gebhart/patrepeval huggingface dataset:
Identification of Fungal Limonene-3-Hydroxylase for Biotechnological Menthol Production (2021)

More than 30,000 tons of menthol are produced every year as a flavor and fragrance compound or as a medical component. So far, only extraction from plant material and chemical synthesis are possible. An alternative approach for menthol production could be a biotechnological-chemical process with ideally only two conversion steps, starting from (+)-limonene, which is a side product of the citrus processing industry. The first step requires a limonene-3-hydroxylase (L3H) activity that specifically catalyzes hydroxylation of limonene at carbon atom 3. Several protein engineering strategies have already attempted to create limonene-3-hydroxylases from bacterial cytochrome P450 monooxygenases (CYPs, or P450s), which can be efficiently expressed in bacterial hosts. However, their regiospecificity is rather low compared to that of the highly selective L3H enzymes from the biosynthetic pathway for menthol in <i>Mentha</i> species. The only naturally occurring limonene-3-hydroxylase activity identified in microorganisms so far was reported for a strain of the black yeast-like fungus <i>Hormonema</i> sp. in South Africa. We have discovered additional fungi that can catalyze the intended reaction and identified potential CYP-encoding genes within the genome sequence of one of the strains. Using heterologous gene expression and biotransformation experiments in yeasts, we were able to identify limonene-3-hydroxylases from <i>Aureobasidium pullulans</i> and <i>Hormonema carpetanum</i> Further characterization of the <i>A. pullulans</i> enzyme demonstrated its high stereospecificity and regioselectivity, its potential for limonene-based menthol production, and its additional ability to convert α- and β-pinene to verbenol and pinocarveol, respectively.<b>IMPORTANCE</b> (-)-Menthol is an important flavor and fragrance compound and furthermore has medicinal uses. To realize a two-step synthesis starting from renewable (+)-limonene, a regioselective limonene-3-hydroxylase enzyme is necessary. We identified enzymes from two different fungi which catalyze this hydroxylation reaction and represent an important module for the development of a biotechnological process for (-)-menthol production from renewable (+)-limonene.
Superfluidity of indirect excitons in a quantum dot (1998)

The superfluidity and Bose-Einstein condensation of indirect excitons in two-dimensional quantum dot are studied by path-integral Monte Carlo simulations. The temperature dependence of superfluid and bose-condensed fraction are calculated at different strengths of interaction. Using the Kosterlitz-Thouless recursion relations, we also predict behavior of superfluid fraction in macroscopic large systems.
On codes for structured bursts (2012)

We introduce a technique for constructing codes for bursts of errors that have some known structure; for example bursts of length at most b and Hamming weight at most t. This technique is based on modifying existing codes for generic bursts by replacing a portion of their check matrix with a more efficient one, in light of the additional constraints on the burst. We illustrate this procedure by modifying the Fire, Burton and Gilbert codes to address bursts with maximum Hamming weight, bursts with solid errors, or bursts with internal “mini-bursts”. We provide evidence that the redundancy of the codes we construct can be very good through examples, one of which is optimal within the class of cyclic codes.
Influence of Dietary Histidine on Basophil Release, Circulating Concentration, and Urinary Excretion of Histamine in Domestic Felines (2012)

Dietary histidine has been shown to elevate circulating free histidine and plasma histamine concentration in murine models as much as 6- fold. Bladder mastocytosis is a hallmark of feline interstitial cystitis, and histidine is stored in mast cells and converted to histamine for signaling and inflamma tion by the enzyme histidine decarboxylase. Elevated dietary histidine may represent a risk factor for heightened mast cell responses. Nine healthy adult female shorthair cats were used in random crossover experiment with fixed treatment sequences to test the effects of dietary histidine (0.6, 1.0, and 1.4% DM) on histamine in blood and urine. The dry-extruded test foods were fed in sufficient amounts to maintain ideal body weight. Each experimental period was preceded by a 7-day wash out period, in which the 0.6% histidine diet was fed, followed by a 14-day feeding period of
A Genome-Wide Haploid Genetic Screen Identifies Heparan Sulfate-Associated Genes and the Macropinocytosis Modulator TMED10 as Factors Supporting Vaccinia Virus Infection (2019)

Vaccinia virus is a promising viral vaccine and gene delivery candidate and has historically been used as a model to study poxvirus-host cell interactions. We employed a genome-wide insertional mutagenesis approach in human haploid cells to identify host factors crucial for vaccinia virus infection. A library of mutagenized HAP1 cells was exposed to modified vaccinia virus Ankara (MVA). Deep-sequencing analysis of virus-resistant cells identified host factors involved in heparan sulfate synthesis, Golgi organization, and vesicular protein trafficking. We validated EXT1, TM9SF2, and TMED10 (TMP21/p23/p24δ) as important host factors for vaccinia virus infection. The critical roles of EXT1 in heparan sulfate synthesis and vaccinia virus infection were confirmed. TM9SF2 was validated as a player mediating heparan sulfate expression, explaining its contribution to vaccinia virus infection. In addition, TMED10 was found to be crucial for virus-induced plasma membrane blebbing and phosphatidylserine-induced macropinocytosis, presumably by regulating the cell surface expression of the TAM receptor Axl.<b>IMPORTANCE</b> Poxviruses are large DNA viruses that can infect a wide range of host species. A number of these viruses are clinically important to humans, including variola virus (smallpox) and vaccinia virus. Since the eradication of smallpox, zoonotic infections with monkeypox virus and cowpox virus are emerging. Additionally, poxviruses can be engineered to specifically target cancer cells and are used as a vaccine vector against tuberculosis, influenza, and coronaviruses. Poxviruses rely on host factors for most stages of their life cycle, including attachment to the cell and entry. These host factors are crucial for virus infectivity and host cell tropism. We used a genome-wide knockout library of host cells to identify host factors necessary for vaccinia virus infection. We confirm a dominant role for heparin sulfate in mediating virus attachment. Additionally, we show that TMED10, previously not implicated in virus infections, facilitates virus uptake by modulating the cellular response to phosphatidylserine.
Linearization of Power Amplifiers Using the Reverse MM-LINC Technique (2010)

A new mode-multiplexing linear amplification with nonlinear components (MM-LINC) technique is proposed in this brief. This technique, which is referred to as reverse MM-LINC, consists of using linear amplification with nonlinear components (LINC) hardware, along with two signal decomposition modes, depending on the power of the input signal. This decomposition guarantees acceptable linearity of the signal when the power amplifiers (PAs) are operating at their full power potential. This linearity improvement requires only relatively light computational complexity, which makes this technique a suitable alternative to digital predistortion for mobile and medium-power wireless transmitters. The implementation of the reverse MM-LINC concept for mobile WiMAX applications showed an improvement of 15 dB in the adjacent channel power ratio and a reduction in the error vector magnitude from 10% to 2.2%, when compared with a nonlinearized class-AB PA operating at full power potential. At this operation point, the efficiency of the reverse MM-LINC amplification system was not significantly different from the efficiency of the class-AB PA.
ChemInform Abstract: Steroids. Part 383. Pregnane‐Type Brassinosteroids with a Four‐Carbon Ester Functionality in Position 20. (1996)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Pompe Disease Results in a Golgi-based Glycosylation Deficit in Human Induced Pluripotent Stem Cell-derived Cardiomyocytes (2014)

Infantile-onset Pompe disease is an autosomal recessive disorder caused by the complete loss of lysosomal glycogen-hydrolyzing enzyme acid α-glucosidase (GAA) activity, which results in lysosomal glycogen accumulation and prominent cardiac and skeletal muscle pathology. The mechanism by which loss of GAA activity causes cardiomyopathy is poorly understood. We reprogrammed fibroblasts from patients with infantile-onset Pompe disease to generate induced pluripotent stem (iPS) cells that were differentiated to cardiomyocytes (iPSC-CM). Pompe iPSC-CMs had undetectable GAA activity and pathognomonic glycogen-filled lysosomes. Nonetheless, Pompe and control iPSC-CMs exhibited comparable contractile properties in engineered cardiac tissue. Impaired autophagy has been implicated in Pompe skeletal muscle; however, control and Pompe iPSC-CMs had comparable clearance rates of LC3-II-detected autophagosomes. Unexpectedly, the lysosome-associated membrane proteins, LAMP1 and LAMP2, from Pompe iPSC-CMs demonstrated higher electrophoretic mobility compared with control iPSC-CMs. Brefeldin A induced disruption of the Golgi in control iPSC-CMs reproduced the higher mobility forms of the LAMPs, suggesting that Pompe iPSC-CMs produce LAMPs lacking appropriate glycosylation. Isoelectric focusing studies revealed that LAMP2 has a more alkaline pI in Pompe compared with control iPSC-CMs due largely to hyposialylation. MALDI-TOF-MS analysis of N-linked glycans demonstrated reduced diversity of multiantennary structures and the major presence of a trimannose complex glycan precursor in Pompe iPSC-CMs. These data suggest that Pompe cardiomyopathy has a glycan processing abnormality and thus shares features with hypertrophic cardiomyopathies observed in the congenital disorders of glycosylation.
Systemic delivery of siRNA in pumpkin by a plant PHLOEM SMALL RNA‐BINDING PROTEIN 1–ribonucleoprotein complex (2014)

In plants, the vascular system, specifically the phloem, functions in delivery of small RNA (sRNA) to exert epigenetic control over developmental and defense-related processes. Although the importance of systemic sRNA delivery has been established, information is currently lacking concerning the nature of the protein machinery involved in this process. Here, we show that a PHLOEM SMALL-RNA BINDING PROTEIN 1 (PSRP1) serves as the basis for formation of an sRNA ribonucleoprotein complex (sRNPC) that delivers sRNA (primarily 24 nt) to sink organs. Assembly of this complex is facilitated through PSRP1 phosphorylation by a phloem-localized protein kinase, PSRPK1. During long-distance transport, PSRP1-sRNPC is stable against phloem phosphatase activity. Within target tissues, phosphatase activity results in disassembly of PSRP1-sRNPC, a process that is probably required for unloading cargo sRNA into surrounding cells. These findings provide an insight into the mechanism involved in delivery of sRNA associated with systemic gene silencing in plants.
The stability of free fermi Hamiltonians (2019)

Recent results have shown the stability of frustration-free Hamiltonians to weak local perturbations, assuming several conditions. In this paper, we prove the stability of free fermion Hamiltonians which are gapped and local. These free fermion Hamiltonians are not necessarily frustration-free, but we are able to adapt previous work to prove stability. The key idea is to add an additional copy of the system to cancel topological obstructions. We comment on applications to quantization of Hall conductance in such systems.
Distinctive Expression of Cancer/Testis-X Antigens in a Subset of ER Negative Breast Carcinomas. (2009)

Abstract Background: Cancer/testis-X antigens are a multigene family that are predominantly expressed in human germ line cells, with little or no expression in somatic adult tissues, but become aberrantly activated in various malignancies. Some such CT-X antigens represent ideal targets for cancer immunotherapy and have already been used in clinical testing. In contrast to melanomas, bladder, lung, ovarian and hepatocellular carcinomas which show higher levels of CT-X antigen expression, the reports in breast cancers have been inconclusive to date and a comprehensive gene expression and clinicopathological analysis has yet to be performed.Material and Methods: Using sequencing data as well as nine publicly available gene expression data sets, we analyzed the expression of Cancer/testis-X antigens in more than 1900 primary breast cancers. Complementary analysis was performed on three tissue microarrays comprising a total of 201 primary breast carcinomas and 53 brain metastases. Clinical information on the ER-, PR-, HER2, Ki67, p53, EGFR and basal markers was available for statistical analysis.Results: A significantly higher expression of Cancer/testis-X antigens was found in ER negative breast carcinomas over different data sets with a concordant gene expression pattern of several Cancer/testis-X antigens. Members of the MAGEA family and NY-ESO-1/CTAG1B were consistently the most prevalent. Immunohistochemical analyses confirmed a significant correlation of MAGEA family and NY-ESO-1/CTAG1B with ER negative (pValue &amp;lt; 0.0001), PR negative (pValue &amp;lt; 0.01) and Ki67 staining (pValue &amp;lt; 0.0001). Many of these tumors were also positive for basal markers.Discussion: Previous studies of Cancer/testis-X antigens in breast have focused on ER positive cancers, in smaller subsets and provided inconclusive results. Using comprehensive gene expression data sets and tissue microarrays, we have demonstrated a significant association of MAGEA family and NY-ESO-1/CTAG1B with ER/PR negative breast cancer. Since these cancers represent a subgroup for which less therapeutic modalities are available, we propose the use of MAGEA and NY-ESO-1/CTAG1B cancer vaccines in the adjuvant setting as an approach to restricting tumor growth and metastases. Clinical trails using MAGEA and NY-ESO-1/CTAG1B are warranted. Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 3139.
Singlet oxygen oxidation of substituted furans to 5-hydroxy-2(5H)-furanone (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSinglet oxygen oxidation of substituted furans to 5-hydroxy-2(5H)-furanoneGary C. M. Lee, Elizabeth T. Syage, Dale A. Harcourt, Judy M. Holmes, and Michael E. GarstCite this: J. Org. Chem. 1991, 56, 25, 7007–7014Publication Date (Print):December 1, 1991Publication History Published online1 May 2002Published inissue 1 December 1991https://pubs.acs.org/doi/10.1021/jo00025a012https://doi.org/10.1021/jo00025a012research-articleACS PublicationsRequest reuse permissionsArticle Views1409Altmetric-Citations48LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Artistic screening (1995)

Artistic screening is a new image reproduction technique incorporating freely created artistic screen elements for generating halftones. Fixed predefined dot contours associated with given intensity levels determine the screen dot shape's growing behavior. Screen dot contours associated with each intensity level are obtained by interpolation between the fixed predefined dot contours. A user-defined mapping transforms screen elements from screen element definition space to screen element rendition space. This mapping can be tuned to produce various effects such as dilatations, contractions and nonlinear deformations of the screen element grid. Discrete screen elements associated with all desired intensity levels are obtained by rasterizing the interpolated screen dot shapes in the screen element rendition space. Since both the image to be reproduced and the screen shapes can be designed independently, the design freedom offered to artists is very great. The interaction between the image to be reproduced and the screen shapes enables the creation of graphic designs of high artistic quality. Artistic screening is particularly well suited for the reproduction of images on large posters. When looked at from a short distance, the poster's screening layer may deliver its own message. Furthermore, thanks to artistic screening, both full size and microscopic letters can be incorporated into the image reproduction process. In order to avoid counterfeiting, banknotes may comprise grayscale images with intensity levels produced by microletters of varying size and shape.
Ingenol Disoxate: A Novel 4-Isoxazolecarboxylate Ester of Ingenol with Improved Properties for Treatment of Actinic Keratosis and Other Non-Melanoma Skin Cancers (2016)

LEO Pharma A/S.
Shape-Directed Assembly of a “Macromolecular Barb” into Nanofibers: Stereospecific Cyclopolymerization of Isopropylidene Diallylmalonate (2010)

Cyclopolymerization of isopropylidene diallylmalonate (1) in CH(2)Cl(2) using as the initiator a crystallographically defined alpha-diimine Pd(II) complex with a trans-azobenzene strap (trans-3) proceeds stereospecifically to give a cycloolefinic polymer that is rich in threo-disyndiotactic sequences (st(rich)-2; syndiotactic tetrad content = 60% at -10 to 0 degrees C). Polymer 2, when perfectly threo-disyndiotactic, adopts a "barb"-shaped geometry with its cyclic malonate pendants sticking out alternately up and down along the rigid main chain. Under appropriate conditions, st(rich)-2 regularly self-assembles, not only in the solid state but also in solution, into nanofibers that eventually give rise to physical gelation of halogenated solvents such as CH(2)Cl(2). In sharp contrast, a reference polymer 2 that is rich in threo-diisotactic sequences (it(rich)-2), which likely adopts a helical geometry, has poor self-assembly capability in solution and neither forms nanofibers nor induces physical gelation of CH(2)Cl(2).
On Link Scheduling Under Blockage and Interference in 60-GHz Ad Hoc Networks (2015)

In this paper, we tackle the problem of minimum time length link scheduling in 60-GHz ad hoc wireless networks using directional antennas with directional beamforming, under both traffic demand and signal to interference and noise ratio constraints. Both single-hop and multi-hop cases are considered. For the single-hop scenario, a binary integer programming problem is formulated by incorporating a general interference model for directional transmissions and a Markov chain-based blockage model. Two effective solution algorithms are proposed, including a greedy algorithm that maximizes the instant throughput for each time slot, and a column generation-based algorithm that iteratively improves the current link schedule. For the multi-hop scenario, we develop a more complicated problem formulation incorporating both route selection and flow conservation constraints. We also develop an effective algorithm to solve the multi-hop problem. The performance of the proposed algorithms is validated with simulations.
Stereoconvergent and -divergent Synthesis of Tetrasubstituted Alkenes by Nickel-Catalyzed Cross-Couplings (2021)

We report the development of a method to diastereoselectively access tetrasubstituted alkenes via nickel-catalyzed Suzuki-Miyaura cross<b>-</b>couplings of enol tosylates and boronic acid esters. Either diastereomeric product was selectively accessed from a mixture of enol tosylate starting material diastereomers in a convergent reaction by judicious choice of the ligand and reaction conditions. A similar protocol also enabled a divergent synthesis of each product isomer from diastereomerically pure enol tosylates. Notably, high-throughput optimization of the monophosphine ligands was guided by chemical space analysis of the <i>kraken</i> library to ensure a diverse selection of ligands was examined. Stereoelectronic analysis of the results provided insight into the requirements for reactive and selective ligands in this transformation. The synthetic utility of the optimized catalytic system was then probed in the stereoselective synthesis of various tetrasubstituted alkenes, with yields up to 94% and diastereomeric ratios up to 99:1 <i>Z</i>/<i>E</i> and 93:7 <i>E</i>/<i>Z</i> observed. Moreover, a detailed computational analysis and experimental mechanistic studies provided key insights into the nature of the underlying isomerization process impacting selectivity in the cross<b>-</b>coupling.
ChemInform Abstract: Translocation of Radical Sites by Intramolecular 1,5‐Hydrogen Atom Transfer. (1988)

Abstract Two variants are described for the preparation of cyclopentanes such as (II) or (IV) via a radical cyclization procedure, involving halogen abstraction, 1,5‐H atom transfer, cyclization and chain transfer.
Supplementary Figure 10 from Somatic Epigenetic Silencing of <i>RIPK3</i> Inactivates Necroptosis and Contributes to Chemoresistance in Malignant Mesothelioma (2023)

&lt;p&gt;Expression levels of MLKL, CASP8 and FADD were not significantly correlated with MM patient survival. Data are from TCGA dataset of 87 primary pleural MM patients. A, C and E, Box plots of mRNA expression of MLKL, CASP8 and FADD where each X-axis shows quartile-based mRNA expression categories, and each Y-axis indicates the log-transformed RSEM mRNA expression values. In box plots, color code orange indicates high gene expression, and blue indicates low expression. B, D and F, Kaplan-Meier curves indicating OS of MM patients based on mRNA expression of MLKL, CASP8 and FADD, with MM patients having low expression of each gene shown with blue line and MM patients with high levels of expression of each of gene shown with an orange line.&lt;/p&gt;
The Alzheimer's Association international guidelines for handling of cerebrospinal fluid for routine clinical measurements of amyloid β and tau (2021)

The core cerebrospinal fluid (CSF) Alzheimer's disease (AD) biomarkers amyloid beta (Aβ42 and Aβ40), total tau, and phosphorylated tau, have been extensively clinically validated, with very high diagnostic performance for AD, including the early phases of the disease. However, between-center differences in pre-analytical procedures may contribute to variability in measurements across laboratories. To resolve this issue, a workgroup was led by the Alzheimer's Association with experts from both academia and industry. The aim of the group was to develop a simplified and standardized pre-analytical protocol for CSF collection and handling before analysis for routine clinical use, and ultimately to ensure high diagnostic performance and minimize patient misclassification rates. Widespread application of the protocol would help minimize variability in measurements, which would facilitate the implementation of unified cut-off levels across laboratories, and foster the use of CSF biomarkers in AD diagnostics for the benefit of the patients.