gebhart/patrepeval huggingface dataset:
Multivariate analysis of microarray data by principal component discriminant analysis: prioritizing relevant transcripts linked to the degradation of different carbohydrates in Pseudomonas putida S12 (2005)

The value of the multivariate data analysis tools principal component analysis (PCA) and principal component discriminant analysis (PCDA) for prioritizing leads generated by microarrays was evaluated. To this end, Pseudomonas putida S12 was grown in independent triplicate fermentations on four different carbon sources, i.e. fructose, glucose, gluconate and succinate. RNA isolated from these samples was analysed in duplicate on an anonymous clone-based array to avoid bias during data analysis. The relevant transcripts were identified by analysing the loadings of the principal components (PC) and discriminants (D) in PCA and PCDA, respectively. Even more specifically, the relevant transcripts for a specific phenotype could also be ranked from the loadings under an angle (biplot) obtained after PCDA analysis. The leads identified in this way were compared with those identified using the commonly applied fold-difference and hierarchical clustering approaches. The different data analysis methods gave different results. The methods used were complementary and together resulted in a comprehensive picture of the processes important for the different carbon sources studied. For the more subtle, regulatory processes in a cell, the PCDA approach seemed to be the most effective. Except for glucose and gluconate dehydrogenase, all genes involved in the degradation of glucose, gluconate and fructose were identified. Moreover, the transcriptomics approach resulted in potential new insights into the physiology of the degradation of these carbon sources. Indications of iron limitation were observed with cells grown on glucose, gluconate or succinate but not with fructose-grown cells. Moreover, several cytochrome- or quinone-associated genes seemed to be specifically up- or downregulated, indicating that the composition of the electron-transport chain in P. putida S12 might change significantly in fructose-grown cells compared to glucose-, gluconate- or succinate-grown cells.
Individual charge traps in silicon nanowires: Measurements of location, spin and occupation number by Coulomb blockade spectroscopy (2005)

We study anomalies in the Coulomb blockade spectrum of a quantum dot formed in a silicon nanowire. These anomalies are attributed to electrostatic interaction with charge traps in the device. A simple model reproduces these anomalies accurately and we show how the capacitance matrices of the traps can be obtained from the shape of the anomalies. From these capacitance matrices we deduce that the traps are located near or inside the wire. Based on the occurrence of the anomalies in wires with different doping levels we infer that most of the traps are arsenic dopant states. In some cases the anomalies are accompanied by a random telegraph signal which allows time resolved monitoring of the occupation of the trap. The spin of the trap states is determined via the Zeeman shift.
Interworking of switched ethernet and ATM flow control mechanisms (2002)

Abstract In this paper, we evaluate the performance of TCP in a network where the IEEE 802.3x flow control and the ATM Available Bit Rate flow control mechanisms are interworked. The objective is to examine whether an interworking of the two flow control mechanisms can improve the performance of upper‐layer protocols like TCP which is an end‐to‐end connection‐based transport protocol. The simulation studies show that the two interworked flow control mechanisms result in high link utilization while providing very low loss rates when used in conjunction with TCP. The flow control mechanisms complement each other. Copyright © 2002 John Wiley &amp; Sons, Ltd.
Polarization-Based Image Understanding Research for Automatic Target Recognition (2000)

Abstract : Major developments in a new promising approach to Automatic Target Detection and Recognition have taken place this year building off of previous research developments in Polarization Vision. Preliminary results have already demonstrated tangible enhanced capabilities for RSTA in the UGV program for Detection of heavily occluded military vehicles, woodland camouflage nets, and, augmented features for Target Recognition. Basic research in Polarization Vision has continued with the development of a material classification method having the capability of detecting metallic materials under polarized illumination of clear skylight, complementary in nature to existing methods. New photometric invariants have been discovered for object recognition under multiple light illumination based upon the relationship between the local covariance matrix of photometric values and Gaussian curvature. For 3-D images in Medical Imaging of complex tubular anatomy (e.g., lung bronchial and vascular trees) accurate automated methods have been developed for extraction of central axis geometry which is of large importance to medical researchers.
Argument Structure Analysis of Event-nouns Using Lexico-syntactic Patterns of Noun Phrases (2010)

形態素解析や構文解析など自然言語処理の要素技術は成熟しつつあり，意味解析・談話解析といった，より高次な言語処理の研究が盛んになってきた．特に文の意味理解のためには「誰が」「何を」「誰に」といった要素（項）を同定することが重要である．動詞や形容詞を対象にした項構造解析のことを述語項構造解析と呼ぶが，文中の事態を表す表現は動詞や形容詞の他にも名詞も存在することが知られている．そこで，我々は日本語の名詞を対象とした項構造解析タスクを取り上げ，機械学習を用いた自動的な解析手法を提案する．日本語の事態性名詞には事態を指すか否か曖昧性のある名詞があるため，まず事態性の有無を判定する事態性判別タスクと項同定タスクの 2 つに分解し，それぞれ大規模なコーパスから抽出した語彙統語パターンを用いた手法と述語・事態性名詞間の項の共有現象に着目した手法を提案する．
Double Haploidentical Hematopoietic Stem Cell Transplantation (HSCT) Enhances Anti-Tumor Activity After Transplant (2012)

Abstract Abstract 1897 We have previously shown that haploidentical (HI) HSCT with low dose donor T-cell infusion provides a survival advantage in tumor bearing mice when compared to parent F1 or MHC-matched transplant models. We suggest that MHC difference in HI-HSCT generates early T-cell clonal activation against the unshared MHC haplotype, which eliminates residual tumor cells that express the unshared MHC haplotype. However, alteration in MHC antigen expression is a significant contributor to tumor escape from graft-versus-tumor (GVT) activity. Recent haploidentical transplant data revealed that uniparental disomy, the loss of the HLA haplotype, is a clinically relevant mechanism of tumor escape that leads to post-transplant leukemia relapse. Murine renal cell carcinoma, RENCA-TGL, cell line normally expresses only H2Kd as a MHC molecule. Therefore, in our haploidentical transplant model, T cell clonal activity is usually restricted against H2Kd molecule only. For circumventing the single haplotype expression of tumor model, we transfected this cell line with a H2Kb expressing vector, pAcGFP-NeoR-H2Kb, and generated stable clones with G418 selection. The clone that has more than 95% H2Kb expression used for in vivo experiments. Both tumor cell lines, i.e. parental and transfected clone, had similar in vivo tumor growth acceptance and growth rate. We then used two different haploidentical donors that were targeting different MHC haplotypes. Lethally irradiated B6D2F1 (H2Kb/d) mice were transplanted with T cell depleted bone marrow (TCD-BM) from either B6C3F1 (H-2Kb/k) (single haplo-1; SH1), or C3D2F1 (H2Kk/d) (single haplo 2; SH2) or both donor mice with low-dose (1×105) T-cells. In some experiments, animals were also injected either H2Kd or H2Kb/d expressing RENCA-TGL cells for the evaluation of GVT activity. Bone marrow (BM), spleens and thymi were harvested from recipients of single and double HI-HSCT at day 35 and showed similar cellularities. Interestingly, spleen and bone marrow had similar chimerism from both donors in DH-HSCT. There were no early transplant mortality, graft failure, weight loss and GVHD scoring difference among the double or single-haploidentical transplant recipients. In two other sets of experiments, we followed the tumor growth and the survival of tumor bearing mice after transplant. The recipients of DH-HSCT showed a better survival and GVT activity than the recipients of SH-HSCT in RENCA-TGL (H2Kb/d) bearing tumor model. These observations confirmed that MHC targeting plays a prominent role in tumor surveillance, and immune targeting the unshared MHC haplotype with haploidentical transplant induce remarkable survival advantage. Double HI-HSCT provides an unique anti-tumor activity that continues to exert GVT effect, even in case of MHC haplotype loss. Disclosures: No relevant conflicts of interest to declare.
Imaging poly(ADP ribose) polymerase-1 activity for personalized cancer medicine using a novel PET tracer (2015)

2 Objectives Poly(ADP ribose) polymerase-1 (PARP-1) is a DNA damage logic gate, selecting repair or cell death depending on the extent of therapy-induced DNA damage. PARP-1 enzymatic activity, not protein expression level, is prognostic of DNA damage response, however no biomarker for its activity currently exists. Objective 1: develop an 18F-labelled substrate-based PARP-1 activity PET tracer (18F-SuPAR). Objective 2: monitor radiation therapy response and determine PARP-1 inhibitor efficacy in mouse models of human cervical and breast cancers. Methods Rational tracer design based on endogenous PARP-1 substrate yielded 18F-SuPAR with high substrate activity. Radiolabelling occurred by ligand-assisted copper-catalyzed click chemistry (RCY = 8.2%). Mice bearing HeLa (cervical) or MDA-MB-231 (breast) tumors received 5 Gy or 10 Gy radiation, and 18F-SuPAR imaging was performed 8 or 24 hr post-treatment. PARP-1 inhibition by BMN673 (1 mg/kg) was also investigated. Ex vivo autoradiography and immunofluorescence of the endogenous product of PARP-1 activity was used to assess radiotracer specificity for PARP-1. Results 18F-SuPAR provided the non-invasive measurement of PARP-1 activity in living subjects, indicating a differential response to radiation therapy between tumor types. PARP-1 activity was significantly inhibited in breast tumors following administration of BMN673, but not in cervical tumors. 18F-SuPAR signal correlated strongly with PARP-1 activity in breast (r=0.93, p Conclusions 18F-SuPAR measures PARP-1 activity in vivo, with target specificity confirmed through PARP-1 inhibition. Breast but not cervical cancer was identified to benefit from PARP-1 inhibition therapy, mimicking clinical data. By imaging PARP activity, this novel tracer may enable selection of patients suited to PARP-1 inhibitor therapy, and the monitoring radiation therapy response early after administration. Research Support Susan G. Komen For The Cure Post-doctoral Fellowship (AJS); Stanford Cancer Institute Translational Research Award; Department of Defense Prostate Cancer Research Program IDEA award.
Antitumor Activity of Interleukin-18 Against the Murine T-Cell Leukemia/Lymphoma EL-4 in Syngeneic Mice (2002)

Interleukin (IL)-18 induces interferon (IFN)-gamma production by T cells and natural killer (NK) cells, and augments NK cell activity in mouse spleen cell cultures. It has recently been demonstrated that in vivo administration of IL-18 to mice results in considerable antitumor effects against syngeneic Meth A sarcoma. In this study, the antitumor effects of IL-18 against murine T-cell leukemia (EL-4) were evaluated. EL-4 proliferation was resistant in vitro to IL-18 and IFN-gamma. When 4 x 10(6) EL-4 cells were transplanted intravenously, the antitumor effects of IL-18 were not pronounced, and only a slight prolongation of the mean survival times was observed. The antitumor effects of IFN-gamma were even less apparent than those of IL-18. However, when mice were transplanted intravenously with 5 x 10(5) EL-4 cells, the extent of experimental visceral dissemination of EL-4 was markedly reduced in mice treated subcutaneously with IL-18, resulting in an increase in survival time with some mice even cured. Although IL-18 was highly effective at inhibiting the development of EL-4 lymphoma dissemination in C57BL/6 mice, it could not inhibit the development of dissemination in mutant C57BL/6 beige (bg/bg) mice lacking NK cell activity. The efficacy of IL-18 was also significantly reduced in nude mice lacking T cells. These results suggest that antitumor efficacy of IL-18 is mediated primarily by NK cells, but that T cells are also required for the complete antitumor efficacy of IL-18.
Secretory production of a beta-mannanase and a chitosanase using a Lactobacillus plantarum expression system (2016)

ManB and CsnA were efficiently produced and secreted in L. plantarum using pSIP-based expression vectors containing either an erythromycin resistance or the alr gene as selection marker.
Friction testing and torque sensing systems (2023)

The present invention relates, in part, to systems for characterizing force (e.g., friction, wear, and/or torque). In one embodiment, the system allows for wear testing of samples in a high throughput manner. In another embodiment, the system allows for torque sensing in a non-contact manner.
Chiral antiferromagnetic Josephson junctions as spin-triplet supercurrent spin valves and d.c. SQUIDs (2023)

Spin-triplet supercurrent spin valves are of practical importance for the realization of superconducting spintronic logic circuits. In ferromagnetic Josephson junctions, the magnetic-field-controlled non-collinearity between the spin-mixer and spin-rotator magnetizations switches the spin-polarized triplet supercurrents on and off. Here we report an antiferromagnetic equivalent of such spin-triplet supercurrent spin valves in chiral antiferromagnetic Josephson junctions as well as a direct-current superconducting quantum interference device. We employ the topological chiral antiferromagnet Mn<sub>3</sub>Ge, in which the Berry curvature of the band structure produces fictitious magnetic fields, and the non-collinear atomic-scale spin arrangement accommodates triplet Cooper pairing over long distances (>150 nm). We theoretically verify the observed supercurrent spin-valve behaviours under a small magnetic field of <2 mT for current-biased junctions and the direct-current superconducting quantum interference device functionality. Our calculations reproduce the observed hysteretic field interference of the Josephson critical current and link these to the magnetic-field-modulated antiferromagnetic texture that alters the Berry curvature. Our work employs band topology to control the pairing amplitude of spin-triplet Cooper pairs in a single chiral antiferromagnet.
Digitally Encoded Drug Tablets to Combat Counterfeiting (2007)

Designer labels: “In-drug labeling”, that is, the labeling of the drug instead of the packaging (see figure), would be a major step forward to combat counterfeiting. The digitally encoded microparticles described in this paper can be successfully incorporated in drug tablets and may become a major tool in combating counterfeiters of pharmaceuticals. The microparticles are also shown not to be toxic.
Tissue Damage due to Mechanical Stresses as applied during Minimally Invasive Surgery (2006)

While there are many benefits to minimally invasive surgery, force feedback, or touch sensation, is lacking in the currently available MIS tools, including surgical robots, creating the potential for excessive force application during surgery. The goal of this work was to develop a methodology with which to identify stress magnitudes and durations that can be safely applied with a grasper to different tissues, helping to improve MIS device design and reduce potential for clinically relevant consequences. Using the porcine model, stresses typically applied in MIS were applied to liver, ureter, and small bowel using a motorized endoscopic grasper. Acute indicators of tissue damage including cellular death, activation of the coagulation cascade, and infiltration of inflammatory cells were measured using histological and image analysis techniques. ANOVA and post-hoc analyses were used to detect stress magnitudes and durations that caused significantly increased tissue damage with the goal to ultimately identify safe stress ‘thresholds’ during grasping of the studied tissues. Preliminary data suggests a graded non-linear response between applied stress magnitude and apoptosis in liver and small bowel as well as granulocyte infiltration in small bowel.
Compact, High-Isolation 110-140-GHz SPST and SPDT Switches Using a 250-nm InP HBT Process (2022)

A low insertion-loss (IL) and high isolation (ISO) single-pole single-throw (SPST) and single-pole double-throw (SPDT) is demonstrated in 250-nm Indium Phosphide (InP) heterojunction bipolar transistor (HBT). The switch employs a 90° hybrid coupler with independent reflective loads to break tradeoffs in IL and ISO ratio. Measurement results of the implemented SPST show IL of 0.77-2.7 dB and ISO of 22.5-40dB in 110–140 GHz. Measured results of the proposed SPDT show 1.42-3.8 dB IL and ISO of 33.8-53 dB in 110–132 GHz.
Safety and efficacy outcomes of atrial fibrillation ablation in patients with rheumatoid arthritis (2022)

Patients with RA are at higher risk of clinical AF recurrence, and are more likely to be taking AADs and require repeat ablation. Preablation CRP and ESR are independent predictors of AF recurrence, and CRP is an independent predictor of repeat catheter ablation.
Sequencing of Partially Methyl-Esterified Oligogalacturonates by Tandem Mass Spectrometry and Its Use To Determine Pectinase Specificities (1999)

Complex mixtures of acidic oligosaccharides were produced by enzymatic digestion of partially methyl-esterified pectin with Aspergillus niger pectin lyase, endopolygalacturonase II, and exopolygalacturonase. To determine the specificities of these pectolytic enzymes toward non-esterified and methyl-esterified galacturonic acid residues, we have studied the methyl esterification patterns of selected oligomers in unseparated pectin digests. Collision-induced dissociation in a nanoelectrospray ionization ion trap mass spectrometer was used to locate methyl-esterified galacturonic acid residues in oligomers up to a degree of polymerization of 10. Analysis of the methyl esterification patterns gave insight into the substrate specificities of these pectolytic enzymes. Isomeric fragment ions containing the reducing and nonreducing ends were differentiated by 18O-labeling of the reducing end.
Episomal editing of synthetic constructs in yeast using CRISPR (2022)

Abstract Use of synthetic genomics to design and build “big” DNA has revolutionized our ability to answer fundamental biological questions by employing a bottom-up approach. S. cerevisiae , or budding yeast, has become the major platform to assemble large synthetic constructs thanks to its powerful homologous recombination machinery and the availability of well-established molecular biology techniques. However, efficiently and precisely introducing designer variations to episomal assemblies remains challenging. Here, we describe CRISPR Engineering of EPisomes in Yeast, or CREEPY, for rapid engineering of mammalian DNA constructs larger than 100 kb. We demonstrate that editing of circular episomes presents unique challenges compared to modifying native yeast chromosomes with CRISPR. After optimizing CREEPY for episomal editing, we achieve efficient simplex and multiplex editing as demonstrated by engineering a mouse Sox2 -harboring episome.
Synthesis, Structure and Reactivity of .eta.3-Allenyl/Propargyl Dinuclear Palladium Complexes (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis, Structure and Reactivity of .eta.3-Allenyl/Propargyl Dinuclear Palladium ComplexesSensuke Ogoshi, Ken Tsutsumi, Motohiro Ooi, and Hideo KurosawaCite this: J. Am. Chem. Soc. 1995, 117, 41, 10415–10416Publication Date (Print):October 1, 1995Publication History Published online1 May 2002Published inissue 1 October 1995https://pubs.acs.org/doi/10.1021/ja00146a040https://doi.org/10.1021/ja00146a040research-articleACS PublicationsRequest reuse permissionsArticle Views337Altmetric-Citations56LEARN 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 (4)»Supporting Information Supporting Information Get e-Alerts
Ventricular Ectopy and QTc‐Interval Prolongation Associated with Dronedarone Therapy (2013)

Amiodarone is an effective treatment for atrial and ventricular arrhythmias, but its use is limited by a toxic adverse-effect profile. Although dronedarone has been touted as an antiarrhythmic agent devoid of both solid organ toxicity and proarrhythmic properties, its potential for prolonging ventricular repolarization may augment triggered ectopy. We describe a 66-year-old man who began dronedarone 400 mg twice/day for new-onset paroxysmal atrial fibrillation; he had no left ventricular dysfunction or clinical heart failure. Three months after starting the drug, he complained of malaise, fatigue, and rare palpitations. Twenty four-hour Holter monitoring revealed increased premature ventricular complexes, and the rate-corrected QT (QTc) interval was prolonged (range 525-760 msec). Dronedarone was discontinued and the patient's symptoms gradually resolved over the next 3 weeks. Holter monitoring revealed a marked reduction in ventricular ectopy burden, and the QTc interval decreased to his baseline values. Even in the absence of documented symptomatic torsade de pointes, this case suggests that caution should be exercised when prescribing dronedarone and that serial QTc interval monitoring may be appropriate. In addition, clinicians should have a low threshold to perform Holter monitoring if symptoms develop during dronedarone therapy.