in mice. Our results revealed previously unknown structural roles for LM and LAM and further demonstrated that they are important for the pathogenesis of tuberculosis. IMPORTANCE Tuberculosis (TB) is a global burden, affecting millions of people worldwide. Mycobacterium tuberculosis is a causative agent of TB, and understanding the biology of M. tuberculosis is essential for tackling this devastating disease. The cell wall of M. tuberculosis is highly impermeable and plays a protective role in establishing infection. Among the cell wall components, LM and LAM are major glycolipids found in all Mycobacterium species, show various immunomodulatory activities, and have been thought to play roles in TB pathogenesis. However, the roles of LM and LAM as integral parts of the cell wall structure have not been elucidated. Here we show that LM and LAM play critical roles in the integrity of mycobacterial cell wall and the pathogenesis of TB. These findings will now allow us to seek the possibility that the LM/LAM biosynthetic pathway is a chemotherapeutic target.
Accelerating Refractive Rendering of Transparent Objects (2007)

Abstract In this paper, a technique is proposed for the rendering of transparent objects interactively using the method of refractive rendering. In the proposed technique, the refractive rendering algorithm is performed in two stages, namely the pre‐computation stage and the shading stage. In the pre‐computation stage, ray‐traced information, including directions and positions of rays, are generated by a ray tracing process and are stored in a set of ray lists. In the shading stage, these data are retrieved from the ray lists for computing the shading of an object. Using the proposed technique, photorealistic image of transparent objects and gemstones with various cuttings, material properties, lighting and background can be rendered interactively. By combining the refractive rendering technique with conventional shading techniques, jewelry and crystal designs can be rendered at a much higher speed comparing with conventional ray tracing techniques.
A linear, featured-data scheme for image reconstruction in time-domain fluorescence molecular tomography (2006)

Fluorescence diffuse optical tomography (DOT) has attracted many attentions from the community of biomedical imaging, since it provides effective enhancement in imaging contrast. This modality is now rapidly evolving as a potential means of monitoring molecular events in small living organisms with help of molecule-specific contrast agents, referred to as fluorescence molecular tomography (FMT). FMT could greatly promote pathogenesis research, drug development, and therapeutic intervention. Although FMT in steady-state and frequency-domain modes have been heavily investigated, the extension to time-domain scheme is imminent for its several unique advantages over the others. By extending the previously developed generalized pulse spectrum technique for time-domain DOT, we propose a linear, featured-data image reconstruction algorithm for time-domain FMT that can simultaneously reconstruct both fluorescent yield and lifetime images of multiple fluorophores, and validate the methodology with simulated data.
Changing the Way the Enterprise Works: Operational Transformations. (2005)

The communication and information revolution is caused by a fast changing sets of technologies that have already caused changes in the enterprise. Furthermore the expectations of the customers of the enterprise have changed because of personal use of the internet and web. Customers expect the Time of response for any transaction to be instantaneous. Managing the pace of change is today’s big enterprise problem. The technologies of computers, networks, software that enable very fast response are complex and themselves fast changing .To use the new versions of technologies requires both learning new skills and changing internal operational procedures. Operational Transformation is the next frontier of business advantage. Because of global competition in uncertain times, Any enterprise of any size must be configured to change; change the way they conduct business and change basic operations. Failure to do this will mean losing to competitors who do change. These issues will be examined and a possible solution to the problem offered.
Epstein-Barr Virus Induces Cellular Transcription Factors to Allow Active Expression of EBER Genes by RNA Polymerase III (2006)

The EBER genes of Epstein-Barr virus (EBV) are transcribed by RNA polymerase (pol) III to produce untranslated RNAs that are implicated in oncogenesis. These EBER transcripts are the most highly expressed viral gene products in EBV-transformed cells. We have identified changes to the cellular transcription machinery that may contribute to the high levels of EBER RNA. These include phosphorylation of ATF2, which interacts with EBER promoters. A second is induction of TFIIIC, a pol III-specific factor that activates EBER genes; all five subunits of TFIIIC are overexpressed in EBV-positive cells. In addition, EBV induces BDP1, a subunit of the pol III-specific factor TFIIIB. Although BDP1 is the only TFIIIB subunit induced by EBV, its induction is sufficient to stimulate EBER expression in vivo, implying a limiting function. The elevated levels of BDP1 and TFIIIC in EBV-positive cells stimulate production of tRNA, 7SL, and 5S rRNA. Abnormally high expression of these cellular pol III products may contribute to the ability of EBV to enhance growth potential.
Inhibition of neuroretinal cell death by insulin-like growth factor-1 and its analogs. (2000)

IGF-1, as well as IGF-1 analogs, improves survival of neuroretinal cells in vitro, under conditions of hypoxia or serum-starvation. Since all three IGF-1 analogs inhibit cell death to some degree, we interpret these results to mean that IGF-1-mediated inhibition of cell death does not depend upon strong affinities for the IGF-1 receptor or IGF-1 binding proteins. Further studies will reveal additional information as to the pathways responsible for IGF-1-mediated neuroprotection of retinal cells.
Characterization of Silicon Native Oxide Formed in SC-1, H<sub>2</sub>O<sub>2</sub> and Wet Ozone Processes (1997)

The structures of silicon native oxides formed in the SC-1, H 2 O 2 and wet ozone processes were characterized using X-ray photoelectron spectroscopy (XPS), transmission electron microscopy (TEM) and Fourier transform infrared spectroscopy (FT-IR). Spectral simulation was performed to clarify the FT-IR spectra, assuming that the native oxide was pure silicon dioxide. Effective medium theories were applied to understand deviations of the observed spectra from the calculated ones. The deviations between the native oxide thickness evaluated by XPS and the absolute thickness obtained by TEM were also discussed. These deviations can be explained if the void is incorporated in the native oxides and the interface between the native oxide and the basal silicon obtained by the wet ozone process has a relatively smooth surface and a structure more similar to that of pure silicon dioxide, compared with that obtained by SC-1 or H 2 O 2 treatment.
On the frame error rate of turbo-codes (2002)

In spite of the excellent bit error rate performance of the original turbo-code, simulations indicate that this code yields relatively poor frame error rate performance. In this paper we show that "primitive" turbo-codes and "asymmetric" turbo-codes provides both good bit error rate and frame error rate performance.
Anti-tumor antibody BR96 blocks cell migration and binds to a lysosomal membrane glycoprotein on cell surface microspikes and ruffled membranes. (1994)

BR 96 is an internalizing antibody that binds to Lewis Y (Le(y)), a carbohydrate determinant expressed at high levels on many human carcinomas (Hellström, I., H. J. Garrigues, U. Garrigues, and K. E. Hellström. 1990. Cancer Res. 50:2183-2190). Breast carcinoma cell lines grown to confluence bind less BR96 than subconfluent cultures (Garrigues, J., U. Garrigues, I. Hellström, and K. E. Hellström. 1993. Am. J. Path. 142:607-622). However, when the confluent cells are induced to migrate by scratch wounding, they again bind BR96 suggesting that antigens bearing the Le(y) determinant may promote cell migration. In the present study, BR96 was found to be highly enriched on microspikes and ruffled membranes, cell surface structures involved in cell migration. In addition, BR96 was a potent inhibitor of cell migration in vitro. When stationary BR96 treated cells were exposed to fresh culture media, membrane ruffles and microspikes developed at the cell margin and migration resumed. Immunogold microscopy showed that BR96 antigens were enriched on these membrane protrusions. BR96 cell surface immunoprecipitation analysis of 3H-glucosamine labeled breast carcinoma cells identified antigens with approximate molecular weights of 135 kd (upper antigen) and 85 kd (lower antigen). A short amino terminal sequence (8 residues) of the upper antigen matched that of human lysosomal membrane glycoprotein 1 (LAMP-1). In addition, the upper antigen was detected on immunoblots probed with anti-LAMP-1, and within the intracellular compartment BR96 was found predominantly in endosomes and lysosomes. A soluble LAMP-1/immunoglobulin fusion protein (LAMP-1/Ig) was transiently expressed in both BR96 binding and nonbinding cell lines. Immunoblot analysis of LAMP-1/Ig's from the various cell lines showed that (a) acquisition of the BR96 epitope is probably controlled at the level of polylactosamine modification (e.g., fucosylation) rather than LAMP-1 gene expression; (b) alternate forms of LAMP-1/Ig comigrate with the lower BR96 antigen raising the possibility that it may be a degradation product of the upper antigen; and (c) LAMP-1/Ig expressed in 3396 breast carcinoma cells has approximately 30-fold more BR96 epitopes than LAMP-1/Ig from non-tumorigenic mammary epithelial cells. Together these data indicate that a major BR96 antigen, LAMP-1, is present on unique cell surface domains involved in cell locomotion as well as membranes of the endocytic compartment. Altered glycosylation of LAMP-1 expressed in transformed cells may contribute to their ability to disseminate.
Selenoprotein synthesis in archaea (2001)

The availability of the genome sequences from several archaea has facilitated the identification of the encoded selenoproteins and also of most of the components of the machinery for selenocysteine biosynthesis and insertion. Until now, selenoproteins have been identified solely in species of the genera Methanococcus (M.) and Methanopyrus. Apart from selenophosphate synthetase, they include only enzymes with a function in energy metabolism. Like in bacteria and eukarya, selenocysteine insertion is directed by a UGA codon in the mRNA and involves the action of a specific tRNA and of selenophosphate as the selenium donor. Major differences to the bacterial system, however, are that no homolog for the bacterial selenocysteine synthase was found and, especially, that the SECIS element of the mRNA is positioned in the 3' nontranslated region. The characterisation of a homolog for the bacterial SelB protein showed that it does not bind to the SECIS element necessitating the activity of at least a second protein. The use of the genetic system of M. maripaludis allowed the heterologous expression of a selenoprotein gene from M. jannaschii and will facilitate the elucidation of the mechanism of the selenocysteine insertion process in the future.
Prism-array lenses for energy filtering in medical x-ray imaging (2007)

Conventional energy filters for x-ray imaging are based on absorbing materials which attenuate low energy photons, sometimes combined with an absorption edge, thus also discriminating towards 'photons of higher energies. These filters are fairly inefficient, in particular for photons of higher energies, and other methods for achieving a narrower bandwidth have been proposed. Such methods include various types of monochromators, based on for instance mosaic crystals or refractive multi-prism x-ray lenses (MPL's). Prism-array lenses (PAL's) are similar to MPL's, but are shorter, have larger apertures, and higher transmission. A PAL consists of a number of small prisms arranged in columns perpendicular to the optical axis. The column height decreases along the optical axis so that the projection of lens material is approximately linear with a Resnel phase-plate pattern superimposed on it. The focusing effect is one dimensional, and the lens is chromatic. Hence, unwanted energies can be blocked by placing a slit in the image plane of a desired energy. We present the first experimental and theoretical results on an energy filter based on a silicon PAL. The study includes an evaluation of the spectral shaping properties of the filter as well as a quantification of the achievable increase in dose efficiency compared to standard methods. Previously, PAL's have been investigated with synchrotron radiation, but in this study a medical imaging setup, based on a regular x-ray tube, is considered.
A 4.9-dB NF 53.5&#x2013;62-GHz micro-machined CMOS wideband LNA with small group-delay-variation (2010)

A 53.5-62-GHz wideband CMOS low-noise amplifier (LNA) with excellent phase linearity property is reported. Current-sharing technique is adopted to reduce power dissipation. The LNA (STD LNA) consumed 29.1 mW and achieved input return loss (S <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">11</sub> ) of -10.3~ -19.5 dB, output return loss (S <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">22</sub> ) of -13.8~ -27.8 dB, forward gain (S <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">21</sub> ) of 8.1~ 11.1 dB, and reverse isolation (S <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">12</sub> ) of -49.9~ -60.2 dB over the 53.5-62-GHz-band. The minimum NF (NF <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">min</sub> ) is 5.4 dB at 62 GHz. To reduce the substrate loss, the CMOS process compatible backside inductively-coupled-plasma (ICP) deep trench technology is used to remove the silicon underneath the LNA. After the ICP etching, the LNA (ICP LNA) achieved maximum S <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">21</sub> (S <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">21-max</sub> ) of 13.2 dB, 2.1 dB higher than that (11.1 dB) of the STD LNA. In addition, the ICP LNA achieved NF <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">min</sub> of 4.9 dB, 0.5 dB lower than that (5.4 dB) of the STD LNA. These results demonstrate the proposed LNA architecture in conjunction with the backside ICP technology is very promising for 60-GHz-band RFIC applications.
Indoleamine 2,3‐dioxygenase activity associates with cardiovascular risk factors: The Health 2000 study (2008)

Indoleamine 2,3-dioxygenase (IDO) is an important immunomodulator suppressing the activation of T lymphocytes, and its level in blood is increased in several autoimmune and inflammatory diseases. We have previously shown that this activity associates with several signs and risk factors of atherosclerosis in 24 to 39-year-old females. Now we repeat this analysis in an older population (n = 921, age range 46-76 years), i.e. in a population with more advanced atherosclerosis. IDO activity had a significant positive correlation in both sexes with carotid artery intima/media thickness (IMT), an early marker of atherosclerosis. In females, a significant negative correlation with HDL cholesterol and a positive correlation with triglycerides levels was observed. The association with IMT did not remain significant after adjustment with classical risk factors of atherosclerosis. It is thus concluded that IDO is a sensitive marker of atherosclerosis--or the inflammatory response associated with it--but does not have an independent role in the pathogenesis of this disease.
A Drug over the Millennia : Pharmacognosy, Chemistry, and Pharmacology of Licorice (2000)

Licorice, the root of Glycyrrhiza spp. (Fabaceae), has been used since ancient Egyptian, Greek, and Roman times in the West and since the Former Han era (the 2nd-3rd century B.C.) in ancient China in the East. In traditional Chinese medicine, licorice is one of the most frequently used drugs. In Japan, the oldest specimen of licorice introduced from China in the middle of the 8th century still exists in Shosoin, the Imperial Storehouse, in Nara. Extracts of licorice were recommended as a remedy for gastric ulcer by Revers of the Netherlands in 1946, which was soon withdrawn owing to its side effects. Carbenoxolon sodium, glycyrrhetinic acid (GA) hemisuccinate Na, was prepared from licorice to treat peptic ulcer in the UK. In Japan for the past 60 years, a glycyrrhizin (GL) preparation under the name of Stronger Neo-Minophagen C (SNMC) has been used clinically as an antiallergic and antihepatitis agent. GL and GA sometimes induce edema, hypertension, and hypokalemia in patients treated with higher doses and long-term administration. The mechanism of this side effect, pseudoaldosteronism, has been explained as due to the 11-hydroxy-steroid dehydrogenase inhibitory activity of GL and GA. The excess of endogenous cortisol produced combines with the renal mineral corticoid receptor, which promotes an aldosterone-like action. GL and GA reduce alanine transaminase (ALT) and aspartate transaminase (AST) values in the serum. This hepatoprotective effect has recently been explained as the inhibitory effects of GL and GA on immune-mediated cytotoxicity against hepatocytes and on nuclear factor (NF)-kappa B, which activates genes encoding inflammatory cytokines in the liver. To exclude the side effects and enhance the therapeutic activities, chemical modification of GL and GA has been performed. Deoxoglycyrrhetol (DG), homo- and heteroannular diene homologs of dihemiphthalates, showed a remarkable improvement in antiinflammatory, antiallergic, and antiulcer activities in animal experiments. Immunomodulating effects of GL, GA, and DG derivatives, which induce interferon-gamma and some other cytokines, have been demonstrated in relation with their antiviral activities. Antiinflammatory, antitumorigenic, and antimalarial effects of licorice flavonoids have also been investigated.
Determination of tocopherols, sterols, and steryl esters in vegetable oil distillates and residues (1974)

Abstract A twofold technique for determination of tocopherols and a gas liquid chromatography procedure for determination of sterols and steryl esters are described. Incorporated herein are a modified Emmerie‐Engel procedure for total tocopherols and gas liquid chromatographic analysis for tocopherols and sterols as their propionate esters. The approach is directly applicable to quality control and production use.