gebhart/patrepeval huggingface dataset:
Functional analysis of the promoter of the 3-phosphoglycerate kinase gene of Aspergillus nidulans. (1990)

Sequence elements contributing to high level expression of the 3-phosphoglycerate kinase (pgk) gene of Aspergillus nidulans have been investigated by the construction of gene fusion vectors using lacZ (?-galactosidase) of Escherichia coli as an assay system, and including the catabolic dehydroquinase (qutE) gene as a selective marker for the transformation of A.nidulans. The importance of targeting these constructs to a specific gene locus has been demonstrated by the analysis of a large number of transformed strains which reveals that the expression of the lacZ reporter gene is dependent upon the site of integration of the vector into the genome, and that when targeted to the qutE locus, is directly proportional to its copy number. The analysis of transformed strains in which single copies of lacZ fusions have been targeted to the qutE locus has identified three constitutive positively acting sequence elements in the pgk gene. Firstly, sequence located between -161 and -120bp (possibly spanning -120) relative to the transcript start site is essential for expression, thus demonstrating that the putative core promoter, including potential TATA and CCAAT boxes, and a pyrimidine rich region, is not alone sufficient to enable expression. A comparison of this sequence to known promoter elements has revealed the presence of an octamer AAGCAAAT (-131 to -124), with a seven out of eight base pair match to the consensus octamer sequence ATGCAAAT characterized as being essential for the expression of several higher eukaryotic genes. Whilst the octamer containing sequence contributes almost a residual 40% of the maximum expression recorded, a second region encompassing codons 14 to 183 and including the two introns of pgk has been shown to account for over 30% of the total activity. However, the full effect of the internal sequence may be greater, since the large 3-galactosidase fusion proteins studied here have been shown to be unstable. Thirdly, an extensive region extending from 0.5 to over 3Kb upstream of the start site has been shown to be required for full expression, accounting for almost 30% of the total recorded activity. Furthermore, sequence located between -638 and -488bp, and including an eight bp consensus element TGAGGTGT common to the four cloned A.nidulans glycolytic genes, has been shown to modulate expression: increasing activity about 1.5-fold on gluconeogenic compared to glycolytic carbon sources. In a separate exercise, the native pgk gene has been replaced with disrupted sequence to generate a pgk mutant strain of A.nidulans. This replacement has been achieved in a diploid strain, from which both pgk+ and pgk-segregants have been isolated, and the analysis of these has allowed the pgk locus to be assigned to chromosome VIII. The pgk- mutant strain that has been isolated is deficient in 3-phosphoglycerate kinase activity, requires both acetate and glycerol for growth, conidiates poorly, and is poisoned by even moderate concentrations of hexoses.
Real-Time Control of Self-collision Avoidance for Mobile Manipulator using RoBE : Self-collision avoidance motion using redundancy (2003)

RoBEという弾性要素を用いる手法でロボット形状を表現し, その反力を用いたモバイルマニピュレータにおける実時間自己衝突制御を提案, 双腕型移動ロボット"MR Helper"に実装して, その有効性を検証する。
Mechanism of free radical formation in metal carbonyl + halide systems. Solvent effects; Part 2 (1966)

The polymerization of methyl methacrylate initiated by molybdenum carbonyl and carbon tetrachloride has been studied in dioxan, acetic anhydride, and benzonitrile solutions. Kinetic evidence suggests that monomer is involved in initiation, and that dioxan and acetic anhydride can also participate in the initiation process by a similar mechanism. A modified reaction scheme has been proposed to explain the unusual features of the benzonitrile system, in which two slow steps appear to be involved. Kinetic parameters have been evaluated, and experimental observations are in excellent agreement with theoretically determined rates. The implications of the values of the kinetic parameters have been discussed.
Long‐Term Clinical Outcome of Right Bundle Branch Radiofrequency Catheter Ablation for Treatment of Bundle Branch Reentrant Ventricular Tachycardia (1995)

The study assessed the long-term outcome of patients undergoing radiofrequency ablation of the right bundle for bundle branch reentrant ventricular tachycardia. Bundle branch reentrant tachycardia was diagnosed in 16 patients (ejection fraction 31% +/- 15%) who underwent electrophysiology study in our laboratory. All patients had His-Purkinje system conduction delay with mean HV interval of 68 +/- 8 ms. After ablation, right bundle branch block developed in 15 patients. One patient developed complete heart block, which was anticipated. One patient died of heart failure 9 months after ablation. Two patients were successfully bridged to heart transplantation 0.5 and 13 months, respectively, after ablation. Two patients received implantable defibrillators for other ventricular tachycardias. One patient had syncope 11 months after ablation, but there was no evidence of ventricular tachycardia or heart block in repeat electrophysiology study. This patient died suddenly 29 months after ablation. The remaining nine patients were alive and well for a mean follow-up of 19 +/- 10 months. Radiofrequency ablation of the right bundle branch is an effective therapy for treatment of bundle branch reentrant ventricular tachycardia. Survival is excellent provided that other types of ventricular tachycardia, when present, are treated as well. This technique may be helpful in management of patients who have unacceptable frequent shocks from their implanted defibrillators and may be helpful in avoiding implantation of such a device completely in others. In some patients with terminal heart failure and incessant ventricular tachycardia, this procedure can function as a bridge to cardiac transplantation.
Titania Nanotube Arrays as Interfaces for Blood-Contacting Implantable Devices: A Study Evaluating the Nanotopography-Associated Activation and Expression of Blood Plasma Components (2012)

The constant exposure of implantable biomaterials such as titanium and titanium alloys to blood-introducesserious and ongoing concerns regarding poor blood-material interactions. To date, all blood-contacting materials have been shown to initiate immunological events in the form of inflammation, thrombosis, fibrosis and infection; potentially leading to complete implant failure. Material surfaces that provide biomimetic cues such as nanoscale architectures have been shown to elicit improved cellular interaction; and thus, may provide possible solutions for enhancing blood-compatibility. However, limited information exists about the thrombogenicityof nanoscalesurface architectures. In this study, we have evaluated the efficacy of titania nanotube arrays as interfaces for blood contacting devices by investigating the thrombogenic effects using whole blood plasma. Thus, platelet/leukocyte adhesion, activation and interaction, morphology, complement activation, contact activation, platelet release reaction, fibrinogen expression and material cytotoxicity were evaluated to determine the in vitro thrombogenicity. The results presented here indicate a decrease in thrombogenic effects of titania nanotube arrays as compared to biomedical grade titanium after 2 hours of contact with whole blood plasma. This work shows the improved blood-compatibility of titania nanotube arrays, identifying this specific nanoarchitecture as a potentially optimal interface for promoting the long-term success of blood contacting biomaterials.
Scalable, Ad Hoc Deployable, RF-Based Localization (2002)

Spatial localization or the ability to locate nodes is an important building block for next generation pervasive computing systems, but a formidable challenge, particularly, for very small hardware and energy constrained devices, for noisy, unpredictable environments and for very large ad hoc deployed and networked systems. In this paper, we describe, validate and evaluate in real environments a very simple self localization methodology for RF-based devices based only on RF-connectivity constraints to a set of beacons (known nodes), applicable outdoors. Beacon placement has a significant impact on the localization quality in these systems. To self-configure and adapt the localization in noisy environments with unpredictable radio propagation vagaries, we introduce the novel concept of adaptive beacon placement. We propose several novel and density adaptive algorithms for beacon placement and demonstrate their effectiveness through evaluations. We also outline an approach in which beacons leverage a software controllable variable transmit power capability to further improve localization granularity. These combined features allow a localization system that is scalable and ad hoc deployable, long-lived and robust to noisy environments. The unique aspect of our localization approach is our emphasis on adaptive self-configuration.
CCDC 896059: Experimental Crystal Structure Determination (2012)

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
Sympathetic activation of brown-adipose-tissue thermogenesis in cachexia (1981)

Tumour-bearing mice spontaneously lose weight 8-9 weeks after implantation of a human hypernephroma, in spite of a normal food intake. Resting oxygen consumption was up to 40% higher in these animals than in sham-operated controls, but was significantly reduced by beta-adrenergic blockade with propranolol in the former group. The injection of noradrenaline caused a marked stimulation of the metabolic rate in all the animals, but the greatest response was seen in the cachectic mice. The brown-adipose-tissue mass was similar for both groups, but guanosine diphosphate binding to brown-adipose-tissue mitochondria (an index of thermogenic capacity) was significantly increased in tumor-bearing mice, and the injection of noradrenaline 1 h prior to sacrifice caused the greatest stimulation of binding in the cachectic group. These data suggest that the rapid weight loss of tumor-bearing animals may be due to a high metabolic rate which results from sympathetic stimulation of brown-adipose-tissue metabolism. The relevance of these results to cancer-induced cachexia in man is discussed.
Effect of Zwitterionic Polymers on Wound Healing (2008)

The effect of a thin film of a zwitterionic random copolymer composed of carboxybetaine [1-carboxy-N,N-dimethyl-N-(2'-methacryloyloxyethyl)methanaminium inner salt] (CMB) and n-butyl methacrylate (BMA), poly(CMB-r-BMA) (CMB, 30 mol%), on the healing of a full-thickness excisional and incisional wound in hairless rats was examined. The poly(CMB-r-BMA) film significantly enhanced wound closure and complete healing of a full-thickness excisional wound compared with the effect of the poly(n-butyl methacrylate) (PBMA) and the poly(ethylene terephthalate) (PET) films. However, the poly(CMB-r-BMA) film did not enhance healing of a full-thickness incisional wound in hairless rats. The amount of proteins adsorbed and that of neutrophiles adhered onto the poly(CMB-r-BMA) film were significantly smaller than those onto the PBMA and PET films. The results suggested that various cells and growth factors in the wound exudate are utilized effectively by covering an excisional wound with the poly(CMB-r-BMA) film, resulting in acceleration of healing. In addition, the poly(CMB-r-BMA) film significantly enhanced healing of a full-thickness excisional wound in hairless rats compared with the effect of Tegaderm as wound dressings. The poly(CMB-r-BMA) film has potential as a new wound dressing.
Activation of the alternative pathway of complement by mycobacteria and cord factor (1980)

The ability of a number of mycobacteria and some of their components to activate complement was examined. Mycobacterium bovis BCG (Glaxo strain), Mycobacterium leprae, Mycobacterium lepraemurium, and cord factor activated the alternative pathway of complement in normal human serum and normal and C4-deficient guinea pig sera and generated biologically active products. BCG (Pasteur strain) and muramyl dipeptide did not activate complement. The relevance of activation of complement by mycobacteria to their induction of granulomas is discussed.
Lymphocyte transformation test in leprosy: decreased lymphocyte reactivity to Mycobacterium leprae in lepromatous leprosy, with no evidence for a generalized impairment (1978)

Untreated leprosy patients were examined with respect to lymphocyte transformation in vitro after stimulation with mycobacterial and other microbial antigens, allogeneic lymphocytes, or nonspecific mitogens. Methods were used to circumvent technical variability. The results were compared with those obtained in controls matched for age, sex, race, and environment. No evidence was found for a generalized impairment of lymphocyte transformation in vitro, whereas a specific defect towards Mycobacterium leprae was demonstrable in lepromatous leprosy patients. The response to M. leprae, investigated in untreated and treated leprosy patients, decreased along the leprosy spectrum. Moreover, the results of the one-way mixed lymphocyte cultures showed that lymphocytes from leprosy patients had a normal stimulator and responder capacity, when they were tested against a panel of allogeneic lymphocytes. The influence of serum factors was investigated in untreated leprosy patients in the mixed lymphocyte culture. On average, tuberculoid as well as lepromatous sera showed a low-level depressive effect, but some sera showed a stimulatory effect. Therefore, a depressive effect of serum factors cannot be considered to be a general feature of leprosy. The correlation between the Mitsuda type of lepromin skin test and the lymphocyte reactivity in vitro to M. leprae was studied, and a positive correlation was found.
Low-Energy Atomic Collisions. I. The Schrödinger Equation for H+–H (1966)

The Schrödinger equation for the system H+–H is considered. After the usual separation of the center-of-mass coordinates, group theoretic methods are used to eliminate three degrees of freedom associated with the rotational motion of the system. This is done in a manner which treats the protons symmetrically, thereby enabling one to easily establish the symmetry character of the wavefunctions. The result is in a form which is convenient in the study of scattering.
<i>Cob</i> gene pyrosequencing enables characterization of benthic dinoflagellate diversity and biogeography (2013)

Dinoflagellates in marine benthic habitats living epiphytically on macroalgae are an important but highly understudied group of protists. Many produce toxins that can have severe economic impacts on marine-based economies, and improved monitoring tools are required to enhance the management of toxin-related hazards. We analysed the distribution and diversity of epibenthic dinoflagellates inhabiting eight sites in Cocos (Keeling) Islands, Papua New Guinea, and Broome and Exmouth, Western Australia. We used pyrosequencing approaches based on two DNA barcoding marker genes - 18S ribosomal RNA (rRNA) and mitochondrial cytochrome b (cob) - and compared these to an approach based on clone libraries (197 sequences) using the cob gene. Dinoflagellate sequences accounted for 133 [64 unique operational taxonomic units (OTU)] out of 10 529 18S rRNA gene sequences obtained from all samples. However, using the dinoflagellate specific assay targeting the cob gene marker, we obtained 9748 (1217 unique OTU) dinoflagellate sequences from the same environmental samples, providing the largest, to date, set of dinoflagellate cob gene sequences and reliable estimates of total dinoflagellate richness within the samples and biogeographic comparisons between samples. This study also reports the presence of potentially toxic species of the genera Gambierdiscus, Ostreopsis, Coolia, Prorocentrum and Amphidinium from the above-mentioned geographical regions.
The role of ERK2 in germinal center B cell selection (2019)

Abstract The regulation of B cell activation and survival is a crucial control point for the maintenance of B cell tolerance in the germinal center (GC) and involves the coordination of several intracellular signaling pathways. Dysregulation of these pathways can lead to the production and survival of autoreactive memory B cells and plasma cells (PCs), resulting in autoimmune disease. The mitogen-activated protein kinase (MAPK) pathway is involved in the transduction of stimulating and apoptotic signals such as those received through the B cell receptor (BCR) and the Fas receptor (CD95), respectively. Extracellular signal regulated kinases 1 and 2 (ERK1/2), important effectors of this pathway, play a major role in B cell activation and survival. Though ERK2 specifically regulates the pro-apoptotic protein, Bmf, its role in regulating GC B cell selection is unknown. Our lab has developed a novel mouse model in which the deletion of Erk2 is accompanied by the expression of the fluorescent reporter protein, eYFP, allowing us to identify and isolate viable Erk2Δ B cells using flow cytometry. Preliminary data using this model has shown that peripheral Erk2Δ B cells express several surface markers associated with follicular T helper cell interactions and immunoglobulin class switching, such as DEC205 and CD80, respectively. Thus we hypothesize that ERK2 is a critical regulator of GC B cell selection. We are currently investigating the ability of Erk2Δ B cells to respond to various activating stimuli in vitro as well as to differentiate into antigen-specific PCs. Our results will contribute to a better understanding of the molecular programs involved in B cell selection, potentially offering new approaches to treating B cell-driven autoimmune diseases.
Dynamic Wavelet Neural Network Model for Traffic Flow Forecasting (2005)

Accurate and timely forecasting of traffic flow is of paramount importance for effective management of traffic congestion in intelligent transportation systems. In this paper, a novel nonparametric dynamic time-delay recurrent wavelet neural network model is presented for forecasting traffic flow. The model incorporates the self-similar, singular, and fractal properties discovered in the traffic flow. The concept of wavelet frame is introduced and exploited in the model to provide flexibility in the design of wavelets and to add extra features such as adaptable translation parameters desirable in traffic flow forecasting. The statistical autocorrelation function is used for selection of the optimum input dimension of traffic flow time series. The model incorporates both the time of the day and the day of the week of the prediction time. As such, it can be used for long-term traffic flow forecasting in addition to short-term forecasting. The model has been validated using actual freeway traffic flow data. The model can assist traffic engineers and highway agencies to create effective traffic management plans for alleviating freeway congestions.
The Platelet-Derived Growth Factor Receptor beta Fuses to Two Distinct Loci at 3p21 in Imatinib Responsive Chronic Eosinophilic Leukemia. (2005)

Abstract We have identified three patients (2 adults, one infant) who presented with BCR-ABL negative eosinophilic myeloproliferative disorders. Cytogenetic analysis revealed a t(1;3;5)(p36;p21;q33) for case 1 and a t(3;5)(p21–25;q31–35) for cases 2 and 3. Two-color fluorescence in situ hybridization (FISH) using differentially labelled probes flanking PDGFRB indicated that this gene was disrupted in all three cases. 5′ rapid amplification of cDNA ends (5′RACE) for case 1 identified an in-frame mRNA fusion of exon 9 of the WDR48 gene at 3p21 to exon 12 of PDGFRB. The chimeric mRNA is predicted to encode a 872 amino acid fusion protein that retains the amino terminal WD repeat region of WDR48 fused to the transmembrane and intracellular tyrosine kinase domains of PDGFRbeta. Cases 2 and 3 were negative for the WDR48-PDGFRB fusion mRNA by RT-PCR using several combinations of primers. 5′RACE PCR from case 2 RNA identified a fusion involving a second 3p21 gene: GOLGA4 exon 11 was fused in-frame to exon 11 of PDGFRB. Exactly the same fusion was found in case 3. The predicted 991 amino acid protein included the amino terminal coiled-coil domain of GOLGA4 fused to the transmembrane and intracellular tyrosine kinase domains of PDGFRbeta. Interestingly, both WDR48 and GOLGA4 are involved in endocytic shuttling pathways. The presence of all fusions was confirmed by RT-PCR and identification of the genomic breakpoints. Imatinib, a known inhibitor of PDGFRbeta, selectively blocked the growth of patient CFU-GM for case 2. Following the identification of PDGFRB rearrangements, all three patients were treated with imatinib. Case 1 was in transformation, but responded rapidly to minimal doses of imatinib (800mg daily for 4 days) with complete cytogenetic remission but remained pancytopenic. Blast crisis recurred 8 months later, responded similarly to 3 days of imatinib, but the patient died 2 months later of invasive fungal infection. Case 2 responded clinically and remains in sustained cytogenetic and molecular remission (nested RT-PCR negative for GOLGA4-PDGFRB). Case 3 (a 13 month old boy) had a complete hematologic response to 50mg/day imatinib but the t(3;5) was still seen in 40% of metaphases at 3 months. We conclude that PDGFRB fuses to diverse partner genes to give rise to atypical MPDs. Although very rare, identification of these fusions is critical for proper management of affected individuals.
Studies in Stereochemistry. V. The Effect of F-Strain on the Relative Base Strengths of Ammonia and Trimethylamine<sup>1</sup> (1945)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStudies in Stereochemistry. V. The Effect of F-Strain on the Relative Base Strengths of Ammonia and Trimethylamine1Herbert C. BrownCite this: J. Am. Chem. Soc. 1945, 67, 3, 374–378Publication Date (Print):March 1, 1945Publication History Published online1 May 2002Published inissue 1 March 1945https://doi.org/10.1021/ja01219a007RIGHTS & PERMISSIONSArticle Views282Altmetric-Citations51LEARN 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 InReddit PDF (600 KB) Get e-Alerts Get e-Alerts