gebhart/patrepeval huggingface dataset:
A defined medium for rumen bacteria and identification of strains impaired in de novo biosynthesis of certain amino acids (1995)

A completely defined growth medium has been developed to determine the nitrogen requirements for several species of ruminal bacteria, and has revealed two strains which are impaired in de novo biosynthesis of certain amino acids. Using NH4Cl as a sole nitrogen source, the medium supported growth of Butyrivibrio, Selenomonas, Prevotella and Streptococcus species. One strain of B. fibrisolvens (E14) and one strain of P. ruminicola (GA33) did not grow in the presence of NH4Cl until the medium was supplemented with amino acids or peptides. For B. fibrisolvens strain E14, methionine was identified as the specific growth-limiting amino acid although methionine alone did not support growth in the absence of NH4Cl. For P. ruminicola strain GA33, any individual amino acid other than methionine or cysteine could supplement the medium and support growth. Enzyme assays confirmed a lack of NADH and NADPH-dependent glutamate dehydrogenase (GDH) activities in this strain.
Digital Information Processing in Molecular Systems (2008)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTDigital Information Processing in Molecular SystemsKonrad Szaciłowski*View Author Information Uniwersytet Jagielloński, Wydział Chemii, ul. Romana Ingardena 3, 30-060 Kraków, Poland* Corresponding author. Tel: +48 12 663 2208. Fax: +48 12 634 0515. E-mail: [email protected]Cite this: Chem. Rev. 2008, 108, 9, 3481–3548Publication Date (Web):June 27, 2008Publication History Received8 November 2007Published online27 June 2008Published inissue 10 September 2008https://pubs.acs.org/doi/10.1021/cr068403qhttps://doi.org/10.1021/cr068403qreview-articleACS PublicationsCopyright © 2008 American Chemical SocietyRequest reuse permissionsArticle Views10345Altmetric-Citations767LEARN 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 SUBJECTS:Absorption,Cations,Fluorescence,Molecules,Reaction mechanisms Get e-Alerts
The Receptor for the Cytotoxic Ligand TRAIL (1997)

TRAIL (also known as Apo-2L) is a member of the tumor necrosis factor (TNF) ligand family that rapidly induces apoptosis in a variety of transformed cell lines. The human receptor for TRAIL was found to be an undescribed member of the TNF-receptor family (designated death receptor-4, DR4) that contains a cytoplasmic "death domain" capable of engaging the cell suicide apparatus but not the nuclear factor kappa B pathway in the system studied. Unlike Fas, TNFR-1, and DR3, DR4 could not use FADD to transmit the death signal, suggesting the use of distinct proximal signaling machinery. Thus, the DR4-TRAIL axis defines another receptor-ligand pair involved in regulating cell suicide and tissue homeostasis.
Embryonic stem cells attenuate myocardial dysfunction and inflammation after surgical global ischemia via paracrine actions (2008)

Stem cell treatment may positively influence recovery and inflammation after shock by multiple mechanisms, including the paracrine release of protective growth factors. Embryonic stem cells (ESCs) are understudied and may have greater protective power than adult bone marrow stem cells (BMSCs). We hypothesized that ESC paracrine protective mechanisms in the heart (decreased injury by enhanced growth factor-mediated reduction of proinflammatory cytokines) would be superior to the paracrine protective mechanisms of the adult stem cell population in a model of surgically induced global ischemia. Adult Sprague-Dawley rat hearts were isolated and perfused via Langendorff model. Hearts were subjected to 25 min of warm global ischemia and 40 min of reperfusion and were randomly assigned into one of four groups: 1) vehicle treated; 2) BMSC or ESC preischemic treatment; 3) BMSC or ESC postischemic treatment; and 4) BMSC- or ESC-conditioned media treatment. Myocardial function was recorded, and hearts were analyzed for expression of tissue cytokines and growth factors (ELISA). Additionally, ESCs and BMSCs in culture were assessed for growth factor production (ELISA). ESC-treated hearts demonstrated significantly greater postischemic recovery of function (left ventricular developed pressure, end-diastolic pressure, and maximal positive and negative values of the first derivative of pressure) than BMSC-treated hearts or controls at end reperfusion. ESC-conditioned media (without cells) also conferred cardioprotection at end reperfusion. ESC-infused hearts demonstrated increased VEGF and IL-10 production compared with BMSC hearts. ESC hearts also exhibited decreased proinflammatory cytokine expression compared with MSC hearts. Moreover, ESCs in cell culture demonstrated greater pluripotency than MSCs. ESC paracrine protective mechanisms in surgical ischemia are superior to those of adult stem cells.
A Novel LPS-Inducible C-Type Lectin Is a Transcriptional Target of NF-IL6 in Macrophages (1999)

C-type lectins serve multiple functions through recognizing carbohydrate chains. Here we report a novel C-type lectin, macrophage-inducible C-type lectin (Mincle), as a downstream target of NF-IL6 in macrophages. NF-IL6 belongs to the CCAAT/enhancer binding protein (C/EBP) of transcription factors and plays a crucial role in activated macrophages. However, what particular genes are regulated by NF-IL6 has been poorly defined in macrophages. Identification of downstream targets is required to elucidate the function of NF-IL6 in more detail. To identify downstream genes of NF-IL6, we screened a subtraction library constructed from wild-type and NF-IL6-deficient peritoneal macrophages and isolated Mincle that exhibits the highest homology to the members of group II C-type lectins. Mincle mRNA expression was strongly induced in response to several inflammatory stimuli, such as LPS, TNF-alpha, IL-6, and IFN-gamma in wild-type macrophages. In contrast, NF-IL6-deficient macrophages displayed a much lower level of Mincle mRNA induction following treatment with these inflammatory reagents. The mouse Mincle proximal promoter region contains an indispensable NF-IL6 binding element, demonstrating that Mincle is a direct target of NF-IL6. The Mincle gene locus was mapped at 0.6 centiMorgans proximal to CD4 on mouse chromosome 6.
A Glu113Ala Mutation within a Factor VIII Ca2+-Binding Site Enhances Cofactor Interactions in Factor Xase (2005)

We recently identified an acidic-rich segment in the A1 domain of factor VIII (residues 110-126) that functions in the coordination of Ca(2+), an ion necessary for cofactor activity [Wakabayashi et al. (2004) J. Biol. Chem. 279, 12677-12684]. Mutagenesis studies showed that replacement of residue Glu113 with Ala (E113A) yielded a factor VIII point mutant possessing increased specific activity as determined by a one-stage clotting assay. Mutagenesis at this site suggested that substitution with relatively small, nonpolar residues was well tolerated, whereas replacement with a number of polar or charged residues appeared detrimental to activity. Ala substitution resulted in the greatest enhancement, yielding an approximately 2-fold increased specific activity. Time course experiments following reaction with thrombin revealed similar rates of activation and inactivation of E113A as observed for the wild type. Results from factor Xa generation assays showed minimal differences in kinetic parameters and factor IXa affinity for E113A and wild-type factor VIIIa when run in the presence of synthetic phospholipid vesicles, whereas factor VIIIa E113A displayed an approximately 4-fold greater affinity for factor IXa compared with factor VIIIa wild type in reactions run on the platelet membrane surface. This latter effect may be attributed, in part, to a 2-fold increased affinity of factor VIIIa E113A for the platelet membrane. Considering that low levels of factors VIIIa and IXa are generated during clotting in plasma, the increased cofactor specific activity observed for E113A factor VIII may result from its enhanced affinity for factor IXa on the physiological membrane.
Microfluorimeter with disposable polymer chip for detection of coeliac disease toxic gliadin (2009)

Coeliac disease is an inflammatory disease of the upper small intestine and results from gluten ingestion in genetically susceptible individuals, and is the only life-long nutrient-induced enteropathy. The only treatment is a strict gluten-free diet and the longer the individual fails to adhere to this diet, the greater the chance of developing malnutrition and other complications. The existence of reliable gluten free food is crucial to the well-being of the population. Here we report on a microfluorimeter device for the in situ detection of gliadin in foodstuffs, which could be used for a rapid control of raw materials in food processing, as well as for process control of gliadin contamination. The microfluorimeter is based on a reflector that is used inside a microfluidic chip, exploiting various strategically placed reflective or totally metallised mirrors for efficient collection of the fluorescent light emitted in a large solid angle. The chip is capable of executing five assays in parallel and has been demonstrated to possess detection sensitivity applicable to fluoroimmunoassays. Various immunoassay formats exploiting fluorescence detection, using enzyme/fluorophore labels were developed and compared in terms of sensitivity, ease of assay, assay time and compatibility with buffer used to extract gliadin from raw and cooked foodstuffs, with the best performance observed with an indirect competition assay using a fluorophore-labelled anti-mouse antibody. This assay was exploited within the microfluorimeter device, and a very low detection limit of 4.1 ng/mL was obtained. The system was observed to be highly reproducible, with an RSD of 5.9%, for a concentration of 50 ng/mL of gliadin applied to each of the five channels of the microfluorimeter. Biofunctionalised disposable strips incorporated into the microfluorimeter were subjected to accelerated Arrhenius thermal stability studies and it was demonstrated that strips pre-coated with gliadin could be stored for approximately 2 years at 4 degrees C, with no discernable loss in sensitivity or detectability of the assay. Finally, the microfluorimeter was applied to the analysis of commercial gluten-free food samples, and an excellent correlation with routine ELISA measurements was obtained. The developed microfluorimeter should find widespread application for on-site execution of fluoroimmunoassays.
Exceptional chemopreventive activity of low-dose dehydroepiandrosterone in the rat mammary gland. (1996)

To determine if the chemopreventive activity of dehydroepiandrosterone (DHEA) in the rat mammary gland can be dissociated from its toxicity, two studies were conducted in which low doses of DHEA were administered alone and in combination with other agents to rats treated with N-methyl-N-nitrosourea. Beginning 1 week prior to administration of 35 mg N-methyl-N-nitrosourea per kg body weight, groups of 20 female Sprague-Dawley rates were fed AIN-76A diet supplemented with DHEA alone (800 or 400 mg/kg diet), DHEA + tamoxifen (80 or 40 microgram/kg diet), DHEA + carbenoxolone (3500 or 1750 mg/kg diet), or DHEA + tamoxifen + carbenoxolone. When administered alone at either 800 or 400 mg/kg diet, DHEA reduced mammary cancer incidence from >70% in dietary controls to 0%; mammary cancer incidence from >70% in dietary controls to 0%; mammary cancer incidence in all DHEA combination regimens was also < or = 5%. The dose levels of DHEA used induced no toxicity or alteration in body weight gain. These results indicate that dietary supplementation with low doses of DHEA has chemopreventive efficacy greater than or equal to that of endocrine ablation. This protection may be mediated by the induction of differentiation in the mammary parenchyma.
New Two-Photon Absorbing Fluorene Derivatives:  Synthesis and Nonlinear Optical Characterization (1999)

Efficient Pd-catalyzed Heck coupling methodology was employed to provide two new fluorene derivatives with phosphonate (2) and nitro (3) electron-withdrawing functionalities. Both derivatives exhibit two-photon absorption (2PA), as determined by nonlinear absorption measurements using a femtosecond pump/white light continuum probe “NLO spectrometer”. Both fluorene derivatives have high 2PA cross sections (650 and 1300 × 10-50 cm4 s photon-1 molecule-1 for compounds 2 and 3, respectively).
Grape seed extract (Vitis vinifera) partially reverses high fat diet-induced obesity in C57BL/6J mice (2008)

The aim of the present study was to assess the anti-obesity effects of grape seed extract (GSE) supplement in C57BL/6J mice. Thirty mice were divided into three groups; normal diet control group (ND), high fat diet control group (HD) and high fat diet plus grape seed extract supplemented group (HD+GSE). Results were as follows: 1. GSE supplement reduced the weight gain in mice fed high fat diets; epididymal and back fat weights were lower compared to non-supplemented HD group. 2. Blood lipid concentrations were lower in the HD+GSE group than in the HD group. Serum HDL-C concentrations were higher in the HD+GSE group compared with the other groups. 3. The concentrations of acid-insoluble acylcarnitines (AIAC) in serum and liver were higher in the HD+GSE group than in the HD group. 4. GSE supplementation increased mRNA levels of lipolytic genes such as carnitine palmitoyltransferase-1 (CPT-1) and decreased mRNA levels of lipogenic genes such as acetyl CoA carboxylase (ACC). These findings suggest that grape seed extract supplements in high fat diet might normalize body weight, epididymal and back fat weights, lipid concentrations, and carnitine levels through controlling lipid metabolism.
Microtubule assembly dynamics: An attractive target for anticancer drugs (2008)

Microtubules, composed of alphabeta tubulin dimers, are dynamic polymers of eukaryotic cells. They play important roles in various cellular functions including mitosis. Microtubules exhibit differential dynamic behaviors during different phases of the cell cycle. Inhibition of the microtubule assembly dynamics causes cell cycle arrest leading to apoptosis; thus, qualifying them as important drug targets for treating several diseases including cancer, neuronal, fungal, and parasitic diseases. Although several microtubule-targeted drugs are successfully being used in cancer chemotherapy, the development of resistance against these drugs and their inherent toxicities warrant the development of new agents with improved efficacy. Several antimicrotubule agents are currently being evaluated for their possible uses in cancer chemotherapy. Benomyl, griseofulvin, and sulfonamides have been used as antifungal and antibacterial drugs. Recent reports have shown that these drugs have potent antitumor potential. These agents are shown to inhibit proliferation of different types of tumor cells and induce apoptosis by targeting microtubule assembly dynamics. However, unlike vincas and taxanes, which inhibit cancer cell proliferation in nanomolar concentration range, these agents act in micromolar range and are considered to have limited toxicities. Here, we suggest that these drugs may have a significant use in cancer chemotherapy when used in combination with other anticancer drugs.
Modification of cerebral ischemia with Fluosol. (1985)

Fluosol-DA (Perfluorochemical Blood Substitute) was investigated in a previous study and found to provide some protection from ischemia and possible usefulness in limiting the size of infarction. In the present study, larger doses over longer periods of acute focal cerebral ischemia were used. Twenty four cats had transorbital ligation of the middle cerebral artery (MCA). The 12 experimental animals were given 20% Fluosol-DA. The control group of 12 received isotonic saline solution. Twenty-four hours after the MCA occlusion, the cats were perfused with saline and phosphate-buffered formalin. The brains were removed and immersed in 10% formalin for 2 weeks. The results of macroscopic and histological examination suggested that, although Fluosol-DA did not provide complete protection from ischemic injury to the brains of the cats treated, it may have helped to slow the development of the pathological changes.
Computer‐generated three‐dimensional reconstructions of serially sectioned mouse embryos (1998)

We have been involved with a group of computer scientists and anatomists in the development of computer-based methodologies that not only combine the advantages of scanning electron microscopy and conventional histology, but provide the additional dimension of tissue recognition. The latter is achieved by the appropriate labelling of tissues and structures by delineation or 'painting'. Individually segmented anatomically defined tissues can be highlighted in a particular colour and viewed either in isolation or in combination with other appropriately labelled tissues and organs. Tissues can be shown in any orientation either as a transparent overlay on computer-generated histological sections or as 3-D images without the histological background. An additional feature of the system is that computer graphics technology combined with 3-D glasses now also allows the viewer to see the object under analysis in stereo. This facility has been found to be particularly helpful in drawing attention to topological relationships that had not previously been readily noted. As the mouse is now the mammalian model of choice in many areas of developmental research, it is of critical importance that a basic level of skill is available in the research community in the interpretation of serially sectioned material, for example, for the rapidly expanding field in which gene expression studies play a significant role. It is equally important that there is an understanding of the dynamic changes that occur in relation to the differentiation of the various organ systems seen in these early stages of development. What we emphasise here is the additional information that it is possible to gain from the use of this tool which, in our view, could not readily have been gained from the analysis of scanning electron micrographs or by studying conventional serial histological sections of similar stages of mouse embryonic development. The methodology has been developed as part of a large project to prepare a database of mouse developmental anatomy covering all stages from fertilisation to birth in order to allow the accurate spatial mapping of gene expression and cell lineage data onto the digital Atlas of normal mouse development. In this paper we show how this digital anatomical Atlas also represents a valuable teaching aid and research tool in anatomy.
Distributed turbo coded diversity for relay channel (2003)

A novel coding technique is proposed for the quasi-static fading relay channel. The source broadcasts a recursive code to both relay and destination. The relay decodes, interleaves, and re-encodes the message prior to forwarding. Because the destination receives both codes in parallel, a distributed turbo code is embedded in the relay channel. Results indicate a combined diversity and coding gain, which is significant even for simple constituent codes.
Methicillin-resistant Staphylococcus aureus bacteremia in children (1986)

We reviewed the records of 20 patients with bacteremia caused by methicillin-resistant Staphylococcus aureus (MRSA) and 49 patients with methicillin-susceptible S. aureus (MSSA) bacteremia occurring during a 39-month period. Sixteen of the MRSA bacteremias were clinically significant, as were 42 of the MSSA bacteremias. MRSA bacteremia was almost always nosocomial and occurred mainly in very young patients who were often prematurely born and severely compromised by underlying diseases. In contrast patients with MSSA bacteremia were frequently older children who had no underlying disease and acquired their bacteremic illness in the community. The seven patients with nosocomial MSSA bacteremia had characteristics similar to those of the patients with MRSA bacteremia. Fatality rates for patients with clinically significant bacteremia were 50% for MRSA and 2% for MSSA. Treatment of MRSA bacteremia with vancomycin was effective, provided it was begun early. At hospitals with endemic MRSA it may be necessary to use vacomycin in the initial treatment of nosocomial bacteremia in high risk patients until the identity and antimicrobial susceptibility of the bloodstream pathogen can be determined.
Universal Linkage System: versatile nucleic acid labeling technique (2001)

Over the last two decades nonradioactive nucleic acid labeling and detection systems have overcome the safety, disposal, stability and cost problems that are associated with radioactive techniques. Besides traditional, enzyme-mediated, nonradioactive labeling methods (e.g., random priming, nick translation or labeling by PCR), several chemical labeling systems have been developed (e.g., ULS, psoralen, alkylating agents). These methods provide fluorescent (or hapten) labeled probes for fluorescence in situ hybridization (FISH), comparative genomic hybridization (CGH) and microarray-based techniques. In this review the DNA-based molecular diagnostic applications and perspectives of the Universal Linkage System (ULS) technology will be described.
Nasal airway positive pressure in patients with occlusive sleep apnea. Methods and feasibility. (1984)

Nasal airway positive pressure (NAPP) effectively eliminates obstructive sleep apnea. This report describes construction and evaluation of a convenient NAPP apparatus used successfully in 15 patients with obstructive sleep apnea. An impeller blower with high flow, low pressure characteristics delivers room air to a flow divider and then to an injector attached to a custom-fitted nose mask. Of the total naris pressure supplied by the system, a large fraction derives from the kinetic energy of the air stream delivered to the naris by the injectors. This, together with the high flow rate of the system, promotes a constant naris pressure. Naris pressure is determined by the size of the flow divider and the aperture of the exhaust port(s) of the injector. A series of 10 flow divider-injector combinations are described that provide a variety of naris pressures between 2.5 and 13.6 cm H2O. Fourteen of 15 patients found the NAPP apparatus acceptable and effective. No maintenance or repair appears to be required.
Surgical Treatment of Pancreatic Cancer (2008)

Pancreatic cancer is an aggressive disease with an overall 5-year survival rate of less than 5%. Up to date, surgical resection represents the basis of treatment for localized pancreatic cancer and remains the only chance for cure. Due to continuous improvements in surgical techniques and perioperative care, pancreatic resections have evolved into safe surgical procedures with low mortality and acceptable morbidity rates for experienced surgeons in high-volume centers. Recently, more aggressive approaches including extended lymphadenectomy, vascular resection, surgery for metastastic or recurrent disease, and multimodal regimens have been suggested to improve long-term outcome. This article provides an overview on current standard procedures and summarizes new strategies in the surgical treatment of pancreatic cancer.