gebhart/patrepeval huggingface dataset:
Site-Directed Mutations in the Lanthipeptide Mutacin 1140 (2013)

The oral bacterium Streptococcus mutans, strain JH1140, produces the antibiotic mutacin 1140. Mutacin 1140 belongs to a group of antibiotics called lanthipeptides. More specifically, mutacin 1140 is related to the epidermin type A(I) lanthipeptides. Mutagenesis experiments of this group of lanthipeptides have been primarily restricted to the posttranslationally modified meso-lanthionine and 3-methyllanthionine residues. Site-directed mutagenesis of the core peptide of mutacin 1140 was performed using the suicide vector pVA891. Substitutions of the N-terminal residue, the charged residue in the hinge region, and residues in ring A and intertwined rings C and D were investigated. A truncation and insertion of residues in ring A and intertwined rings C and D were also performed to determine whether or not they would alter the antimicrobial activity of the producing strain. Bioassays revealed that five of 14 mutants studied had improved antimicrobial activity against the indicator strain Micrococcus luteus ATCC 10240. MICs against Streptococcus mutans UA159, Streptococcus pneumoniae ATCC 27336, Staphylococcus aureus ATCC 25923, Clostridium difficile UK1, and Micrococcus luteus ATCC 10240 were determined for three mutacin 1140 variants that had the most significant increases in bioactivity in the M. luteus bioassay. This mutagenesis study of the epidermin group of lanthipeptides shows that antimicrobial activity can be significantly improved.
Gradient boosting factorization machines (2014)

Recommendation techniques have been well developed in the past decades. Most of them build models only based on user item rating matrix. However, in real world, there is plenty of auxiliary information available in recommendation systems. We can utilize these information as additional features to improve recommendation performance. We refer to recommendation with auxiliary information as context-aware recommendation. Context-aware Factorization Machines (FM) is one of the most successful context-aware recommendation models. FM models pairwise interactions between all features, in such way, a certain feature latent vector is shared to compute the factorized parameters it involved. In practice, there are tens of context features and not all the pairwise feature interactions are useful. Thus, one important challenge for context-aware recommendation is how to effectively select "good" interaction features. In this paper, we focus on solving this problem and propose a greedy interaction feature selection algorithm based on gradient boosting. Then we propose a novel Gradient Boosting Factorization Machine (GBFM) model to incorporate feature selection algorithm with Factorization Machines into a unified framework. The experimental results on both synthetic and real datasets demonstrate the efficiency and effectiveness of our algorithm compared to other state-of-the-art methods.
Low-Complexity Soft-Output Decoding of Polar Codes (2014)

The state-of-the-art soft-output decoder for polar codes is a message-passing algorithm based on belief propagation, which performs well at the cost of high processing and storage requirements. In this paper, we propose a low-complexity alternative for soft-output decoding of polar codes that offers better performance but with significantly reduced processing and storage requirements. In particular we show that the complexity of the proposed decoder is only 4% of the total complexity of the belief propagation decoder for a rate one-half polar code of dimension 4096 in the dicode channel, while achieving comparable error-rate performance. Furthermore, we show that the proposed decoder requires about 39% of the memory required by the belief propagation decoder for a block length of 32768.
Genomic and Genetic Analysis of <i>Bordetella</i> Bacteriophages Encoding Reverse Transcriptase-Mediated Tropism-Switching Cassettes (2004)

Liu et al. recently described a group of related temperate bacteriophages that infect Bordetella subspecies and undergo a unique template-dependent, reverse transcriptase-mediated tropism switching phenomenon (Liu et al., Science 295: 2091-2094, 2002). Tropism switching results from the introduction of single nucleotide substitutions at defined locations in the VR1 (variable region 1) segment of the mtd (major tropism determinant) gene, which determines specificity for receptors on host bacteria. In this report, we describe the complete nucleotide sequences of the 42.5- to 42.7-kb double-stranded DNA genomes of three related phage isolates and characterize two additional regions of variability. Forty-nine coding sequences were identified. Of these coding sequences, bbp36 contained VR2 (variable region 2), which is highly dynamic and consists of a variable number of identical 19-bp repeats separated by one of three 5-bp spacers, and bpm encodes a DNA adenine methylase with unusual site specificity and a homopolymer tract that functions as a hotspot for frameshift mutations. Morphological and sequence analysis suggests that these Bordetella phage are genetic hybrids of P22 and T7 family genomes, lending further support to the idea that regions encoding protein domains, single genes, or blocks of genes are readily exchanged between bacterial and phage genomes. Bordetella bacteriophages are capable of transducing genetic markers in vitro, and by using animal models, we demonstrated that lysogenic conversion can take place in the mouse respiratory tract during infection.
Chiral Catalyst Controlled Diastereoselection and Regioselection in Intramolecular Carbon−Hydrogen Insertion Reactions of Diazoacetates (1996)

Individual enantiomers of substituted cyclohexyl diazoacetates or 2-octyl diazoacetates matched with a configurationally suitable chiral dirhodium(II) carboxamidate catalyst provide an effective methodology for the synthesis of lactones with exceptional diastereo- and regiocontrol. Enantiomerically pure (1S,2R)-cis-2-methylcyclohexyl diazoacetate forms the all-cis-(1R,5R,9R)-9-methyl-2-oxabicyclo[4.3.0]nonan-3-one with complete diastereocontrol in reactions catalyzed by dirhodium(II) tetrakis[methyl 1-(3-phenylpropanoyl)-2-oxoimidazolidine-4(R)-carboxylate], Rh2(4(S)-MPPIM)4, but the configurational mismatch results in a mixture of products. The same diazoacetate produces (1S,5R)-5-methyl-2-oxabicyclo[4.3.0]nonan-3-one with virtually complete selectivity by catalysis with dirhodium(II) tetrakis[methyl 2-oxopyrrolidine-5(S)-carboxylate], Rh2(5(S)-MEPY)4. Similarly high stereo- and regiocontrol is also achieved with enantiomerically pure trans-2-methylcyclohexyl diazoacetates. Product control from insertion reactions of d- or l-menthyl diazoacetate and (+)-neomenthyl diazoacetate from the configurational match with dirhodium(II) catalyst results in the formation of one C−H insertion product in high yield. The exceedingly high product diastereoselection observed in these reactions is consistent with virtually exclusive insertion into equatorial C−H bonds. The catalyst-dependent selective formation of a cis-disubstituted γ-butyrolactone or a β-lactone from 2-octyl diazoacetate has been achieved. Control of product diastereoselectivity and regioselectivity in C−H insertion reactions is explained by conformational suitability in configurational match/mismatch of catalyst and carbene.
Real-time 3D Thermal Modeling of a Magnetically Levitated Planar Actuator (2011)

A transient thermal model used to track the temperature distribution in real-time in a planar actuator is presented. The temperature distribution in the stator coils of the planar actuator depends on the trajectory of the levitated magnet plate. With the help of the presented real-time thermal model the possibility is established that the input power of the coils is no longer limited by the worst case assumption. A performance increase for the actuator will be achieved due to the possibility to monitor the temperature of each coil.
Cost-effectiveness of <i>nab</i>-paclitaxel plus gemcitabine versus erlotinib plus gemcitabine in metastatic pancreatic cancer. (2014)

353 Background: In a recent phase III trial nab-paclitaxel (albumin-bound paclitaxel) + gemcitabine (nab-P/G) demonstrated a 1.8 month, or 27%, improvement in median overall survival (OS) (HR = 0.72, P < 0.001) vs gemcitabine (G) in first-line metastatic pancreatic cancer (mPC). nab-P/G had higher 1 year OS (35% vs 22%) and improved PFS by 1.8 months (HR = 0.69, P < 0.01). nab-P/G is the first taxane based therapy to show a significant OS improvement in a phase III mPC trial. Erlotinib + gemcitabine (E/G) has also demonstrated activity in mPC, with a 0.3 month OS benefit vs G (HR = 0.82, P = 0.04), a 1 year OS of 23% vs 17%, and 0.2 months PFS benefit (HR = 0.77, P = 0.004) vs G. A cost-effectiveness analysis measuring the cost per life year (LY) gained for nab-P/G and E/G was conducted from the US payer perspective. Methods: Costs and clinical outcomes were evaluated fromnab-P/G vs G and E/G vs G trials of mPC. Health care resource use and the management of grade III/IV adverse events (AE) were collected from a large multisite US oncology clinic, expert opinion, and literature (2012 US dollars). Drug cost per cycle was multiplied by the median cycles delivered from the trials for nab-P/G and E/G. Results: Duration of therapy was 4 months for nab-P/G vs 3.9 months for E/G. Total cost for nab-P/G was $24,984 vs $23,044 for E/G, including drug, administration and AE management. AE costs were similar between the two therapies (Table). Differences of > 5% were noted in neutropenia (rates: nab-P/G = 33%; E/G = 24%), neuropathy (nab-P/G = 17%; E/G = 1%), and rash (nab-P/G = 0%; E/G = 6%). The net survival advantage for nab-P/G vs E/G was 1.5 incremental life months gained. Nab-P/G was cost-effective relative to E/G, at a cost of $15,522 per incremental life year gained. Conclusions: nab-P/G is a cost-effective alternative to E/G in mPC, bringing more months of OS at < $16,000 cost per incremental life year gained. [Table: see text]
Time-domain channel estimator for polarization interleaving direct-detection orthogonal frequency-division multiplexing passive optical network (2016)

We propose an efficient time-domain channel estimation method for polarization interleaving orthogonal frequency-division multiplexing passive optical network with direct detection. Compared with the frequency-domain least-square channel estimator and intrasymbol frequency-domain averaging, the time-domain channel estimator with overhead reduction demonstrates better system robustness against transmission impairments, such as optical noise, chromatic dispersion, and polarization mode dispersion.
A Second-Generation Synthesis of the C1−C28 Portion of the Altohyrtins (Spongistatins) (2003)

A practical second-generation synthesis of an advanced intermediate in our total synthesis of altohyrtin C (spongistatin 2) has been developed. A new approach to the C1-C15 (AB) portion features a vinyllithium addition to an aldehyde followed by a palladium-catalyzed allylic reduction to install the troublesome C13-C15 segment. Our general approach to the C16-C28 (CD) spiroketal has been retained, but some improvements have been made. Most notably, the kinetically controlled CD-spiroketalization reaction now proceeds in high yield with excellent diastereoselection. This new strategy uses the anti-aldol coupling used in our first-generation synthesis to join AB and CD fragments. A total of 9.6 g of intermediate 57 has been produced using this improved route.
Coprecipitation of mercury(II) with iron(III) hydroxide (1979)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCoprecipitation of mercury(II) with iron(III) hydroxideYoshikazu Inoue and Makoto MunemoriCite this: Environ. Sci. Technol. 1979, 13, 4, 443–445Publication Date (Print):April 1, 1979Publication History Published online1 May 2002Published inissue 1 April 1979https://pubs.acs.org/doi/10.1021/es60152a001https://doi.org/10.1021/es60152a001research-articleACS PublicationsRequest reuse permissionsArticle Views355Altmetric-Citations42LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Targeting of CDK8 to a promoter-proximal RNA element demonstrates catalysis-dependent activation of gene expression (1998)

During transcription of mRNA genes, there is a correlation between the phosphorylation state of the C-terminal domain (CTD) of the large subunit of RNA polymerase II (RNAP II) and the ability of the RNAP II complex to processively transcribe the gene. To examine the involvement of CTD phosphorylation in modulation of RNAP II function, we have analyzed the ability of a known CTD kinase, human Cdk8, to modulate HIV-1 LTR-driven gene expression upon directed targeting to a promoter-proximal nascent RNA element. The results indicated that Cdk8, when localized to an RNA element, activates gene expression in a catalysis-dependent manner. Also, Cdk8 targeted to RNA was observed to act in a synergystic manner with DNA-targeted Sp1 but not with DNA-targeted HIV-1 Tat, suggesting that RNA-targeted Cdk8 acts on similar rate limiting post-initiation events as Tat. As recent observations suggest that Tat/TAR-mediated transcription of the proviral genome of HIV depends on specific phosphorylation of RNAP II in its CTD by the Tat-associated kinase (TAK/p-TEFb/Cdk9), our results indicate that Cdk8 shares with Cdk9 the ability to modulate transcription upon targeting to a nascent RNA element.
Control of MHC class II gene expression in autoimmune, infectious, and neoplastic diseases. (1993)

The major histocompatibility complex (MHC) class II genes encode surface molecules that are required for presentation of antigenic peptides to helper T-cells. The concentration of these proteins on the surface of effector cells (antigen-presenting cells such as B-cells and macrophage) is one of the parameters affecting the intensity of the immune response. Many studies have thus focused their attention on the mechanisms that control the expression of class II genes, particularly in B-cells. The anatomy of MHC class II promoters has been dissected in detail, and many trans-acting factors and their cognate DNA regulatory elements have been identified and characterized, thus helping to elucidate the molecular circuitry which determines tissue-specific, coordinate expression of these genes. In most cases, regulation has been investigated at the level of mRNA transcription. MHC class II gene expression has been observed as well, under physiological conditions, in many other tissues and organs such as brain, thyroid, thymus, and intestine, thus implying that class II molecules may be involved, whether directly or indirectly, in the modulation of other important biological responses in addition to the control of the immune reaction against soluble antigens. Spurious MHC class II activity is also detected in tumor cells and in other pathological conditions such as those found in autoimmune, inflammatory, and infectious diseases. In autoimmunity, cells that express class II molecules may present tissue-specific antigens, thus triggering a mechanism of self-destruction. In tumors, instead, unscheduled MHC class II expression may be part of a mechanism that prevents tumor progression. Comprehension of the regulatory functions operating in pathological conditions as compared to those active in B-cells and in macrophages is still rudimentary. Because of the possible pathogenetic importance of aberrant class II expression, knowledge of the cis- and trans-acting elements controlling gene expression at either the transcriptional or posttranscriptional level may allow the development of strategies for immunointervention against these diseases.
Electrically small antennas with dimensions down to one-fifteenth and one-thirtieth of wavelength (2015)

This paper presents two electrically small meander line antennas operating at 915 MHz. The first antenna has dimensions λ <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</inf> /30 by λ <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</inf> /30. It is constructed from a Vivaldi antenna whose two edges are connected through a meander line. The feeding is achieved via a slot line excited by a microstrip located at the backside of the substrate. The antenna has gain, efficiency and bandwidth of −3.75 dBi, 31%, and 28 MHz (3%) respectively. The size of the second antenna is λ <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</inf> /15 by λ <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</inf> /15. It consists of two antennas of the first design which are placed back-to-back. This antenna has gain, efficiency and bandwidth of −0.3 dBi, 76%, and 73 MHz (8%) respectively.
5‐Fluorouracil preferentially sensitizes mutant KRAS non‐small cell lung carcinoma cells to TRAIL‐induced apoptosis (2015)

Mutations in the KRAS gene are very common in non-small cell lung cancer (NSCLC), but effective therapies targeting KRAS have yet to be developed. Interest in tumor necrosis factor-related apoptosis-inducing ligand (TRAIL), a potent inducer of cell death, has increased following the observation that TRAIL can selectively kill a wide variety of human cancer cells without killing normal cells both in vitro and in xenograft models. However, results from clinical trials of TRAIL-based therapy are disappointingly modest at best and many have demonstrated a lack of therapeutic benefit. Current research has focused on selecting a subpopulation of cancer patients who may benefit from TRAIL-based therapy and identifying best drugs to work with TRAIL. In the current study, we found that NSCLC cells with a KRAS mutation were highly sensitive to treatment with TRAIL and 5-fluorouracil (5FU). Compared with other chemotherapeutic agents, 5FU displayed the highest synergy with TRAIL in inducing apoptosis in mutant KRAS NSCLC cells. We also found that, on a mechanistic level, 5FU preferentially repressed survivin expression and induced expression of TRAIL death receptor 5 to sensitize NSCLC cells to TRAIL. The combination of low-dose 5FU and TRAIL strongly inhibited xenograft tumor growth in mice. Our results suggest that the combination of TRAIL and 5FU may be beneficial for patients with mutant KRAS NSCLC.
Assessing the value of branches with what-if analysis (2012)

Branches within source code management systems (SCMs) allow a software project to divide work among its teams for concurrent development by isolating changes. However, this benefit comes with several costs: increased time required for changes to move through the system and pain and error potential when integrating changes across branches. In this paper, we present the results of a survey to characterize how developers use branches in a large industrial project and common problems that they face. One of the major problems mentioned was the long delay that it takes changes to move from one team to another, which is often caused by having too many branches (branchmania). To monitor branch health, we introduce a novel what-if analysis to assess alternative branch structures with respect to two properties, isolation and liveness. We demonstrate with several scenarios how our what-if analysis can support branch decisions. By removing high-cost-low-benefit branches in Windows based on our what-if analysis, changes would each have saved 8.9 days of delay and only introduced 0.04 additional conflicts on average.
<i>In Vitro</i> and <i>In Vivo</i> Effectiveness of an Innovative Silver-Copper Nanoparticle Coating of Catheters To Prevent Methicillin-Resistant Staphylococcus aureus Infection (2016)

In this study, silver/copper (Ag/Cu)-coated catheters were investigated for their efficacy in preventing methicillin-resistant Staphylococcus aureus (MRSA) infection in vitro and in vivo Ag and Cu were sputtered (67/33% atomic ratio) on polyurethane catheters by direct-current magnetron sputtering. In vitro, Ag/Cu-coated and uncoated catheters were immersed in phosphate-buffered saline (PBS) or rat plasma and exposed to MRSA ATCC 43300 at 10(4) to 10(8) CFU/ml. In vivo, Ag/Cu-coated and uncoated catheters were placed in the jugular vein of rats. Directly after, MRSA (10(7) CFU/ml) was inoculated in the tail vein. Catheters were removed 48 h later and cultured. In vitro, Ag/Cu-coated catheters preincubated in PBS and exposed to 10(4) to 10(7) CFU/ml prevented the adherence of MRSA (0 to 12% colonization) compared to uncoated catheters (50 to 100% colonization; P < 0.005) and Ag/Cu-coated catheters retained their activity (0 to 20% colonization) when preincubated in rat plasma, whereas colonization of uncoated catheters increased (83 to 100%; P < 0.005). Ag/Cu-coating protection diminished with 10(8) CFU/ml in both PBS and plasma (50 to 100% colonization). In vivo, Ag/Cu-coated catheters reduced the incidence of catheter infection compared to uncoated catheters (57% versus 79%, respectively; P = 0.16) and bacteremia (31% versus 68%, respectively; P < 0.05). Scanning electron microscopy of explanted catheters suggests that the suboptimal activity of Ag/Cu catheters in vivo was due to the formation of a dense fibrin sheath over their surface. Ag/Cu-coated catheters thus may be able to prevent MRSA infections. Their activity might be improved by limiting plasma protein adsorption on their surfaces.
Reproduction of the reniform nematode on thirty soybean cultivars. (1994)

In greenhouse experiments conducted in 1991 and 1992, the 30 soybean (Glycine max) cultivars most commonly grown in Arkansas in 1990 were tested for resistance to the reniform nematode, Rotylenchulus reniformis. 'Forrest' was the most resistant cultivar, whereas 'Braxton' was the most susceptible to R. reniformis. Cultivars Coker 485, Centennial, Stonewall, and Sharkey did not differ from Forrest (P = 0.01). Cultivars Lee 74, Coker 6955, Waiters, Davis, Pioneer 9442, and Narow did not differ from Braxton (P = 0.01). Cultivar Lloyd had the second highest reproductive index (Pf/Pi) in 1992 and for the combined test, but was significantly different from Braxton in 1991. The remaining cultivars were inconsistent in their reproductive indices. Two cultivars, Leflore and Lloyd, exhibited large variation in Pf/Pi. This may be due to multiple resistance genes and (or) segregation for resistance among individual seedlings. Segregation is possible because these varieties were not selected or tested for reniform nematode resistance during the cultivar development process.