gebhart/patrepeval huggingface dataset:
The epicardium and epicardially derived cells (EPDCs) as cardiac stem cells (2003)

After its initial formation the epicardium forms the outermost cell layer of the heart. As a result of an epithelial-to-mesenchymal transformation (EMT) individual cells delaminate from this primitive epicardial epithelium and migrate into the subepicardial space (Pérez-Pomares et al., Dev Dyn 1997; 210:96-105; Histochem J 1998a;30:627-634). Several studies have demonstrated that these epicardially derived cells (EPDCs) subsequently invade myocardial and valvuloseptal tissues (Mikawa and Fischman, Proc Natl Acad Sci USA 1992;89:9504-9508; Mikawa and Gourdie, Dev Biol 1996;174:221-232; Dettman et al., Dev Biol 1998;193:169-181; Gittenberger de Groot et al., Circ Res 1998;82:1043-1052; Manner, Anat Rec 1999;255:212-226; Pérez-Pomares et al., Dev. Biol. 2002b;247:307-326). A subset of EPDCs continue to differentiate in a variety of different cell types (including coronary endothelium, coronary smooth muscle cells (CoSMCs), interstitial fibroblasts, and atrioventricular cushion mesenchymal cells), whereas other EPDCs remain in a more or less undifferentiated state. Based on its specific characteristics, we consider the EPDC as the ultimate 'cardiac stem cell'. In this review we briefly summarize what is known about events that relate to EPDC development and differentiation while at the same time identifying some of the directions where EPDC-related research might lead us in the near future.
Learning from Data: Concepts, Theory, and Methods (1998)

From the Publisher:
This is an interdisciplinary book on neural networks, statistics and fuzzy systems. A unique feature is the establishment of a general framework for adaptive data modeling within which various methods from statistics, neural networks and fuzzy logic are presented. Chapter summaries, examples and case studies are also included.[Includes companion Web site with ... Software for use with the book.
Oxidative Stress: Emerging Mitochondrial and Cellular Themes and Variations in Neuronal Injury (2010)

Oxidative stress plays a central role in neuronal injury and cell death in acute and chronic pathological conditions. The cellular responses to oxidative stress embrace changes in mitochondria and other organelles, notably endoplasmic reticulum, and can lead to a number of cell death paradigms, which cover a spectrum from apoptosis to necrosis and include autophagy. In Alzheimer's disease, and other pathologies including Parkinson's disease, protein aggregation provides further cellular stresses that can initiate or feed into the pathways to cell death engendered by oxidative stress. Specific attention is paid here to mitochondrial dysfunction and programmed cell death, and the diverse modes of cell death mediated by mitochondria under oxidative stress. Novel insights into cellular responses to neuronal oxidative stress from a range of different stressors can be gained by detailed transcriptomics analyses. Such studies at the cellular level provide the key for understanding the molecular and cellular pathways whereby neurons respond to oxidative stress and undergo injury and death. These considerations underpin the development of detailed knowledge in more complex integrated systems, up to the intact human bearing the neuropathology, facilitating therapeutic advances.
A Comparative Analysis of the Production Characteristics of Cavity Completions and Hydraulic Fractures in Coalbed Methane Reservoirs (1999)

Abstract Coalbed methane wells usually require a stimulation technique because their initial flow rates are often quite low. Hydraulic fracturing is the most common type of stimulation technique applied to coalgas reservoirs. Recently, open-hole cavity completions have become an alternative stimulation technique in coalbed methane reservoirs. In this study, a three-dimensional, two-phase fluid flow model is used to compare production performances of the cavity-completed and hydraulically fractured wells in coalbed methane reservoirs. A static local grid refinement (LGR) technique is embedded into the model to adequately capture the flow behavior around cavity completions and hydraulic fractures without using excessively large number of grid cells. The model utilizes a residual equation rather than a wellbore equation to determine the flow rates into the cavity and hydraulic fracture. Both cavity completions and hydraulic fractures are approximated as a combination of fine rectangular grid blocks. The constructed fine grid lines are terminated at the coarse and fine grid block interfaces by implementing the LGR technique developed. The generated flow equations for fine and coarse blocks are, then, solved simultaneously. Flow performances of cavity completions and hydraulic fractures are compared for various coal seam permeabilities. It is demonstrated that permeability damage during fracturing may have significant impact on the flow performance of the hydraulic fracture. Hydraulic fractures without permeability damage associated perform better than cavity completions if permeability contrast in the coal seam is not significant. In strongly anisotropic systems, however, even if there is no formation damage due to fracturing fluid, cavity completions outperform hydraulic fractures.
Requirement of an intact microtubule cytoskeleton for aggregation and inclusion body formation by a mutant huntingtin fragment (2002)

Huntington's disease is caused by the expansion of CAG repeats coding for a polyglutamine tract in the huntingtin protein. The major pathological feature found in Huntington's disease neurons is the presence of detergent-insoluble ubiquitinated inclusion bodies composed of the huntingtin protein. However, the mechanisms that underlie inclusion body formation, and the precise relationship between inclusion bodies and events that initiate toxicity, remain unclear. Here, we analyzed the effects of drugs or genetic mutations that disrupt the microtubule cytoskeleton in a Saccharomyces cerevisiae model of the aggregation of an amino-terminal polyglutamine-containing fragment of huntingtin exon 1 (HtEx1). Treatment of yeast with drugs that disrupt microtubules resulted in less than 2% of the detergent-insoluble HtEx1 observed in mock-treated cells and prevented the formation of large juxtanuclear inclusion bodies. Disruption of microtubules also unmasked a potent glutamine length-dependent toxicity of HtEx1 under conditions where HtEx1 exists in an entirely detergent-soluble nonaggregated form. Results from the yeast model paralleled those from neuronal pheochromocytoma cells, where disruption of microtubules eliminated the formation of juxtanuclear and intranuclear inclusion bodies by HtEx1. Our results suggest that active transport along microtubules may be required for inclusion body formation by HtEx1 and that inclusion body formation may have evolved as a cellular mechanism to promote the sequestration or clearance of soluble species of HtEx1 that are otherwise toxic to cells.
Proton exchange in biotin: a reinvestigation, with implications for the mechanism of carbon dioxide transfer (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTProton exchange in biotin: a reinvestigation, with implications for the mechanism of carbon dioxide transferCharles L. Perrin and Tammy J. DwyerCite this: J. Am. Chem. Soc. 1987, 109, 17, 5163–5167Publication Date (Print):August 1, 1987Publication History Published online1 May 2002Published inissue 1 August 1987https://pubs.acs.org/doi/10.1021/ja00251a020https://doi.org/10.1021/ja00251a020research-articleACS PublicationsRequest reuse permissionsArticle Views142Altmetric-Citations26LEARN 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-Alertsclose Get e-Alerts
Laser-chemical three-dimensonal writing of multimaterial structures for microelectromechanics (2002)

A patterning machine capable of 5*10/sup 4/ pixel per second random access scanning has been developed as a tool for laser microchemical fabrication of three-dimensional parts. The tool is designed to implement precision laser deposition and etching reactions through a direct interface to solid modeling CAD/CAM (computer-aided design/manufacturing) software. Initial results with the three-dimensional laser patterning machine demonstrate clean etching of germanium and silicon with micrometer depth control and speeds one to two orders of magnitude faster than electric discharge machining. High material selectivity has been exploited to write buried flow channels under oxide membranes.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Iron-Binding Antioxidant Potential of Plasma Albumin (1997)

1. The extracellular proteins caeruloplasmin and transferrin have important antioxidant properties by virtue of the fact that they inhibit iron-dependent free radical production, and ensuing damage to cells. 2. Albumin is a plasma protein which can loosely bind iron, but the redox activity of this iron has not been fully investigated. 3. The ability of albumin to bind iron and to prevent iron-dependent lipid peroxidation in vitro was investigated using liposomes and a rat brain homogenate system. 4. The iron-binding capacity of albumin was found to be substantial, and albumin inhibited lipid peroxidation in a concentration-dependent manner in both systems used. 5. This antioxidant property of albumin may be especially important in the plasma of babies born prematurely, in whom transferrin and caeruloplasmin concentrations are often very low, and in whom non-transferrin-bound iron has been detected in the plasma.
Regulation of human fetal hemoglobin: new players, new complexities (2005)

The human globin genes are among the most extensively characterized in the human genome, yet the details of the molecular events regulating normal human hemoglobin switching and the potential reactivation of fetal hemoglobin in adult hematopoietic cells remain elusive. Recent discoveries demonstrate physical interactions between the beta locus control region and the downstream structural gamma- and beta-globin genes, and with transcription factors and chromatin remodeling complexes. These interactions all play roles in globin gene expression and globin switching at the human beta-globin locus. If the molecular events in hemoglobin switching were better understood and fetal hemoglobin could be more fully reactivated in adult cells, the insights obtained might lead to new approaches to the therapy of sickle cell disease and beta thalassemia by identifying specific new targets for molecular therapies.
Preparation and Stability of Template-Synthesized Metal Nanorod Sols in Organic Solvents (1998)

Gold and silver nanorods of diameter 40 and 90 nm and having a variety of aspect ratios (length/diameter) were prepared using the template synthesis approach. After template synthesis, the nanorods were freed from the template membrane and dispersed in either hexafluoro-2-propanol (HFIP) or CHCl3. The stability of these nanorod sols was monitored using visible absorption spectroscopy. For both the Au and Ag nanorods (in both solvents), sols prepared from the 90-nm diameter nanorods were found to be less stable than sols prepared from the 40-nm diameter nanorods. The addition of the polymeric stabilizers poly(vinylpyridine) or poly(vinylpyrrolidone) did not enhance the stability of these nanorod sols. In addition to these studies of sol stability, UV−vis absorption spectroscopy was used to investigate the plasmon absorption band of these sols. The wavelength of maximum absorbance of the plasmon resonance band (λmax) for both Ag and Au sols was shifted to higher wavelengths when the nanorod diameter was increased from 40 to 90 nm. In addition, the λmax values for sols prepared in CHCl3 were red-shifted relative to analogous sols prepared in HFIP.
The Increasing Problem of Asthma in the United States (1992)

"The Increasing Problem of Asthma in the United States." American Review of Respiratory Disease, 146(4), pp. 823–824
NMR Studies of Structure and Function of Biological Macromolecules (Nobel Lecture) (2003)

The structure of proteins (such as that of bovine prion protein, see picture) and further information on the dynamics and structural, thermodynamic, and kinetic aspects of their interactions with other components in solution can be obtained by NMR methods developed by K. Wüthrich and his group. In his Nobel Lecture, Wüthrich delves into the past, present, and future of these techniques, and offers us a glimpse into his life.
Identification of differentialy expressed genes by restirction endonuclease-based gene expression fingerprinting (1995)

A novel method for identification of differentially expressed genes has been developed. It is based on the consecutive restriction digestions of 3' terminal cDNA fragments to produce a fingerprint of gene expression. cDNA molecules are synthesized using a biotinylated oligo(dT) primer, digested with a frequently cutting restriction endonuclease and the 3'-terminal restriction fragments are isolated using streptavidin microbeads. After amplification by PCR, cDNA fragments are immobilized again on streptavidin beads, radiolabeled and treated sequentially with a set of restriction endonucleases. The products of individual enzymatic reactions from two or more different RNA populations are resolved by polyacrylamide gel electrophoresis and compared to reveal differentially expressed genes. This strategy enabled us to identify and clone the fragments of five genes expressed differentially in murine thymus and spleen. One of the genes was found to encode terminal deoxynucleotidyl transferase; others are apparently previously unknown genes.
Fast radiofrequency flip angle calibration by Bloch–Siegert shift (2011)

Abstract In a recent work, we presented a novel method for B field mapping based on the Bloch–Siegert shift. Here, we apply this method to automated fast radiofrequency transmit gain calibration. Two off‐resonance radiofrequency pulses were added to a slice‐selective spin echo sequence. The off‐resonance pulses induce a Bloch–Siegert phase shift in the acquired signal that is proportional to the square of the radiofrequency field magnitude B 1 2 . The signal is further spatially localized by a readout gradient, and the signal‐weighted average B 1 field is calculated. This calibration from starting system transmit gain to average flip angle is used to calculate the transmit gain setting needed to produce a desired imaging sequence flip angle. A robust implementation is demonstrated with a scan time of 3 s. The Bloch–Siegert‐based calibration was used to predict the transmit gain for a 90° radiofrequency pulse and gave a flip angle of 88.6 ± 3.42° when tested in vivo in 32 volunteers. Magn Reson Med, 2011. © 2011 Wiley Periodicals, Inc.
Chronic intracortical microstimulation (ICMS) of cat sensory cortex using the Utah intracortical electrode array (1999)

In an effort to assess the safety and efficacy of focal intracortical microstimulation (ICMS) of cerebral cortex with an array of penetrating electrodes as might be applied to a neuroprosthetic device to aid the deaf or blind, we have chronically implanted three trained cats in primary auditory cortex with the 100-electrode Utah Intracortical Electrode Array (UIEA). Eleven of the 100 electrodes were hard-wired to a percutaneous connector for chronic access. Prior to implant, cats were trained to "lever-press" in response to pure tone auditory stimulation. After implant, this behavior was transferred to "lever-presses" in response to current injections via single electrodes of the implanted arrays. Psychometric function curves relating injected charge level to the probability of response were obtained for stimulation of 22 separate electrodes in the three implanted cats. The average threshold charge/phase required for electrical stimulus detection in each cat was, 8.5, 8.6, and 11.6 nC/phase respectively, with a maximum charge/phase of 26 nC/phase and a minimum of 1.5 nC/phase thresholds were tracked for varying time intervals, and seven electrodes from two cats were tracked for up to 100 days. Electrodes were stimulated for no more than a few minutes each day. Neural recordings taken from the same electrodes before and after multiple electrical stimulation sessions were very similar in signal/noise ratio and in the number of recordable units, suggesting that the range of electrical stimulation levels used did not damage neurons in the vicinity of the electrodes. Although a few early implants failed, we conclude that ICMS of cerebral cortex to evoke a behavioral response can be achieved with the penetrating UIEA. Further experiments in support of a sensory cortical prosthesis based on ICMS are warranted.
Signature-Tagged Transposon Mutagenesis Studies Demonstrate the Dynamic Nature of Cecal Colonization of 2-Week-Old Chickens by Campylobacter jejuni (2005)

We have constructed plasmids to be used for in vitro signature-tagged mutagenesis (STM) of Campylobacter jejuni and used these to generate STM libraries in three different strains. Statistical analysis of the transposon insertion sites in the C. jejuni NCTC 11168 chromosome and the plasmids of strain 81-176 indicated that their distribution was not uniform. Visual inspection of the distribution suggested that deviation from uniformity was not due to preferential integration of the transposon into a limited number of hot spots but rather that there was a bias towards insertions around the origin. We screened pools of mutants from the STM libraries for their ability to colonize the ceca of 2-week-old chickens harboring a standardized gut flora. We observed high-frequency random loss of colonization proficient mutants. When cohoused birds were individually inoculated with different tagged mutants, random loss of colonization-proficient mutants was similarly observed, as was extensive bird-to-bird transmission of mutants. This indicates that the nature of campylobacter colonization in chickens is complex and dynamic, and we hypothesize that bottlenecks in the colonization process and between-bird transmission account for these observations.
Skeletal Muscle Denervation Increases Satellite Cell Susceptibility to Apoptosis (2002)

Peripheral motor nerve trauma severely compromises skeletal muscle contractile function. Satellite cells respond to denervation by dividing multiple times, ultimately fusing with other satellite cells or myocytes to form new muscle fibers. After chronic denervation, satellite cell numbers decline dramatically, impairing the ability to regenerate and repair myofibers. This satellite cell depletion may contribute to the mechanical deficit observed in denervated or reinnervated muscle. Apoptosis, an evolutionarily conserved form of cell suicide, is a potential mechanism for satellite cell depletion in denervated skeletal muscle. This work tested the hypothesis that skeletal muscle denervation increases satellite cell susceptibility to apoptotic cell death. Adult rats underwent sciatic nerve transection to denervate the distal hindlimb musculature; rats of similar age without the operation served as controls. Two, 6, 10, or 20 weeks after denervation (n = 6 each group), the gastrocnemius and soleus were excised, enzymatically digested, and plated for satellite cell culture. After reaching 95 percent confluence, satellite cells were treated for 24 hours with tumor necrosis factor-alpha (20 ng/ml) and actinomycin D (250 ng/ml), known pro-apoptotic agents. Immunostaining for activated caspases, terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling (TUNEL), and hematoxylin and eosin staining were performed to identify apoptotic satellite cells. Percentages of apoptotic cells were quantified histomorphometrically. In addition, the presence or absence of bcl-2 and bax was determined by Western blot analysis of control, 6 weeks of denervation, and 10 weeks of denervation specimens. At 6 and 10 weeks after nerve transection, TUNEL and caspase activity were increased more than two-fold in satellite cells isolated from denervated muscle compared with those isolated from control muscle (p < 0.05). In all experimental groups, retention of adherence to the collagen-coated substrate was strongly associated with satellite cell survival. Western blot analysis revealed that adherent satellite cells from all groups expressed both bcl-2 and bax. These data support the authors' hypothesis that skeletal muscle denervation increases satellite cell susceptibility to apoptotic cell death. Apoptosis may play a causative role in the depletion of satellite cells in long-term denervated skeletal muscle.
Structure, Expression, and Regulation of the Major Noncollagenous Matrix Proteins of Bone (1992)

The noncollagenous proteins (NCPs) that predominate the bone matrix have recently been the focus of intense investigation because of their potential influence on cell attachment, Ca2+ and hydroxyapatite binding, and the mineralization of bone tissue. With the advent of molecular biology, all of the major NCPs of bone have been cloned and their amino acid sequences completely determined. While each of the proteins has distinct structural properties, some proteins appear to be part of gene families. Examples include the small proteoglycans, decorin and biglycan, as well as the gamma carboxyglutamic acid proteins, such as matrix gla protein and osteocalcin (bone gla protein). Some of the NCPs that are clearly not members of any known gene family still share several common characteristics. One such example of this "convergent evolution" is bone sialoprotein and osteopontin. Both are highly posttranslationally modified glycoproteins that share the cell attachment amino acid sequence RGD (arginine-glycine-aspartic acid), which facilitates the attachment of bone cells in vitro, yet they are clearly not related genetically. Using cDNAs and antisera as probes, the precise temporal localization of NCP expression has been determined, and it has been shown that NCPs are produced in skeletal, and in most cases, nonskeletal tissue as well. This observation implies that the functions of the NCPs are not necessarily limited to bone tissue. Many of the promoters for these genes have been isolated and functional domains determined by a combination of chloramphenicol acetyltransferase assay, gel shift, and footprint analyses. The most extensively studied promoter in the NCP category is osteocalcin, whose sensitivity to 1,25-dihydroxycholecalciferol has been delineated in detail. Future studies on the individual and cooperative activities of the NCPs in bone are likely to involve site-directed mutagenesis of cloned DNA and a combination of in vitro and in vivo functional analyses.