gebhart/patrepeval huggingface dataset:
Maculosin, a host-specific phytotoxin for spotted knapweed from Alternaria alternata (1988)

Several diketopiperazines have been isolated from liquid cultures of Alternaria alternata, the causal agent of black leaf blight of spotted knapweed, Centaurea maculosa Lam. One of these compounds, maculosin [the diketopiperazine cyclo(-L-Pro-L-Tyr-)], was active in the nicked-leaf bioassay at 10(-5) M; synthetic maculosin possessed chemical and biological activities identical to those of the natural product. Other diketopiperazines isolated from the fungus possessed either less activity or none at all. In tests against 19 plant species, maculosin was phytotoxic only to spotted knapweed. Thus maculosin is a host-specific phytotoxin from a weed pathogen.
Nanofabrication of Organic/Inorganic Hybrids of TiO2 with Substituted Phthalocyanine or Polythiophene (2001)

Organic photovoltaic cells, similar to Grätzel type, have been widely investigated in recent years. In the case of Grätzel-type cells, TiO2 colloids are usually spin-coated onto an electrode and then sintered. Later, such electrodes are immersed in dye solution to sensitize the TiO2 layer for fabrication of photovoltaic cells. In the current study, an attempt was made to fabricate photovoltaic cells using a layer-by-layer technique. Based on such a method, ordered substituted phthalocyanine or conducting polythiophene-sensitized TiO2 multilayers were fabricated at the molecular level. Buildup of multilayer films of copper phthalocyanine-capped TiO2 and poly(thiophene-3-acetic acid)/TiO2 was monitored by increments in the UV-visible absorption and the frequency decrease of quartz crystal microbalance. The ordered multilayers were further characterized by infrared spectroscopy, and electrochemical and photoelectrochemical measurements.
FKBP12-Rapamycin-associated Protein (FRAP) Autophosphorylates at Serine 2481 under Translationally Repressive Conditions (2000)

The FKBP12-rapamycin associated protein (FRAP, also RAFT, mTOR) belongs to a family of phosphatidylinositol kinase-related kinases. These kinases mediate cellular responses to stresses such as DNA damage and nutrient deprivation in a variety of eukaryotes from yeast to humans. FRAP regulates G(1) cell cycle progression and translation initiation in part by controlling the phosphorylation states of a number of translational and cell cycle regulators. Although FRAP is known to be phosphorylated in vivo and to phosphorylate several proteins (including itself) in vitro, FRAP's phosphorylation sites and substrate specificity are unknown. We report here the identification of a FRAP autophosphorylation site. This site, Ser-2481, is located in a hydrophobic region near the conserved carboxyl-terminal FRAP tail. We demonstrate that the COOH-terminal tail is required for FRAP kinase activity and for signaling to the translational regulator p70(s6k) (ribosomal subunit S6 kinase). Phosphorylation of wild-type but not kinase-inactive FRAP occurs at Ser-2481 in vivo, suggesting that Ser-2481 phosphorylation is a marker of FRAP autokinase activity in cells. FRAP autophosphorylation is blocked completely by wortmannin treatment but not by rapamycin treatment, amino acid deprivation, or serum withdrawal, treatments that lead to acute dephosphorylation of eIF4E-binding protein (4E-BP1) and p70(s6k). Ser-2481 phosphorylation increases slightly upon c-Akt/PKB activation and dramatically upon calyculin A treatment of T-cells. These results suggest that FRAP-responsive dephosphorylation of 4E-BP1 and p70(s6k) occurs through a mechanism other than inhibition of intrinsic FRAP kinase activity.
Effects of DPP-4 Inhibitors on the Heart in a Rat Model of Uremic Cardiomyopathy (2011)

DPP-4 inhibition increases plasma GLP-1 levels, particularly in uremia, and reduces expression of cardiac mRNA levels of matrix proteins and B-type natriuretic peptides (BNP). Linagliptin may offer a unique approach for treating uremic cardiomyopathy in CKD patients, with no need for dose-adjustment.
Photobiotin Surface Chemistry Improves Label‐Free Interferometric Sensing of Biochemical Interactions (2005)

A highly sensitive and cost-effective biosensor: Simple surface chemistry of photobiotin, bound with a layer of avidin, allows convenient immobilization of any biotinylated molecule of interest onto microfluidic channels molded in poly(dimethylsiloxane) (PDMS). The biosensor obtained this way is capable of monitoring biomolecular interactions in label-free situations and in small (picoliter) volumes. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2006/z502418_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Translational research of VOLTAGE-A: Efficacy predictors of preoperative chemoradiotherapy and consolidation nivolumab in patients with both microsatellite stable and microsatellite instability-high locally advanced rectal cancer. (2021)

100 Background: In VOLTAGE-A, chemoradiotherapy (CRT; 50.4Gy with capecitabine, 1,650mg/m 2 ) followed by five cycles of consolidation nivolumab (nivo) (240mg q2 weeks) showed 30% pathological complete response [pCR; AJCC tumor regression grade (TRG) 0] and 38% major pathological responses (AJCC TRG 0-1) in patients with microsatellite stable (MSS) locally advanced primary rectal cancer (LARC). In addition, 60% pCR was observed in patients with microsatellite instability-high (MSI-H) LARC. In this study, we aimed to determine the predictive biomarkers for efficacy of sequential preoperative CRT and consolidation nivo. Methods: Serial tumor biopsies were performed at four time points:pre-CRT; post-CRT; post-3 cycles of nivo; and pre-surgery. We analyzed the immune status of the patients by flow cytometry using the collected tumor-infiltrating lymphocytes (TILs) dissociated from tumor samples. Whole exome and RNA sequencing analyses were conducted using the extracted DNA and RNA from tumor, respectively. The PD-L1 status of tumor samples was also evaluated by in vitro diagnostic immunohistochemistry staining. Results: Of the 38 MSS patients whose PD-L1 tumor proportion score (TPS) was analyzable in pre-CRT samples, the pCR rates were 67% (6/9) and 17% (5/29) in positive (≥1%) and negative PD-L1 status (p = 0.009), respectively. Among the 24 MSS patients whose samples were serially collected, the pCR rates according to CD8 + T cells/effector regulatory T cells (CD8/eTreg) ratio in TILs of pre-CRT samples ≥2.5 and &lt; 2.5 were 78% (7/9) and 13% (2/15), respectively (p = 0.003). The CD8/eTreg ratio in TILs was consistently high in patients with pCR during the study treatments. Ki-67 and PD-1 expression by CD8 + T cells in TILs was significantly high in pre-CRT samples from patients TRG 0-1. Conversely, in patients with TRG 2-3, CTLA-4 expression by both CD4 + T cells and CD8 + T cells in TILs was significantly high after five cycles of nivo, suggesting the potential resistance mechanisms of nivo monotherapy. Of the 21 MSS patients whose consensus molecular subtype (CMS) was analyzable, those with CMS1 and CMS3 tumors achieved 100% (2/2) and 60% (4/6) TRG 0-1, respectively. In contrast, patients with CMS2 and CMS4 tumors achieved 43% (3/7) and 29% (2/7) TRG 0-1, respectively. The tumor mutational burden (TMB) of pre-CRT samples in five MSI-H patients was higher than that in the 24 MSS patients (median: 13.2 vs. 0.99 mutation/Mbp, p &lt; 0.0001). Among MSS patients, TMB was higher in patients with TRG 0-1 than in patients with TRG 2-3 (median: 1.45 vs. 0.84 mutation/Mbp, p = 0.016). Conclusions: Positive PD-L1 TPS; high CD8/eTreg ratio; Ki-67, PD-1, and CTLA-4 expression by CD8 + T cells in TILs; CMS 1 or 3; and high TMB can be good predictors of efficacy of preoperative CRT followed by nivo. Clinical trial information: NCT02948348.
Simplifying quotient determination in high-radix modular multiplication (2002)

Until now the use of high radices to implement modular multiplication has been questioned, because it involves complex determination of quotient digits for the module reduction. This paper presents algorithms that are obtained through rewriting of Montgomery's algorithm. The determination of quotients becomes trivial and the cycle time becomes independent of the choice of radix. It is discussed how the critical path in the loop can be reduced to a single shift-and-add operation. This implies that a true speed up is achieved by choosing higher radices.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Ruxolitinib: a potent and selective Janus kinase 1 and 2 inhibitor in patients with myelofibrosis. An update for clinicians (2012)

Ruxolitinib became the first US Food and Drug Administration approved therapy for myelofibrosis in 2011 and EU approval is anticipated in summer 2012. Two large phase III trials (known as the COMFORT studies) were the basis for this approval and were published recently. In this review article we discuss the challenges in managing myelofibrosis, the information to date about ruxolitinib and speculate as to the future direction with this and similar agents.
Enhancing Effects of Salt Formation on Catalytic Activity and Enantioselectivity for Asymmetric Hydrogenation of Isoquinolinium Salts by Dinuclear Halide‐Bridged Iridium Complexes Bearing Chiral Diphosphine Ligands (2014)

Asymmetric hydrogenation of 1- and 3-substituted and 1,3-disubstituted isoquinolinium chlorides using triply halide-bridged dinuclear iridium complexes [{Ir(H)(diphosphine)}2 (μ-Cl)3 ]Cl has been achieved by the strategy of HCl salt formation of isoquinolines to afford the corresponding chiral 1,2,3,4-tetrahydroisoquinolines (THIQs) in high yields and with excellent enantioselectivities after simple basic work-up. The effects of salt formation have been investigated by time-course experiments, which revealed that the generation of isoquinolinium chlorides clearly prevented formation of the catalytically inactive dinuclear trihydride complex, which was readily generated in the catalytic reduction of salt-free isoquinoline substrates. Based on mechanistic investigations, including by (1) H and (31) P{(1) H} NMR studies and the isolation and characterization of several intermediates, the function of the chloride anion of the isoquinolinium chlorides has been elucidated, allowing us to propose a new outer-sphere mechanism involving coordination of the chloride anion of the substrates to an iridium dihydride species along with a hydrogen bond between the chloride ligand and the N-H proton of the substrate salt.
Knowledge Guided Disambiguation for Large-Scale Scene Classification With Multi-Resolution CNNs (2017)

Convolutional neural networks (CNNs) have made remarkable progress on scene recognition, partially due to these recent large-scale scene datasets, such as the Places and Places2. Scene categories are often defined by multi-level information, including local objects, global layout, and background environment, thus leading to large intra-class variations. In addition, with the increasing number of scene categories, label ambiguity has become another crucial issue in large-scale classification. This paper focuses on large-scale scene recognition and makes two major contributions to tackle these issues. First, we propose a multi-resolution CNN architecture that captures visual content and structure at multiple levels. The multi-resolution CNNs are composed of coarse resolution CNNs and fine resolution CNNs, which are complementary to each other. Second, we design two knowledge guided disambiguation techniques to deal with the problem of label ambiguity: 1) we exploit the knowledge from the confusion matrix computed on validation data to merge ambiguous classes into a super category and 2) we utilize the knowledge of extra networks to produce a soft label for each image. Then, the super categories or soft labels are employed to guide CNN training on the Places2. We conduct extensive experiments on three large-scale image datasets (ImageNet, Places, and Places2), demonstrating the effectiveness of our approach. Furthermore, our method takes part in two major scene recognition challenges, and achieves the second place at the Places2 challenge in ILSVRC 2015, and the first place at the LSUN challenge in CVPR 2016. Finally, we directly test the learned representations on other scene benchmarks, and obtain the new state-of-the-art results on the MIT Indoor67 (86.7%) and SUN397 (72.0%). We release the code and models at https://github.com/wanglimin/MRCNN-Scene-Recognition.
Online topic model for Twitter considering dynamics of user interests and topic trends (2014)

Latent Dirichlet allocation (LDA) is a topic model that has been applied to various fields, including user profiling and event summarization on Twitter. When LDA is applied to tweet collections, it generally treats all aggregated tweets of a user as a single document. Twitter-LDA, which assumes a single tweet consists of a single topic, has been proposed and has shown that it is superior in topic semantic coherence. However, Twitter-LDA is not capable of online inference. In this study, we extend Twitter-LDA in the following two ways. First, we model the generation process of tweets more accurately by estimating the ratio between topic words and general words for each user. Second, we enable it to estimate the dynamics of user interests and topic trends online based on the topic tracking model (TTM), which models consumer purchase behaviors.
Reverse Signaling through Membrane-bound Interleukin-15 (2004)

The results from this study implicate membrane-anchored interleukin (IL)-15 constitutively expressed on the cell surface of PC-3 human prostate carcinoma cells and interferon-gamma-activated human monocytes in reverse signaling upon stimulation with soluble IL-15 receptor-alpha or anti-IL-15 antibodies, mediating the outside-to-inside signal transduction that involves the activation of members of the MAPK family (ERK and p38) and focal adhesion kinase. The presence of membrane-bound IL-15 was not dependent on the expression of the trimeric IL-15 receptor complex by these cells and resisted treatment with acidic buffer or trypsin. Reverse signaling through membrane-bound IL-15 considerably increased the production of several pro-inflammatory cytokines by monocytes, such as IL-6, IL-8, and tumor necrosis factor-alpha, thereby indicating the relevance of this process to the complex immunomodulatory function of these cells. Furthermore, stimulation of transmembrane IL-15 also enhanced the transcription of IL-6 and IL-8 in the PC-3 cell line and promoted migration of PC-3 cells as well as LNCaP human prostate carcinoma cells stably expressing IL-15 on the cell surface. Thus, IL-15 can exist as a biologically active transmembrane molecule that possesses dual ligand-receptor qualities with a potential to induce bidirectional signaling. This fact highlights a new level of complexity in the biology of IL-15 and offers novel important insights into our understanding of the cellular responses modulated by this pleiotropic cytokine.
Occurrence and diversity of nitrogen-fixingSphingomonasbacteria associated with rice plants grown in Brazil (2009)

So far, the occurrence of nitrogen-fixing Sphingomonas bacteria has been restricted to three strains of Sphingomonas azotifigens. In this work, a group of 46 Sphingomonas-like isolates, which originated from two rice varieties grown in two soils in Brazil, were characterized based on morphological, physiological and genetic analyses. The PCR genus specifically applied indicated that all 46 isolates belonged to the Sphingomonas genus and confirmed the results based on the yellow pigment of the colonies grown on potato agar medium and the BIOLOG data. It was also observed that 22 isolates are nitrogen-fixing bacteria as determined by the acetylene reduction method and confirmed by nifH gene detection. The genetic diversity based on the 16S rRNA analysis (amplified rDNA restriction analysis) showed that the isolates formed two distinct groups at a similarity value of 60%. Furthermore, five clusters at 60% similarity were observed with the 16S-23S intergenic space (ribosomal intergenic space analysis) analysis. Sequencing of the 16S rRNA gene and nifH fragments showed that most of the 22 nitrogen-fixing isolates formed clusters apart from that of the S. azotifigens. This is the first report on the occurrence of nitrogen-fixing Sphingomonas bacteria associated with rice grown in Brazil.
Rosiglitazone Monotherapy Is Effective in Patients with Type 2 Diabetes (2001)

This study evaluated the efficacy and safety of rosiglitazone monotherapy in patients with type 2 diabetes. After a 4-week placebo run-in period, 493 patients with type 2 diabetes were randomized to receive rosiglitazone [2 or 4 mg twice daily (bd)] or placebo for 26 weeks. The primary end point was change in hemoglobin A(1c); other variables assessed included fasting plasma glucose, fructosamine, endogenous insulin secretion, urinary albumin excretion, serum lipids, and adverse events. Rosiglitazone (2 and 4 mg bd) decreased mean hemoglobin A(1c) relative to placebo by 1.2 and 1.5 percentage points, respectively, and reduced fasting plasma glucose concentrations relative to placebo by 3.22 and 4.22 mmol/L, respectively. Fasting plasma insulin and insulin precursor molecules decreased significantly. Homeostasis model assessment estimates indicate that rosiglitazone (2 and 4 mg bd) reduced insulin resistance by 16.0% and 24.6%, respectively, and improved ss-cell function over baseline by 49.5% and 60.0%, respectively. Urinary albumin excretion decreased significantly in the rosiglitazone (4 mg bd) group. There was no increase in adverse events with rosiglitazone. In the short-term, rosiglitazone is an insulin sensitizer that is effective and safe as monotherapy in patients with type 2 diabetes who are inadequately controlled by lifestyle interventions.
Phosphorylation of nuclear proteins directs binding to salicylic acid‐responsive elements (1997)

The cis-located DNA sequence as-1 (Activation Sequence-1) from CaMV 35S promoter has been previously identified as an element that can confer inducibility by salicylic acid (SA) with immediate early kinetics. This sequence specifically binds to ASF-1 (Activation Sequence Factor-1), previously characterized in tobacco nuclear extracts. To assess whether modulation of ASF-1 binding activity can explain the activation of the as-1 sequence observed in vivo, we performed electrophoretic mobility shift assays using nuclear extracts from SA-treated and water-treated tobacco plants. Our results indicate that treatment of plants with SA increases ASF-1 binding to as-1 and to ocs, an as-1-like element from the Agrobacterium octopine synthase gene. In contrast, SA treatment has no effect on the binding of GT-1 factor to its target light-inducible box II element. Furthermore, treatment of nuclear extracts from SA-treated plants with alkaline phosphatase decreases ASF-1 binding to the as-1 element. This can be reversed by pretreatment with 10 mM NaF. Accordingly, pretreatment of nuclear extracts from control water-treated plants with ATP produces an increase in ASF-1 binding activity similar to that observed with SA. This effect of ATP is reversed by treatment with alkaline phosphatase and prevented by quercetin, a casein kinase II inhibitor. These results support the hypothesis that a nuclear protein kinase is involved in the immediate early events of transcriptional activation triggered by SA.
In-Car Positioning and Navigation Technologies—A Survey (2009)

In-car positioning and navigation has been a killer application for Global Positioning System (GPS) receivers, and a variety of electronics for consumers and professionals have been launched on a large scale. Positioning technologies based on stand-alone GPS receivers are vulnerable and, thus, have to be supported by additional information sources to obtain the desired accuracy, integrity, availability, and continuity of service. A survey of the information sources and information fusion technologies used in current in-car navigation systems is presented. The pros and cons of the four commonly used information sources, namely, 1) receivers for radio-based positioning using satellites, 2) vehicle motion sensors, 3) vehicle models, and 4) digital map information, are described. Common filters to combine the information from the various sources are discussed. The expansion of the number of satellites and the number of satellite systems, with their usage of available radio spectrum, is an enabler for further development, in combination with the rapid development of microelectromechanical inertial sensors and refined digital maps.
Oral dabigatran versus enoxaparin for thromboprophylaxis after primary total hip arthroplasty (RE-NOVATE II) (2011)

This trial compared the efficacy and safety of oral dabigatran, a direct thrombin inhibitor, versus subcutaneous enoxaparin for extended thromboprophylaxis in patients undergoing total hip arthroplasty. A total of 2,055 patients were randomised to 28-35 days treatment with oral dabigatran, 220 mg once-daily, starting with a half-dose 1-4 hours after surgery, or subcutaneous enoxaparin 40 mg once-daily, starting the evening before surgery. The primary efficacy outcome was a composite of total venous thromboembolism [VTE] (venographic or symptomatic) and death from all-causes. The main secondary composite outcome was major VTE (proximal deep-vein thrombosis or non-fatal pulmonary embolism) plus VTE-related death. The main safety outcome was major bleeding. In total, 2,013 were treated, of whom 1,577 operated patients were included in the primary efficacy analysis. The primary efficacy outcome occurred in 7.7% of the dabigatran group versus 8.8% of the enoxaparin group, risk difference (RD) -1.1% (95%CI -3.8 to 1.6%); p<0.0001 for the pre-specified non-inferiority margin. Major VTE plus VTE-related death occurred in 2.2% of the dabigatran group versus 4.2% of the enoxaparin group, RD -1.9% (-3.6% to -0.2%); p=0.03. Major bleeding occurred in 1.4% of the dabigatran group and 0.9% of the enoxaparin group (p=0.40). The incidence of adverse events, including liver enzyme elevations and cardiac events, during treatment was similar between the groups. Extended prophylaxis with oral dabigatran 220 mg once-daily was as effective as subcutaneous enoxaparin 40 mg once-daily in reducing the risk of VTE after total hip arthroplasty, and superior to enoxaparin for reducing the risk of major VTE. The risk of bleeding and safety profiles were similar.
Identification of Three Rheumatoid Arthritis Disease Subtypes by Machine Learning Integration of Synovial Histologic Features and RNA Sequencing Data (2018)

Gene expression analysis of RA and OA synovial tissue revealed 3 distinct synovial subtypes. These labels were used to generate a histologic scoring algorithm in which the histologic scores were found to be associated with parameters of systemic inflammation, including the erythrocyte sedimentation rate, CRP level, and autoantibody levels. Comparison of gene expression patterns to clinical features revealed a potentially clinically important distinction: mechanisms of pain may differ in patients with different synovial subtypes.