gebhart/patrepeval huggingface dataset:
Emerging nanotechnology approaches in tissue engineering and regenerative medicine (2014)

Emerging nanotechnology approaches in tissue engineering and regenerative medicine Eung-Sam Kim,1,2 Eun Hyun Ahn,3,4 Tal Dvir,5,6 Deok-Ho Kim1,4,71Department of Bioengineering, University of Washington, Seattle, WA, USA; 2Department of Biological Sciences, Chonnam National University, Gwangju, Korea; 3Department of Pathology, 4Institute of Stem Cell and Regenerative Medicine, School of Medicine, University of Washington, Seattle, WA, USA; 5Department of Molecular Microbiology and Biotechnology, 6Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel; 7Center for Cardiovascular Biology, University of Washington, Seattle, WA, USA The history of human kind suggests that there has been a correlation between global population growth and major events in science and technology over the last three centuries. Sharp increases in the world’s population have been triggered by the industrial revolution and scientific and technological breakthroughs including: the advent of the railways, discovery of penicillin and deoxyribonucleic acid (DNA), and the invention of the computer.1 Since the 20th century, interdisciplinary areas in the physical and biological sciences have accelerated the progress of biomedical applications. The recent integration of emerging nanotechnology into biology and biomedicine has resulted in a range of innovative nanoengineering efforts for the repair and regeneration of tissues and organs.2 Thus, it is expected that nanoengineering approaches to biomedical applications can contribute to addressing the present issue of personal and global health care and its economic burden for more than 7 billion people.Why are we paying attention to nanoengineering for biomedical applications? The size of most biomolecules ranges from 0.2 nm to 200 nm (Figure 1). Research has focused on control of the interaction and localization of biomolecules even at the single-molecule level using ever-evolving nanotechnology.3 The evidence indicates that cells can respond to nanoscale changes in the dynamic extracellular matrix and vice versa. Biomimetic nanopatterns alone can direct the differentiation of stem cells without involvement of exogenous soluble biochemical factors.4,5 This regulation of cellular behavior by nanotechnology is one of many examples demonstrating the significant applications of nanoengineering in biomedicine. This special issue includes four review papers and seven research articles that provide an insight into current nanoengineering approaches to the repair or regeneration of tissues and organs.
Tolerance to the antimicrobial peptide colistin in Pseudomonas aeruginosa biofilms is linked to metabolically active cells, and depends on the pmr and mexAB‐oprM genes (2008)

Bacteria living as biofilm are frequently reported to exhibit inherent tolerance to antimicrobial compounds, and might therefore contribute to the persistence of infections. Antimicrobial peptides are attracting increasing interest as new potential antimicrobial therapeutics; however, little is known about potential mechanisms, which might contribute to resistance or tolerance development towards these compounds in biofilms. Here we provide evidence that a spatially distinct subpopulation of metabolically active cells in Pseudomonas aeruginosa biofilms is able to develop tolerance to the antimicrobial peptide colistin. On the contrary, biofilm cells exhibiting low metabolic activity were killed by colistin. We demonstrate that the subpopulation of metabolically active cells is able to adapt to colistin by inducing a specific adaptation mechanism mediated by the pmr operon, as well as an unspecific adaptation mechanism mediated by the mexAB-oprM genes. Mutants defective in either pmr-mediated lipopolysaccharide modification or in mexAB-oprM-mediated antimicrobial efflux were not able to develop a tolerant subpopulation in biofilms. In contrast to the observed pattern of colistin-mediated killing in biofilms, conventional antimicrobial compounds such as ciprofloxacin and tetracycline were found to specifically kill the subpopulation of metabolically active biofilm cells, whereas the subpopulation exhibiting low metabolic activity survived the treatment. Consequently, targeting the two physiologically distinct subpopulations by combined antimicrobial treatment with either ciprofloxacin and colistin or tetracycline and colistin almost completely eradicated all biofilm cells.
Tetrapeptide DEVD‐aldehyde or YVAD‐chloromethylketone inhibits Fas/Apo‐1 (CD95)‐mediated apoptosis in renal‐cell‐cancer cells (1996)

The apoptotic machinery has been intensively investigated, and interleukin-l-beta-converting enzyme (ICE) and its homologs directly mediate apoptosis by means of their unique protease activity. Fas/Apol (CD95), a member of the TNF-receptor family, mediates apoptosis by binding to its ligand, which is mainly expressed on lymphocytes. Here, we investigated the expression and function of both molecules in renal-cell cancer (RCC). The expression of Fas was examined in 6 RCC cell lines by immunoblotting and all of them expressed Fas. ICE and CPP32/YAMA were also identified among the cell lines. We earlier examined ACHN cells expressing low levels of BCL-2, as well as KRC/Y cells with high levels of BCL-2. Here, we found that the anti-Fas monoclonal antibody, CH-11, induced apoptosis in a dose-dependent fashion more remarkably in ACHN cells. Pre-incubation with the tetrapeptide YVAD-chloromethylketone or DEVD-aldehyde inhibited Fas-mediated apoptosis. These findings suggest that, in RCC, apoptosis is induced by lymphocytes bearing Fas-L, and that it is achieved through the proteolytic action of CPP32/YAMA and/or ICE, or another member of the ICE/ced-3 protease family. © 1996 Wiley-Liss, Inc.
The Impact of Tumor Physiology on Camptothecin-Based Drug Development (2005)

The genomic era has shifted anticancer drug development from its traditional mode concentrated on natural product cytotoxic agents to mechanism-based drug design focused on signal transduction pathways. Yet traditional cytotoxic chemotherapies continue to have an important role in the armamentarium. This is particularly true when one considers that important elements of solid tumor physiology - acidosis and hypoxia - have rarely been incorporated into algorithms for anticancer drug development. It is now well established that a majority of solid tumors exist in an acidic and hypoxic microenvironment that promotes resistance to radiation and chemotherapies apart from any drug-induced target mutations or efflux protein pumps. The acidic extracellular environment leads to a pH gradient unique to tumor cells. This gradient will favor uptake and retention of small molecule drugs that are weak acids. The converse is true for weak bases. The camptothecin class of topoisomerase I inhibitors is one example of a natural product cytotoxic that can exploit the tumor pH gradient. Screening of compounds based on selective activity at acidic pH (pH modulation), rather than potency, reveals analogs that are over ten times more active under the acidic conditions prevalent in vivo. Thus, knowledge of the tumor metabolic phenotype gained at the beginning of the 20(th) century can lead to more effective anticancer drugs in the new millennium.
An Adenosine Deaminase that Generates Inosine at the Wobble Position of tRNAs (1999)

Several transfer RNAs (tRNAs) contain inosine (I) at the first position of their anticodon (position 34); this modification is thought to enlarge the codon recognition capacity during protein synthesis. The tRNA-specific adenosine deaminase of Saccharomyces cerevisiae that forms I(34) in tRNAs is described. The heterodimeric enzyme consists of two sequence-related subunits (Tad2p/ADAT2 and Tad3p/ADAT3), both of which contain cytidine deaminase (CDA) motifs. Each subunit is encoded by an essential gene (TAD2 and TAD3), indicating that I(34) is an indispensable base modification in elongating tRNAs. These results provide an evolutionary link between the CDA superfamily and RNA-dependent adenosine deaminases (ADARs/ADATs).
miR-15 Family Regulates Postnatal Mitotic Arrest of Cardiomyocytes (2011)

These findings suggest that upregulation of the miR-15 family during the neonatal period may be an important regulatory mechanism governing cardiomyocyte cell cycle withdrawal and binucleation.
S-Match: An open source framework for matching lightweight ontologies (2012)

Achieving automatic interoperability among systems with diverse data structures and languages expressing different viewpoints is a goal that has been difficult to accomplish. This paper describes S-Match, an open source semantic matching framework th
In vivo rat pancreatic acinar cell function during supramaximal stimulation with caerulein (1985)

Infusion of a supramaximal dose of caerulein results in acute interstitial pancreatitis in rats. We report studies of in vivo pancreatic acinar cell function during the initial 3.5 h of supramaximal stimulation with caerulein (5 micrograms X kg-1 X h-1). Amino acid [( 3H]phenylalanine) uptake was not altered, and there was no change in the rate or extent of protein synthesis or in intracellular transport of in vivo pulse-labeled proteins from microsome to zymogen granule-enriched fractions. However, the discharge of labeled protein was markedly inhibited. Radioautographic studies indicated that the pulse-labeled proteins retained in the gland were not located extracellularly but had accumulated within acinar cells, with a preferential distribution at the cell apex (presumably in zymogen granules) and in large vacuoles that form within the cell during hyperstimulation. Supramaximal stimulation with caerulein also caused increasing amounts of amylase and labeled proteins to be recovered in the postmicrosomal fraction. These findings suggest that supramaximal stimulation causes digestive enzymes to become localized in organelles that are fragile and subject to disruption during tissue homogenization. These organelles may be the vacuoles noted in morphological studies and believed to represent immature condensing vacuoles and/or crinophagic vacuoles.
<title>Next-generation light delivery system for multitreatment extended-duration photodynamic therapy (MED-PDT)</title> (1997)

The primary focus of laser based oncologic PDT has been on the treatment of skin and hollow organ tumors. Extending PDT to other primary internal lesions and metastasis requires a different approach. Light Sciences has developed a series of semiconductor-based devices which will be completely implanted in the patient using established, minimally invasive surgical techniques. These devices are energized noninvasively utilizing inductive coupling. The light delivery system will allow the clinician to modulate the intensity, spatial distribution, and duration of light delivery in order to maximize the benefits derived from each PDT drug dose. Light Sciences' technology minimizes patient risk and discomfort, is cost competitive, and expands the treatment options available to the clinician. Avoidance of lengthy operations, bone marrow suppression, and an emphasis on organ preservation allow this next generation of PDT light delivery devices to be effectively integrated with other forms of cancer treatment, if desired. We have termed our technique 'Multi-treatment Extended Duration PDT'. In what follows, we shall describe Light Sciences' technology and development of minimally invasive oncologic PDT.
Influence of Site of Uptake of Fluridone on Early Development of Soybean (Glycine max) and Cotton (Gossypium hirsutum) (1979)

The double pot technique was used to study the effects of uptake site of fluridone {1-methyl-3-phenyl-5-[3-(trifluoromethyl—phenyl]-4(1 H )-pyridinone} on early shoot and root development of soybean [ Glycine max (L.) Merr. ‘Williams’] and cotton ( Gossypium hirsutum L. ‘Acala SJ-1′). Soybean is susceptible and cotton is resistant to fluridone. Root uptake in soybean resulted in increased shoot length in the epicotyl and shoot apex, reduced shoot fresh weight, chlorosis of primary and trifoliolate leaves, as well as reduced root length, branching, and fresh weight. Shoot uptake resulted in reduced shoot length above the hypocotyl, reduced shoot weight, severe chlorosis of primary leaves, and inhibition of trifoliolate leaf formation. The reduction in the root length, branching, and weight was less by shoot uptake than by root uptake. In cotton, root uptake resulted in reduced shoot length in the epicotyl and shoot apex, slight reduction in shoot weight, no effect on chlorosis of cotyledon leaves, moderate to slight chlorosis of the true leaves, and no effect on root length, branching, or fresh weight. Shoot uptake resulted in reduced length of all shoot components and shoot weight, chlorosis of cotyledon leaves and the true leaves, and reduced root length, branching, and weight. Compared to soybean, cotton required much higher fluridone concentrations to show the above effects. It was generally concluded that in soybean, uptake by both the root and the shoot contributed significantly to the injury, whereas in cotton, shoot uptake was relatively more important.
An evolutionary classification of the metallo-beta-lactamase fold proteins. (1999)

All the detectable metallo-beta-lactamase fold proteins were identified in the publicly available sequence databases and complete genome sequences using iterative profile searches with the PSI-BLAST program and motif searches with position specific weight matrices. The catalytic site/mechanism and the corresponding structural elements were characterized for these proteins based on the available structure of the Bacillus zinc-dependent beta-lactamase. Based on pair-wise sequence and phylogenetic analysis an evolutionary classification for enzymes of this fold was developed and discussed in terms of implications for substrate specificity. Finally, some predicted inactive members which have been recruited for non-enzymatic functions such as microtubule binding in a cytoskeletal MAP1 are described.
Role of bone marrow transplantation in 90Y antibody therapy of colon cancer xenografts in nude mice. (1990)

The efficacy of bone marrow transplantation (BMT) for the prevention of 90Y toxicity and extension of survival in nude mice with i.p. LS174T carcinomatosis was evaluated. 90Y-labeled monoclonal antibody (MAB) directed against carcinoembryonic antigen (90Y-anti-CEA MAB) at a dose of 120 microCi caused no deaths due to treatment toxicity and increased the duration of animal survival. No long term cures were obtained in these mice. At doses of 160 microCi or more 90Y-anti-CEA MAB led to hematological deaths. Nude mice were given i.p. injections of 10(6) LS174T tumor cells on day 0. On day 7 the mice received 90Y-anti-CEA MAB i.p. at doses of 120-225 microCi. Syngeneic bone marrow cells (10(7) cells) were then injected i.v. into the mice at 1, 3, 5, 7, 10, or 14 days following 90Y treatment. In the absence of BMT, toxic deaths for animals given 175 microCi 90Y were 11 of 24 (46%) with a median survival of 17 days and 13 of 20 (65%) for animals given 225 microCi 90Y with a median survival of 14 days. Animals receiving the same two doses of 90Y and given BMT 5 days following the 90Y treatment showed 0 of 24 (0%) and 0 of 54 (0%) toxicity deaths, respectively. The optimal time of BMT in relation to 90Y therapy was dependent upon the dose of 90Y-anti-CEA MAB (225 microCi, 3-5 days; 175 microCi, 5-14 days). The mean survival in tumor bearing animals was extended from 31.7 +/- 1.2 (SE) to 45.3 +/- 2.0 days by treatment with 120 microCi of 90Y-anti-CEA MAB. By increasing the dose of 90Y-anti-CEA MAB to 225 microCi and undertaking BMT 5 days later the mean survival was further extended to 63.2 +/- 3.6 days (P less than 0.005). BMT administered at the optimal times can prevent toxic deaths and facilitates higher, more effective doses of tumor specific 90Y-MAB.
Exploring the Genomes of Cancer Cells: Progress and Promise (2011)

The description and interpretation of genomic abnormalities in cancer cells have been at the heart of cancer research for more than a century. With exhaustive sequencing of cancer genomes across a wide range of human tumors well under way, we are now entering the end game of this mission. In the forthcoming decade, essentially complete catalogs of somatic mutations will be generated for tens of thousands of human cancers. Here, I provide an overview of what these efforts have revealed to date about the origin and behavioral features of cancer cells and how this genomic information is being exploited to improve diagnosis and therapy of the disease.
Localization of specific binding sites for atrial natriuretic factor in peripheral tissues of the guinea pig, rat, and human. (1986)

Specific, high affinity atrial natriuretic factor (ANF) binding sites were identified and localized by autoradiographic techniques in peripheral tissues of the guinea pig, rat, and human. In the guinea pig kidney, high concentrations of ANF binding sites were located in the glomerular apparatus, outer medulla, and small renal arteries. Other peripheral tissues containing ANF binding sites included the zona glomerulosa of the adrenal cortex, the smooth muscle layer of the aorta and gallbladder, the lung parenchyma, the posterior lobe of the pituitary, the ciliary body of the eye, and the leptomeninges and choroid plexus of the brain. The distribution of ANF binding sites in the rat and human kidney was nearly identical to those seen in the guinea pig kidney; high concentrations were present in the glomerular apparatus, outer medulla, and small renal arteries. These results are consistent with earlier physiological and pharmacological studies that suggested that ANF plays a functional role in the regulation of extracellular fluid volume and blood pressure. There appears to be little species variation in the location and concentration of renal ANF binding sites, suggesting that, at least in the kidney, the results in experimental animals are relevant to the actions of ANF in humans. The finding that ANF binding sites were stable and present in high concentrations in human postmortem kidneys further suggests that these tissues may be amenable to testing for the involvement of ANF receptor dysfunction in diseases such as hypertension and congestive heart failure.
Fluorescein derivatization of fibrinogen for flow cytometric analysis of fibrinogen binding to platelets (1994)

Dog and human fibrinogen were derivatized with N-hydroxysuccinimido-fluorescein and utilized for flow cytometric estimation of fibrinogen binding to activated platelets. Fluorescein-fibrinogen binding fulfilled the criteria for specific binding to platelets; the binding was saturable, dependent on agonist activation, and inhibited by unlabeled fibrinogen. In addition, EDTA and barbourin, a KGD-containing peptide, were found to inhibit the binding of fluorescein-fibrinogen. Fluorescein-fibrinogen bound to dog platelets with an apparent affinity of 0.31 microM after stimulation with either adenosine-5'-diphosphate (ADP) or plateletactivating factor. The labeled fibrinogen was also used to study the fibrinogen binding capacity of aged, biotinylated platelets. Aged platelets were indistinguishable from young platelets with regard to fibrinogen binding in response to ADP. These studies document that direct derivatization of fibrinogen with fluorescein generates a useful probe for analyzing fibrinogen binding to platelets with flow cytometry.
Ultra high‐speed sorting (2005)

Cell sorting has become more stable and predictable and requires less expertise to operate. However, the problems of aerosol containment continue to make droplet-based cell sorting problematical. Fluid physics and cell viability restraints pose practical limits for high-speed sorting that have almost been reached. Over the next 5 years there may be advances in fluidic switching sorting in lab-on-a-chip microfluidic systems that could not only solve the aerosol and viability problems but also make ultra high-speed sorting possible and practical through massively parallel and exponential staging microfluidic architectures.
Imaging of tumor angiogenesis in rat brains in vivo by photoacoustic tomography (2005)

Green laser pulses at a wavelength of 532 nm from a Q-switched Nd:YAG laser were employed as irradiation sources for photoacoustic tomography (PAT). The vascular structure of the brain was imaged clearly, with optimal contrast, because blood has strong absorption near this wavelength. The photoacoustic images of rat brain tumors in this study clearly reveal the angiogenesis that is associated with tumors. Brain tumors can be identified based on the distorted vascular architecture of brain tumorigenesis and related vascular changes, such as hemorrhage. This research demonstrates that PAT can potentially provide a powerful tool for small-animal biological research.
Structural indexing: efficient 3-D object recognition (1992)

The authors present an approach for the recognition of multiple 3-D object models from three 3-D scene data. The approach uses two different types of primitives for matching: small surface patches, where differential properties can be reliably computed, and lines corresponding to depth or orientation discontinuities. These are represented by splashes and 3-D curves, respectively. It is shown how both of these primitives can be encoded by a set of super segments, consisting of connected linear segments. These super segments are entered into a table and provide the essential mechanism for fast retrieval and matching. The issues of robustness and stability of the features are addressed in detail. The acquisition of the 3-D models is performed automatically by computing splashes in highly structured areas of the objects and by using boundary and surface edges for the generation of 3-D curves. The authors present results with the current system (3-D object recognition based on super segments) and discuss further extensions.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Diagnosis of non-palpable breast lesions : ultrasonographically controlled fine-needle aspirations : diagnostic and prognostic implications of cytologic grading, morphometry, DNA cytometry, immunocytochemistry, and color doppler (1993)

Fine-needle aspiration of non-palpable breast lesions, J. Mouriquand mammographic-ultrasonographic-cytologic correlations in different diseases of the breast, J.M. Tournegros, et al non-palpable breast lesions - cytologic examination of breast secretions, J. Mouriquand cytoprognostic classification of breast carcinomas - its predictive value, J. Mouriquand, et al diagnostic and prognostic implications of morphometry and DNA cytometry in breast cytology, P.J. Diest and J.P.A. Baak immunocytochemistry in breast cytopathology - achievements and challenges, J. Abarca-Quinones contribution of colour doppler to the diagnosis of non-palpable breast tumours, E. Escolano and B. Finck the surgeon's attitude when faced with non-palpable breast lesions, J.Y. Pons.
IMP3 Predicts Aggressive Superficial Urothelial Carcinoma of the Bladder (2008)

Our findings indicate that IMP3 is an independent prognostic marker that can identify a group of patients with a high potential to develop progression and who might benefit from early aggressive therapy.
ChemInform Abstract: Synthetic Transformations of 1‐Cyanomethylbenzotriazole. (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.