gebhart/patrepeval huggingface dataset:
Cell surface proteoglycan associates with the cytoskeleton at the basolateral cell surface of mouse mammary epithelial cells. (1986)

The cell surface proteoglycan on normal murine mammary gland mouse mammary epithelial cells consists of an ectodomain bearing heparan and chondroitin sulfate chains and a lipophilic domain that is presumed to be intercalated into the plasma membrane. Because the ectodomain binds to matrix components produced by stromal cells with specificity and high affinity, we have proposed that the cell surface proteoglycan is a matrix receptor that binds epithelial cells to their underlying basement membrane. We now show that the proteoglycan surrounds cells grown in subconfluent or newly confluent monolayers, but becomes restricted to the basolateral surface of cells that have been confluent for a week or more; Triton X-100 extraction distinguishes three fractions of cell surface proteoglycan: a fraction released by detergent and presumed to be free in the membrane, a fraction bound via a salt-labile linkage, and a nonextractable fraction; the latter two fractions co-localize with actin filament bundles at the basal cell surface; and when proteoglycans at the apical cell surface are cross-linked by antibodies, they initially assimilate into detergent-resistant, immobile clusters that are subsequently aggregated by the cytoskeleton. These findings suggest that the proteoglycan, initially present on the entire surface and free in the plane of the membrane, becomes sequestered at the basolateral cell surface and bound to the actin-rich cytoskeleton as the cells become polarized in vitro. Binding of matrix components may cross-link proteoglycans at the basal cell surface and cause them to associate with the actin cytoskeleton, providing a mechanism by which the cell surface proteoglycan acts as a matrix receptor to stabilize the morphology of epithelial sheets.
Construction and characterization of a phage-plasmid hybrid (phagemid), pCAK1, containing the replicative form of viruslike particle CAK1 isolated from Clostridium acetobutylicum NCIB 6444 (1993)

A bacteriophage-plasmid hybrid (phagemid) designated pCAK1 was constructed by ligating 5-kbp Escherichia coli plasmid pAK102 (AprEmr) and the 6.6-kbp HaeIII-linearized replicative form of the CAK1 viruslike particle from Clostridium acetobutylicum NCIB 6444. Phagemid pCAK1 (11.6 kbp) replicated via the ColE1 replication origin derived from pAK102 in E. coli. Single-stranded DNA (ssDNA) molecules complexed with protein in a manner which protected ssDNA from nucleases were recovered from the supernatant of E. coli DH11S transformants containing pCAK1 in the absence of cell lysis. This suggests that the viral-strand DNA synthesis replication origin of CAK1 and associated gene expression are functional in E. coli DH11S. The single-stranded form of pCAK1 isolated from E. coli supernatant was transformed into E. coli DH5 alpha' or DH11S by electroporation. Isolation of ampicillin-resistant E. coli transformants following transformation suggests that the complementary-strand DNA synthesis replication origin of CAK1 is also functional in E. coli. The coat proteins associated with ssDNA of pCAK1 demonstrated sensitivity to proteinase K and various solvents (i.e., phenol and chloroform), similar to the results obtained previously with CAK1. Following phagemid construction in E. coli, pCAK1 was transformed into C. acetobutylicum ATCC 824 and C. perfringens 13 by intact cell electroporation. Restriction enzyme analysis of pCAK1 isolated from erythromycin-resistant transformants of both C. acetobutylicum and C. perfringens suggested that it was identical to that present in E. coli transformants.
Liquid Chromatography: Applications (2013)

This is a single source of authoritative information on all aspects of the practice of modern liquid chromatography suitable for advanced students and professionals working in a laboratory or managerial capacity. It features chapters that are written by authoritative and visionary experts in the field provide an overview and focused treatment of a single topic. Each chapter emphasizes the integration of chromatographic methods and sample preparation, automation, and explains how liquid chromatography is used in different industrial sectors. It focuses on expanding and illustrating the main features of the fundamental section, while demonstrating where and how the best practices of liquid chromatography are utilized. It includes a comprehensive coverage of modern liquid chromatography from theory, to methods, to selected applications. Thorough selected references and tables with commonly used data to facilitate research, practical work, comparison of results, and decision making.
Design, construction, and in vitro analysis of A33scFv::CDy, a recombinant fusion protein for antibody-directed enzyme prodrug therapy in colon cancer (2007)

Antibody-directed enzyme-prodrug therapy (ADEPT) aims at improving the specificity of conventional chemotherapy by employing artificial antibody-enzyme constructs to convert a non-toxic prodrug into a cytotoxic agent specifically localized to the tumor site. The gpA33 antigen is a promising target for ADEPT in colon cancer, as it is expressed by >95% of human colon cancers, but is absent in all non-gastrointestinal tissues. We designed a recombinant fusion construct of a phage display-generated anti-gpA33 single chain fragment, A33scFv, with cytosine deaminase from yeast (CDy), which converts 5-fluorocytosine (5-FC) into 5-fluorouracil (5-FU). The resulting construct, A33scFv::CDy, was overexpressed in Pichia pastoris and secreted into culture supernatant. The fusion protein was purified by affinity chromatography on protein L. Silver-staining after SDS-polyacrylamide gel electrophoresis confirmed molecular mass and purity. Antibody binding and specificity were quantified by flow cytometry. The complete ADEPT system was applied in vitro on gpA33-positive LIM1215 cells, assessing cell survival by a fluorescein diacetate assay. Cytotoxicity of the prodrug 5-FC after A33scFv::CDy binding was equimolar to that of 5-FU, and this effect depended specifically on both antibody and enzyme function. These results demonstrate bifunctional activity of the heterogeneous Pichia-produced A33scFv::CDy fusion protein and proof of principle for the ADEPT system proposed herein.
Efficient Synthesis and Biological Evaluation of 5′-GalNAc Conjugated Antisense Oligonucleotides (2015)

Conjugation of triantennary N-acetyl galactosamine (GalNAc) to oligonucleotide therapeutics results in marked improvement in potency for reducing gene targets expressed in hepatocytes. In this report we describe a robust and efficient solution-phase conjugation strategy to attach triantennary GalNAc clusters (mol. wt. ∼2000) activated as PFP (pentafluorophenyl) esters onto 5'-hexylamino modified antisense oligonucleotides (5'-HA ASOs, mol. wt. ∼8000 Da). The conjugation reaction is efficient and was used to prepare GalNAc conjugated ASOs from milligram to multigram scale. The solution phase method avoids loading of GalNAc clusters onto solid-support for automated synthesis and will facilitate evaluation of GalNAc clusters for structure activity relationship (SAR) studies. Furthermore, we show that transfer of the GalNAc cluster from the 3'-end of an ASO to the 5'-end results in improved potency in cells and animals.
Damage detection with small data set using energy-based nonlinear features (2015)

This study proposes a new algorithm for damage detection in structures. The algorithm employs an energy-based method to capture linear and nonlinear effects of damage on structural response. For more accurate detection, the proposed algorithm combines multiple damage sensitive features through a distance-based method by using Mahalanobis distance. Hypothesis testing is employed as the statistical data analysis technique for uncertainty quantification associated with damage detection. Both the distance-based and the data analysis methods have been chosen to deal with small size data sets. Finally, the efficacy and robustness of the algorithm are experimentally validated by testing a steel laboratory prototype, and the results show that the proposed method can effectively detect and localize the defects. Copyright © 2015 John Wiley & Sons, Ltd.
Natural killer cells (2014)

Natural killer (NK) cells constitute our bodies' frontline defense system, guarding against tumors and launching attacks against infections. The activities of NK cells are regulated by the interaction of various receptors expressed on their surfaces with cell surface ligands. While the role of NK cells in controlling tumor activity is relatively clear, the fact that they are also linked to various other disease conditions is now being highlighted. Here, we present an overview of the role of NK cells during normal body state as well as under diseased state. We discuss the possible utilization of these powerful cells as immunotherapeutic agents in combating diseases such as asthma, autoimmune diseases, and HIV-AIDS. This review also outlines current challenges in NK cell therapy.
Rabbit Liver Phosphofructokinase (1971)

A relatively simple procedure was devised for the purification of phosphofructokinase from rabbit liver extracts. The enzyme was purified more than 2600-fold with a yield of close to 50%. Liver phosphofructokinase migrates faster on zone electrophoresis than rabbit skeletal muscle phosphofructokinase. It also differs from muscle enzyme in stability, molecular weight, and kinetic properties. The liver enzyme behaves on Sepharose chromatography as a polymer of various states of aggregation with the largest aggregate having a particle weight of many millions. A comparison of the kinetic properties of liver and muscle phosphofructokinase revealed similarities in pH optimum, cation activation, and substrate affinity at pH 8.2. On the other hand, striking differences in kinetic control properties were observed at pH 7.0. The liver enzyme was more inhibited by ATP, less sensitive to the deinhibiting action of AMP, ADP, and cyclic 3',5'-AMP, less inhibited by citrate, phosphoenolpyruvate, phosphocreatine, 2-phosphoglycerate, and 3-phosphoglycerate, and more inhibited by 2,3-diphosphoglycerate than muscle phosphofructokinase. The results suggest that liver phosphofructokinase is less suited for anaerobic energy production than the skeletal muscle enzyme and may not be subject to the same control mechanism in vivo.
Electroorganic synthesis : A novel route of green synthesis (2009)

Electrochemical Laboratory of Green Synthesis, Department of Chemistry, University of Allahabad, Allahabad-211 002, Uttar Pradesh, India <em>E-mail</em> : rkp.singh@rediffmail.com Fax : 91-532-2461157 <em>Manuscript received 17 April 2009, accepted 3 July 2009</em> Electroorganic synthesis of alkanes, alkenes and esters by anodic decarboxylation of potassium salt of palmitic acid, stearic acid, lauric acid and myristic acid, amines by reduction of aromatic nitro compounds, pinacols by reduction of carbonyl compounds, aromatic dimmers by oxidation of aromatic amines, 1,3,4-oxadiazole derivatives by electrocyclization of semicarbazone and acylthiosemicarbazone, aldol condensation of aldehydes, and acetamidation of aromatic compounds were carried out at platinum plate in undivided electrochemical cell at desired potential using simple solvent and supporting electrolyte. All the reactions were carried out at room temperature by using small amount of electricity without involvement of toxic chemicals.
Manual Differential Cell Counts Help Predict Bacterial Infection (2001)

We developed logistic regression models that combine information from the automated CBC and manual 100-cell differential counts to predict bacterial infection. The logistic models were fitted from a case group of 116 patients with proven bacterial infection and a control group of 930 presumably uninfected outpatients. A 4-variable, 15-parameter model, which includes automated absolute neutrophil, manual band, and manual immature granulocyte counts, performed best with a receiver operating characteristic (ROC) curve area of 89%. A more practical 2-variable model including automated absolute neutrophil and manual band counts performed almost as well with an ROC curve area of 86%. The automated neutrophil count-only model is less informative with an ROC curve area of 78%. The combined information from automated and manual differential cell counts more accurately predicts bacterial infection than automated counting alone. Despite these modest improvements, the high cost of manual differential cell counts dictates careful patient selection. The supplemental information gained from manual differential counts is most useful for patients with low to normal neutrophil counts (8,000/microL [8.0 x 10(9)/L] or less). Further studies are indicated to determine the characteristic patient populations deriving maximal benefit from this information.
Mesenchymal Stem Cells in Perichondrium Express Activated Leukocyte Cell Adhesion Molecule and Participate in Bone Marrow Formation (2002)

Perichondrium in fetal limb is composed of undifferentiated mesenchymal cells. However, the multipotency of cells in this region and the role of perichondrium in bone marrow formation are not well understood. In this report, we purified and characterized perichondrial cells using a monoclonal antibody against activated leukocyte cell adhesion molecule (ALCAM) and investigated the role of perichondrial cells in hematopoietic bone marrow formation. ALCAM is expressed on hematopoietic cells, endothelial cells, bone marrow stromal cells, and mesenchymal stem cells and mediates homophilic (ALCAM-ALCAM)/heterophilic (ALCAM-CD6) cell adhesion. Here we show by immunohistochemical staining that ALCAM is expressed in perichondrium. ALCAM+ perichondrial cells isolated by FACS exhibit the characteristics of mesenchymal stem cells. ALCAM+ cells can differentiate into osteoblasts, adipocytes, chondrocytes, and stromal cells, which can support osteoclastogenesis, hematopoiesis, and angiogenesis. Furthermore, the addition of ALCAM-Fc or CD6-Fc to the metatarsal culture, the invasion of the blood vessels to a cartilage was inhibited. Our findings indicate that ALCAM+ perichondrial cells participate in vascular invasion by recruiting osteoclasts and vessels. These findings suggest that perichondrium might serve as a stem cell reservoir and play an important role in the early development of a bone and bone marrow.
Antithrombotic and antineoplastic effects of phyto‐organosulfur compounds (2000)

The antiplatelet activity of methyl allyltrisulfide (MATS), a component commonly present in steam-distilled garlic oil, has been demonstrated by the authors. MATS inhibits arachidonic acid cascade at the reaction site with PGH synthase. However, this enzyme catalyzes two successive reactions, from arachidonic acid to PGG2, and from PGG2 to PGH2. The present study revealed that MATS inhibited the latter reaction. In addition, our recent findings that to a promyelocytic leukemia cell HL60, Allium oils shows marked anti-neoplastic effects representing both growth suppression and differentiation activities are described. The garlic oil and onion oil showed almost equal ability in inducing the proliferation, which measured either by nitroblue-tetrazolium reducing activity assay or by flow cytometry for detecting CD11b expression. The combination use of one of these oils with all-trans retinoic acid or with dimethyl sulfoxide lead to the marked differentiation of the cells, and their effects were estimated to be synergistic.
Algorithms for automatic guided vehicle navigation and guidance based on linear image array sensor data (1988)

Algorithms for path planning of an automatic guided vehicle (hereafter referred to as AGV) using data from a Linear Image Array camera (hereafter referred to as LIAC) are outlined in this dissertation. The use of LIAC data for tracking two guidelines on a factory pathway in order to derive a map of the immediate areas around the AGV is shown.
The prior forms of path sensing and planning systems for an AGV are briefly described, and compared to the requirements for stable control of a practical system. The system requirements are given, based on control stability, robot performance, and execution time for the algorithms.
Based on these requirements, an architecture for a path planner using LIAC data is described with the required algorithms. Conceptually shown as three processor systems (vision, path planning, and motion control), the architecture data rates are shown to match the system requirements for real time guidance of the AGV.
The algorithms for the path planning are described, with changes to the existing algorithms given to improve execution speed from 20 minutes to roughly 20 seconds for planning a route. The known obstacles are avoided by this algorithm, with time delayed penalties within the world model. Unknown obstacles are detected from the sensor data and either passed or retreated from based on the estimate of the obstacle region. The information on the area around the AGV is then used to provide continuous data to the motion control processor through the use of spline functions. The motion processor uses the spline functions at a higher sample rate to control the AGV motors and estimate the world position.
Binol Quinone Methides as Bisalkylating and DNA Cross-Linking Agents (2004)

The photogeneration and detection of new binol quinone methides undergoing mono- and bisalkylation of free nucleophiles was investigated by product distribution analysis and laser flash photolysis in water solution using binol quaternary ammonium derivatives 2 and 12 as photoactivated precursors. The alkylation processes of N and S nucleophiles are strongly competitive with the hydration reaction. DNA cross-linking potency of the water-soluble binol quaternary ammonium salt 2 was investigated as a pH function and compared to that of other quaternary ammonium salts capable of benzo-QM (QM = quinone methide) photogeneration by gel electrophoresis. DFT calculations in the gas phase and in water bulk on the binol and benzo quaternary ammonium salts 2 and 4 evidence structural and electrostatic features of the binol derivative which might offer a rationalization of its promising high photo-cross-linking efficiency.
Topographic patterns of brain activity in response to swim stress: assessment by 2-deoxyglucose uptake and expression of Fos-like immunoreactivity (1993)

Alterations in brain activity patterns were assessed in response to swim stress by immunocytochemical detection of Fos-like immunoreactivity (Fos-LI) and high-resolution autoradiographic imaging of 14C-2-deoxyglucose (2-DG) uptake. The stress paradigm investigated was a classic behavioral screen for antidepressant drug activity, the forced swim test. One of the most pronounced effects produced by swim stress was an increase in 2-DG uptake and induction of Fos-LI in a restricted region of the lateral septal nucleus. Specific "limbic" cortical regions, including the medial prefrontal, ventrolateral orbital, and cingulate cortices, also exhibited both increased 2-DG uptake and expression of Fos-LI in response to swim stress. In the hypothalamic paraventricular nucleus of swim-stressed rats, Fos-LI was induced but no change in 2-DG uptake was apparent. Since the specific swim stress protocol used is a behavioral screen for antidepressant drugs, the effects of imipramine on stress-induced alterations in 2-DG uptake and induction of Fos-LI were examined. The stress-induced increase in 2-DG uptake in the lateral septum was blocked by treatment with imipramine, but treatment with imipramine had no effect on induction of Fos-LI in the same region. Neither 2-DG uptake nor Fos-LI expression was altered by imipramine treatment in the cortical regions influenced by swim stress. Administration of imipramine alone under basal conditions produced a robust induction of Fos-LI in the central nucleus of the amygdala and in the dorsal lateral subdivision of the bed nucleus of the stria terminalis. No effect of imipramine treatment on 2-DG uptake was apparent in these latter regions. The results provide insights into topographic patterns of brain activity associated with swim stress and neuroanatomically selective actions of imipramine. The different and complementary information obtained by assessment of Fos-LI and 2-DG uptake illustrates the utility of applying both functional mapping approaches to examine neuroanatomical correlates of behavioral states and drug treatment.
Nocturnal assisted ventilation using bilevel positive airway pressure: the effect of expiratory positive airway pressure (1995)

Increasing expiratory positive airway pressure (EPAP) has theoretical advantages during overnight nasal ventilation. We wanted to evaluate the effect of the addition of EPAP upon the control of nocturnal hypoventilation. Seven patients with neuromuscular/skeletal (NMS) disorder (mean +/- SD forced vital capacity (FVC) 1.06 +/- 0.28 l, arterial oxygen tension (PaO2) 9.1 +/- 0.6 kPa, and arterial carbon dioxide tension (PaCO2) 6.9 +/- 0.9 kPa), and seven patients with chronic obstructive pulmonary disease (COPD) (FEV1 0.46 +/- 0.14 l, PaO2 6.2 +/- 0.6 kPa, and PaCO2 8.4 +/- 1.1 kPa) all underwent full polysomnography on two nights during bilevel positive airway pressure (BiPAP) ventilation, with and without the addition of expiratory positive airway pressure, which was matched to the level of dynamic positive end-expiratory pressure (PEEP) or set at a minimum value of 5 cmH2O. In the group with neuromuscular/skeletal disorders the maximum transcutaneous carbon dioxide tension (PtcCO2) overnight was lower (inspiratory positive airway pressure (IPAP) 8.1 +/- 1.4 kPa, IPAP/EPAP 7.3 +/- 0.9 kPa) and the minimum level of arterial oxygen saturation (SaO2 min) increased (IPAP 77.1 +/- 6.7%, IPAP/EPAP 83.6 +/- 4.2%) when expiratory positive airway pressure was added. There were no differences in mean PtcCO2 or mean oxygen saturation, but sleep quality was worse (non-rapid eye movement (non-REM) sleep IPAP 266 +/- 44 min, IPAP/EPAP 226 +/- 32 min). In the patients with COPD, expiratory positive airway pressure conferred no advantage.(ABSTRACT TRUNCATED AT 250 WORDS)
Drug-Coupled Poly(Amino Acids) as Polymeric Prodrugs (1988)

Biodegradable poly(α-amino acids) can serve as chemical carriers of active agents. The narcotic antagonist naltrexone and the anti-hypertensive minox idil were covalently coupled to polymer backbones based upon L-glutamic acid to give polymeric prodrugs. The synthesis and release characteristics of these two systems are reviewed. The rate of hydrolytic cleavage of the polymer-drug linkage should be much slower than the rate of diffusion through the polymer matrix; thus release rates approaching zero order can be achieved. In vitro and in vivo release studies demonstrate the potential for these types of polymeric delivery systems.
Prognostic value of simultaneous expression of p21 and mdm2 in breast carcinomas treated by adjuvant chemotherapy with antracyclin. (2000)

One hundred and sixty-two breast carcinomas treated by adjuvant chemotherapy were investigated in immunohistochemistry for expression of p53 and two wild-type p53-regulated induced proteins, mdm2 and p21/waf1. p21 and mdm2 were expression stongly correlated with Ki67 but not with survival. The p53+/p21+, p53+/p21- and p53+/mdm2- phenotypes were associated with the worst prognosis. The p53+/p21+/ mdm2+ tumors were associated with a better outcome than the other phenotypes, they may be tumors expressing wild-type p53 and p21, and a form of mdm2 that might lead to the stabilization of p53. It is suggested that p21/mdm2 expression should be investigated in all cases of p53 positive breast cancer.