gebhart/patrepeval huggingface dataset:
Animal models of cardiorenal syndrome: a review (2011)

The incidence of heart failure and renal failure is increasing and is associated with poor prognosis. Moreover, these conditions do often coexist and this coexistence results in worsened outcome. Various mechanisms have been proposed as an explanation of this interrelation, including changes in hemodynamics, endothelial dysfunction, inflammation, activation of renin-angiotensin-aldosterone system, and/or sympathetic nervous system. However, the exact mechanisms initializing and maintaining this interaction are still unknown. In many experimental studies on cardiac or renal dysfunction, the function of the other organ was either not addressed or the authors failed to show any decline in its function despite histological changes. There are few studies in which the dysfunction of both heart and kidney function has been described. In this review, we discuss animal models of combined cardiorenal dysfunction. We show that translation of the results from animal studies is limited, and there is a need for new and better models of the cardiorenal interaction to improve our understanding of this syndrome. Finally, we propose several requirements that a new animal model should meet to serve as a tool for studies on the cardiorenal syndrome.
The landscape of viral expression and host gene fusion and adaptation in human cancer (2013)

Viruses cause 10-15% of all human cancers. Massively parallel sequencing has recently proved effective for uncovering novel viruses and virus-tumour associations, but this approach has not yet been applied to comprehensive patient cohorts. Here we screen a diverse landscape of human cancer, encompassing 4,433 tumours and 19 cancer types, for known and novel expressed viruses based on >700 billion transcriptome sequencing reads from The Cancer Genome Atlas Research Network. The resulting map confirms and extends current knowledge. We observe recurrent fusion events, including human papillomavirus insertions in RAD51B and ERBB2. Patterns of coadaptation between host and viral gene expression give clues to papillomavirus oncogene function. Importantly, our analysis argues strongly against viral aetiology in several cancers where this has frequently been proposed. We provide a virus-tumour map of unprecedented scale that constitutes a reference for future studies of tumour-associated viruses using transcriptome sequencing data.
A log gamma model and its maximum likelihood estimation (1974)

Journal Article A log gamma model and its maximum likelihood estimation Get access R. L. PRENTICE R. L. PRENTICE Department of Statistics, University of WaterlooOntario Search for other works by this author on: Oxford Academic Google Scholar Biometrika, Volume 61, Issue 3, December 1974, Pages 539–544, https://doi.org/10.1093/biomet/61.3.539 Published: 01 December 1974
Die Pd-katalysierte oxidative Kupplungsreaktion von Methylbenzoesäuremethylester / The Pd-Catalyzed Oxidative Coupling Reaction of Methyl Methylbenzoates (1994)

The Pd-catalyzed oxidative coupling reaction of methyl o-toluate gives, in the presence of a Pd/1,10-phenanthroline(phen)/Cu catalyst, exclusively, the para-linked biphenyldicarboxylates 1, 2, and 3. On the other hand, the meta-linked biphenyldicarboxylates 4 and 5, were predominantly formed in a catalyst system of Pd/2,4-pentanedione(acacH)/Cu, and under similar conditions 6 and 7 were also obtained from the coupling reaction of methyl m-toluate and methyl p-toluate, respectively. A reaction scheme has been proposed.
Hypermethylation-associated inactivation indicates a tumor suppressor role for p15INK4B. (1996)

The recently identified cyclin-dependent kinase inhibitor p15INK4B is localized to a region on chromosome 9p21 frequently deleted in human tumors. Previous evidence has pointed to a related gene, p16INK4A, as the principal target of this deletion. We report that in gliomas and, to a striking degree, in leukemias, the p15 gene is commonly inactivated in association with promoter region hypermethylation involving multiple sites in a 5'-CpG island. In some gliomas and all of the primary leukemias, this event occurs without alteration of the adjacent gene, p16INK4A. In other tumors, including lung, head and neck, breast, prostate, and colon cancer, inactivation of p15INK4B occurs only rarely and only with concomitant inactivation of p16. Aberrant methylation of p15INK4B is associated with transcriptional loss of this gene. Treatment with the demethylating agent 5-aza-2'-deoxycytidine leads to re-expression of p15 mRNA. In selected leukemia cell lines, p15 inactivation correlates with known resistance to the growth-suppressive effects of transforming growth factor-beta. These results suggest that p15INK4B is inactivated selectively in leukemias and gliomas and seems to constitute an important tumor suppressor gene loss in these neoplasms.
Turning carbon dioxide into fuel (2010)

Our present dependence on fossil fuels means that, as our demand for energy inevitably increases, so do emissions of greenhouse gases, most notably carbon dioxide (CO2). To avoid the obvious consequences on climate change, the concentration of such greenhouse gases in the atmosphere must be stabilized. But, as populations grow and economies develop, future demands now ensure that energy will be one of the defining issues of this century. This unique set of (coupled) challenges also means that science and engineering have a unique opportunity-and a burgeoning challenge-to apply their understanding to provide sustainable energy solutions. Integrated carbon capture and subsequent sequestration is generally advanced as the most promising option to tackle greenhouse gases in the short to medium term. Here, we provide a brief overview of an alternative mid- to long-term option, namely, the capture and conversion of CO2, to produce sustainable, synthetic hydrocarbon or carbonaceous fuels, most notably for transportation purposes. Basically, the approach centres on the concept of the large-scale re-use of CO2 released by human activity to produce synthetic fuels, and how this challenging approach could assume an important role in tackling the issue of global CO2 emissions. We highlight three possible strategies involving CO2 conversion by physico-chemical approaches: sustainable (or renewable) synthetic methanol, syngas production derived from flue gases from coal-, gas- or oil-fired electric power stations, and photochemical production of synthetic fuels. The use of CO2 to synthesize commodity chemicals is covered elsewhere (Arakawa et al. 2001 Chem. Rev. 101, 953-996); this review is focused on the possibilities for the conversion of CO2 to fuels. Although these three prototypical areas differ in their ultimate applications, the underpinning thermodynamic considerations centre on the conversion-and hence the utilization-of CO2. Here, we hope to illustrate that advances in the science and engineering of materials are critical for these new energy technologies, and specific examples are given for all three examples. With sufficient advances, and institutional and political support, such scientific and technological innovations could help to regulate/stabilize the CO2 levels in the atmosphere and thereby extend the use of fossil-fuel-derived feedstocks.
Efficient 3D object recognition using foveated point clouds (2013)

Recent hardware technologies have enabled acquisition of 3D point clouds from real world scenes in real time. A variety of interactive applications with the 3D world can be developed on top of this new technological scenario. However, a main problem that still remains is that most processing techniques for such 3D point clouds are computationally intensive, requiring optimized approaches to handle such images, especially when real time performance is required. As a possible solution, we propose the use of a 3D moving fovea based on a multiresolution technique that processes parts of the acquired scene using multiple levels of resolution. Such approach can be used to identify objects in point clouds with efficient timing. Experiments show that the use of the moving fovea shows a seven fold performance gain in processing time while keeping 91.6% of true recognition rate in comparison with state-of-the-art 3D object recognition methods.
Branched and linear poly(ethylene imine)-based conjugates: synthetic modification, characterization, and application (2012)

Poly(ethylene imine)s (PEIs) are widely used in different applications, but most extensively investigated as non-viral vector systems. The high ability of cationic PEIs to complex and condense negatively charged DNA and RNA combined with their inherent proton sponge behavior accounts for the excellent efficiency in gene delivery. Further chemical modifications of the polymer expand the application potential, primarily aiming at increased transfection efficiency, cell selectivity and reduced cytotoxicity. Improvements in the synthesis of tailor-made PEIs in combination with new in-depth analytical techniques offer the possibility to produce highly purified polymers with defined structures. The contemporary strategies towards linear and branched poly(ethylene imine)s with modified surface characteristics, PEI-based copolymers as well as conjugates with bioactive molecules will be discussed. In this regard, the versatile branched PEIs have been successfully modified in a statistical manner, whereas the linear counterparts open avenues to design and synthesize well-defined architectures, in order to exploit their high potential in gene delivery.
The cell cycle inhibitor p27Kip1controls self-renewal and pluripotency of human embryonic stem cells by regulating the cell cycle,BrachyuryandTwist (2011)

The continued turn over of human embryonic stem cells (hESC) while maintaining an undifferentiated state is dependent on the regulation of the cell cycle. Here we asked the question if a single cell cycle gene could regulate the self-renewal or pluripotency properties of hESC. We identified that the protein expression of the p27(Kip)¹ cell cycle inhibitor is low in hESC cells and increased with differentiation. By adopting a gain and loss of function strategy we forced or reduced its expression in undifferentiating conditions to define its functional role in self-renewal and pluripotency. Using undifferentiation conditions, overexpression of p27(Kip)¹ in hESC lead to a G₁phase arrest with an enlarged and flattened hESC morphology and consequent loss of self-renewal ability. Loss of p27(Kip)¹ caused an elongated/scatter cell-like phenotype involving up-regulation of Brachyury and Twist gene expression. We demonstrate the novel finding that p27(Kip)¹ protein occupies the Twist1 gene promoter and manipulation of p27(Kip)¹ by gain and loss of function is associated with Twist gene expression changes. These results define p27(Kip)¹ expression levels as critical for self-renewal and pluripotency in hESC and suggest a role for p27(Kip)¹ in controlling an epithelial to mesenchymal transition (EMT) in hESC.
Ordered Mesoporous Polymers of Tunable Pore Size from Colloidal Silica Templates (1999)

Ordered mesoporous polymers have been prepared by replication of colloidal crystals made from silica spheres 35 nanometers in diameter. The pores in the colloidal crystals were filled with divinylbenzene (DVB), ethyleneglycol dimethacrylate (EDMA), or a mixture of the two. Polymerization and subsequent dissolution of the silica template leaves a polycrystalline network of interconnected pores. When mixtures of DVB and EDMA are used, the pore size of the polymer replicas can be varied continuously between 35 and 15 nanometers because the polymer shrinks when the silica template is removed.
Quantum Theory of Cavity-Assisted Sideband Cooling of Mechanical Motion (2007)

We present a quantum-mechanical theory of the cooling of a cantilever coupled via radiation pressure to an illuminated optical cavity. Applying the quantum noise approach to the fluctuations of the radiation pressure force, we derive the optomechanical cooling rate and the minimum achievable phonon number. We find that reaching the quantum limit of arbitrarily small phonon numbers requires going into the good-cavity (resolved phonon sideband) regime where the cavity linewidth is much smaller than the mechanical frequency and the corresponding cavity detuning. This is in contrast to the common assumption that the mechanical frequency and the cavity detuning should be comparable to the cavity damping.
The Role of the Plasma from Platelet Concentrates in Transfusion Reactions (1994)

Bioreactive substances in the plasma supernatant of the platelet product cause most febrile reactions associated with platelet transfusions. Removing the plasma supernatant before transfusion can minimize or prevent these reactions.
Multimodal error correction for speech user interfaces (2001)

Although commercial dictation systems and speech-enabled telephone voice user interfaces have become readily available, speech recognition errors remain a serious problem in the design and implementation of speech user interfaces. Previous work hypothesized that switching modality could speed up interactive correction of recognition errors. This article presents multimodal error correction methods that allow the user to correct recognition errors efficiently without keyboard input. Correction accuracy is maximized by novel recognition algorithms that use context information for recognizing correction input. Multimodal error correction is evaluated in the context of a prototype multimodal dictation system. The study shows that unimodal repair is less accurate than multimodal error correction. On a dictation task, multimodal correction is faster than unimodal correction by respeaking. The study also provides empirical evidence that system-initiated error correction (based on confidence measures) may not expedite error correction. Furthermore, the study suggests that recognition accuracy determines user choice between modalities: while users initially prefer speech, they learn to avoid ineffective correction modalities with experience. To extrapolate results from this user study, the article introduces a performance model of (recognition-based) multimodal interaction that predicts input speed including time needed for error correction. Applied to interactive error correction, the model predicts the impact of improvements in recognition technology on correction speeds, and the influence of recognition accuracy and correction method on the productivity of dictation systems. This model is a first step toward formalizing multimodal interaction.
Specific targets for antiviral drugs (1982)

Research Article| July 01 1982 Specific targets for antiviral drugs E De Clercq E De Clercq Search for other works by this author on: This Site PubMed Google Scholar Biochem J (1982) 205 (1): 1–13. https://doi.org/10.1042/bj2050001 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter LinkedIn Cite Icon Cite Get Permissions Citation E De Clercq; Specific targets for antiviral drugs. Biochem J 1 July 1982; 205 (1): 1–13. doi: https://doi.org/10.1042/bj2050001 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Journal Search Advanced Search This content is only available as a PDF. © 1982 London: The Biochemical Society1982 Article PDF first page preview Close Modal You do not currently have access to this content.
Degradation of Fluorotelomer Alcohols:  A Likely Atmospheric Source of Perfluorinated Carboxylic Acids (2004)

Human and animal tissues collected in urban and remote global locations contain persistent and bioaccumulative perfluorinated carboxylic acids (PFCAs). The source of PFCAs was previously unknown. Here we present smog chamber studies that indicate fluorotelomer alcohols (FTOHs) can degrade in the atmosphere to yield a homologous series of PFCAs. Atmospheric degradation of FTOHs is likely to contribute to the widespread dissemination of PFCAs. After their bioaccumulation potential is accounted for, the pattern of PFCAs yielded from FTOHs could account for the distinct contamination profile of PFCAs observed in arctic animals. Furthermore, polar bear liver was shown to contain predominately linear isomers (>99%) of perfluorononanoic acid (PFNA), while both branched and linear isomers were observed for perfluorooctanoic acid, strongly suggesting a sole input of PFNA from "telomer"-based products. The significance of the gas-phase peroxy radical cross reactions that produce PFCAs has not been recognized previously. Such reactions are expected to occur during the atmospheric degradation of all polyfluorinated materials, necessitating a reexamination of the environmental fate and impact of this important class of industrial chemicals.
Exploring the effects of group size and table size on interactions with tabletop shared-display groupware (2004)

Interactive tabletops have been previously proposed and studied in the domain of co-located group applications. However, little fundamental research has been done to explore the issue of size. In this paper we identify a number of size considerations for tabletop design, and present an experiment to explore some of these issues, in particular the effects of group size and table size on the speed at which the task was performed, the distribution of work among group members, issues of shared resources, and user preference for table size. Our findings shed light on (1) how work strategies are affected by group size, (2) how social interaction varies with respect to table size, and (3) how the speed of task performance is influenced by group size but not by table size. In addition, our experiments revealed that for larger groups, designers might need to add additional vertical displays for shared information. This finding opens the door for extending single-display groupware to shared-display groupware settings that involve multiple, shared displays.
Two‐dimensional electrophoresis of Malassezia allergens for atopic dermatitis and isolation of Mal f 4 homologs with mitochondrial malate dehydrogenase (1999)

The yeast Malassezia furfur is a natural inhabitant of the human skin microflora that induces an allergic reaction in atopic dermatitis. To identify allergens of M. furfur, we separated a crude preparation of M. furfur antigens as discrete spots by 2-D PAGE and detected IgE-binding proteins using sera of atopic dermatitis patients. We identified the known allergens, Mal f 2 and Mal f 3, and determined N-terminal amino acid sequences of six new IgE-binding proteins including Mal f 4. The cDNA and genomic DNA encoding Mal f 4 were cloned and sequenced. The gene was mitochondrial malate dehydrogenase and encoded Mal f 4 composed of 315 amino acids and a signal sequence of 27 amino acids. We purified Mal f 4, which had a molecular mass of 35 kDa from a membrane fraction of a lysate of cultured cells. Thirty of 36 M. furfur-allergic atopic dermatitis patients (83.3%) had elevated serum levels of IgE to purified Mal f 4, indicating that Mal f 4 is a major allergen. There was a significant correlation of the Phadebas RAST unit values of Mal f 4 and the crude antigen, but not between Mal f 4 and the known allergen Mal f 2.
In vivo measurements document the dynamic cellular kinetics of chronic lymphocytic leukemia B cells (2005)

Due to its relatively slow clinical progression, B cell chronic lymphocytic leukemia (B-CLL) is classically described as a disease of accumulation rather than proliferation. However, evidence for various forms of clonal evolution suggests that B-CLL clones may be more dynamic than previously assumed. We used a nonradioactive, stable isotopic labeling method to measure B-CLL cell kinetics in vivo. Nineteen patients drank an aliquot of deuterated water (2H2O) daily for 84 days, and 2H incorporation into the deoxyribose moiety of DNA of newly divided B-CLL cells was measured by gas chromatography/mass spectrometry, during and after the labeling period. Birth rates were calculated from the kinetic profiles. Death rates were defined as the difference between calculated birth and growth rates. These analyses demonstrated that the leukemic cells of each patient had definable and often substantial birth rates, varying from 0.1% to greater than 1.0% of the entire clone per day. Those patients with birth rates greater than 0.35% per day were much more likely to exhibit active or to develop progressive disease than those with lower birth rates Thus, B-CLL is not a static disease that results simply from accumulation of long-lived lymphocytes. Rather, it is a dynamic process composed also of cells that proliferate and die, often at appreciable levels. The extent to which this turnover occurs has not been previously appreciated. A correlation between birth rates and disease activity and progression appears to exist, which may help identify patients at risk for worsening disease in advance of clinical deterioration.
Danazol. A synthetic steroid with diverse biologic effects. (1990)

Danocrine (danazol) is a synthetic steroid with multiple and diverse biologic effects. It exerts these effects by binding to steroid transport proteins in the circulation and to specific receptors in target tissues. Centrally, danazol inhibits gonadotropins, suppressing gametogenesis and steroidogenesis. Gonadal and adrenal steroidogenesis are suppressed further through danazol's direct effect on specific enzyme systems. Danazol also displays immunoregulatory effects both in vivo and in vitro. In endometriosis, danazol induces amenorrhea and a hypoestrogenic state, resulting in endometrial atrophy. The drug's direct binding to androgen and progesterone receptors in endometriotic tissue may contribute further to the suppression of endometriosis. In women with endometriosis who produce autoantibodies against endometrial cells and endometrial cell-derived phospholipids, histones and nucleotides, danazol may improve reproductive performance through the suppression of abnormal autoantibody levels. In several other autoimmune and genetic disorders danazol brings about a clinical improvement by lowering abnormal autoantibody production or by increasing the concentration of genetically deficient protein. In order to explore the full clinical potential of the drug and to better understand danazol's mechanism of action and especially its immunoregulatory effects in autoimmune diseases and endometriosis, further investigation is necessary.
Effects of Reconstituted High-Density Lipoprotein Infusions on Coronary Atherosclerosis<SUBTITLE>A Randomized Controlled Trial</SUBTITLE> (2007)

clinicaltrials.gov Identifier: NCT00225719
DNA2 Cooperates with the WRN and BLM RecQ Helicases to Mediate Long-range DNA End Resection in Human Cells (2014)

The 5'-3' resection of DNA ends is a prerequisite for the repair of DNA double strand breaks by homologous recombination, microhomology-mediated end joining, and single strand annealing. Recent studies in yeast have shown that, following initial DNA end processing by the Mre11-Rad50-Xrs2 complex and Sae2, the extension of resection tracts is mediated either by exonuclease 1 or by combined activities of the RecQ family DNA helicase Sgs1 and the helicase/endonuclease Dna2. Although human DNA2 has been shown to cooperate with the BLM helicase to catalyze the resection of DNA ends, it remains a matter of debate whether another human RecQ helicase, WRN, can substitute for BLM in DNA2-catalyzed resection. Here we present evidence that WRN and BLM act epistatically with DNA2 to promote the long-range resection of double strand break ends in human cells. Our biochemical experiments show that WRN and DNA2 interact physically and coordinate their enzymatic activities to mediate 5'-3' DNA end resection in a reaction dependent on RPA. In addition, we present in vitro and in vivo data suggesting that BLM promotes DNA end resection as part of the BLM-TOPOIIIα-RMI1-RMI2 complex. Our study provides new mechanistic insights into the process of DNA end resection in mammalian cells.