gebhart/patrepeval huggingface dataset:
Salt tolerant membrane adsorbers for robust impurity clearance (2009)

Clearance of impurities such as viruses, host cell protein (HCP), and DNA is a critical purification design consideration for manufacture of monoclonal antibody therapeutics. Anion exchange chromatography has frequently been utilized to accomplish this goal; however, anion exchange adsorbents based on the traditional quaternary amine (Q) ligand are sensitive to salt concentration, leading to reduced clearance levels of impurities at moderate salt concentrations (50-150 mM). In this report, membrane adsorbers incorporating four alternative salt tolerant anion exchange ligands were examined for impurity clearance: agmatine, tris-2-aminoethyl amine, polyhexamethylene biguanide (PHMB), and polyethyleneimine. Each of these ligands provided greater than 5 log reduction value (LRV) for viral clearance of phage phiX174 (pI approximately 6.7) at pH 7.5 and phage PR772 (pI approximately 4) at pH 4.2 in the presence of salt. Under these same conditions, the commercial Q membrane adsorber provided no clearance (zero LRV). Clearance of host-cell protein at pH 7.5 was the most challenging test case; only PHMB maintained 1.5 LRV in 150 mM salt. The salt tolerance of PHMB was attributed to its large positive net charge through the presence of multiple biguanide groups that participated in electrostatic and hydrogen bonding interactions with the impurity molecules. On the basis of the results of this study, membrane adsorbers that incorporate salt tolerant anion exchange ligands provide a robust approach to impurity clearance during the purification of monoclonal antibodies.
The Database of Ribosomal Cross links (DRC) (1998)

The Database of Ribosomal Cross-links (DRC) provides a complete collection of all the published data produced by cross-linking studies on the Escherichia coli ribosome, as well as on its components and functional ligands. The DRC currently includes data on 986 cross-links from >100 research papers, yielded by >40 different reagents. For each cross-link, information is given concerning its location in the ribosome, the chemical or photochemical reagent applied, a brief description of the method(s) used to locate the cross-link, and the literature reference. The DRC is freely available via the World Wide Web at: http://Ribosome.Genebee.MSU.SU/DRC/ or at http://WWW:MPIMG-Berlin-Dahlem.MPG.DE/[symbol: see text]baranov/DRC/
Functional and Molecular Changes in Colony Stimulating Factor Secretion by Osteoblasts (1989)

Two populations of primary osteoblasts and the cloned murine osteoblast cell line MC3T3 were activated with osteotropic agents and the conditioned media tested for the presence of macrophage colony stimulating factor (M-CSF). Differences in ability of the three populations to secrete the cytokine as well as in the efficacy of the activating agents used to induce it were observed. The ability of these agents to modulate M-CSF mRNA levels was also examined. The data indicate that osteoblasts do not respond uniformly and the reasons for this are discussed. Osteoblasts may exert major regulatory influences on hematopoiesis via CSF secretion as well as function in their more traditional role as the cells responsible for new bone formation.
Thermal and mechanical analysis of an SU8 polymeric actuator using infrared thermography (2008)

In the current paper, report the detailed thermomechanical analysis of a polymeric thermal actuator integrated in a microelectromechanical systems microgripper, is reported. The inclusion of an actuator design which eliminates completely the parasitic resistance of the cold arm improves considerably the thermal efficiency of the system and enables large displacements at lower input voltages and operating temperatures than reported previously. Two different microgrippers built using a trilayer polymer/metal/polymer combination of SU8/gold/SU8 have been modelled, fabricated, and tested. As opposed to standard models, heat transfer by conduction to the ambient as well as between adjacent beams has been modelled. A semi-empirical approach for the calculation of conductive heat transfer coefficients has also been provided. The analysis combines simulations with electrical, deflection, and spatially resolved temperature measurements. The latter was carried out using infrared thermography, its use in polymeric actuators reported here for the first time. The good agreement between the models and the experimental data support the conclusions of the basic analytical model, i.e. thermal losses are dominated by two conduction mechanisms (into the ambient and between the hot and cold arms), and encourage its use for qualitative thermal design assessment and optimization.
Occurrence of Groups A and B of Respiratory Syncytial Virus over 15 Years: Associated Epidemiologic and Clinical Characteristics in Hospitalized and Ambulatory Children (1990)

Over 15 years respiratory syncytial virus (RSV) isolates from 1209 hospitalized and ambulatory children were examined for strain group and in a subset for subgroup to determine the associated epidemiologic and clinical characteristics. Three patterns of yearly outbreaks existed: (1) strong predominance of group A strains (9 years with 83%-100% A strains), (2) relatively equal proportions of group A and B strains (4 years), and (3) strong predominance of group B strains (78%-85%) in 2 years, separated by a decade. The first pattern of highly dominant A strains occurred in cycles of 1 or 2 consecutive years with a single intervening year in which B strains were greater than or equal to 40% of the isolates. Subgroups A1 and A2 predominated, while B2, 3, and 4 occurred almost equally. A greater clinical severity for Group A strains was suggested by children with group A infections requiring intensive care significantly more often (15.4 vs. 8.3%, P = .008). Further, strongly dominant A strain years were associated with higher proportions of RSV admissions requiring intensive care (16.6% vs. 5.5%, P less than .01). Strains of subgroups A2 and B4 were more frequently found in hospitalized patients and A1 in outpatients, and the 2 years with the highest rates of intensive care admissions were those in which subgroup A2 dominated.
Gene expression data analysis (2000)

Microarrays are one of the latest breakthroughs in experimental molecular biology, which allow monitoring of gene expression for tens of thousands of genes in parallel and are already producing huge amounts of valuable data. Analysis and handling of such data is becoming one of the major bottlenecks in the utilization of the technology. The raw microarray data are images, which have to be transformed into gene expression matrices--tables where rows represent genes, columns represent various samples such as tissues or experimental conditions, and numbers in each cell characterize the expression level of the particular gene in the particular sample. These matrices have to be analyzed further, if any knowledge about the underlying biological processes is to be extracted. In this paper we concentrate on discussing bioinformatics methods used for such analysis. We briefly discuss supervised and unsupervised data analysis and its applications, such as predicting gene function classes and cancer classification. Then we discuss how the gene expression matrix can be used to predict putative regulatory signals in the genome sequences. In conclusion we discuss some possible future directions.
Clinical significance of defective dendritic cell differentiation in cancer. (2000)

Defective dendritic cell (DC) function has been described previously in cancer patients and tumor-bearing mice. It can be an important factor in the escape of tumors from immune system control. However, the mechanism and clinical significance of this phenomenon remain unclear. Here, 93 patients with breast, head and neck, and lung cancer were investigated. The function of peripheral blood and tumor draining lymph node DCs was equally impaired in cancer patients, consistent with a systemic rather than a local effect of tumor on DCs. The number of DCs was dramatically reduced in the peripheral blood of cancer patients. This decrease was associated with the accumulation of cells lacking markers of mature hematopoietic cells. The presence of these immature cells was closely associated with the stage and duration of the disease. Surgical removal of tumor resulted in partial reversal of the observed effects. The presence of immature cells in the peripheral blood of cancer patients was closely associated with an increased plasma level of vascular endothelial growth factor but not interleukin 6, granulocyte macrophage colony-stimulating factor, macrophage colony-stimulating factor, interleukin 10, or transforming growth factor-beta and was decreased in lung cancer patients receiving therapy with antivascular endothelial growth factor antibodies. These data indicate that defective DC function in cancer patients is the result of decreased numbers of competent DCs and the accumulation of immature cells. This effect may have significant clinical implications.
Basics of Color in Dentistry: A Review (2014)

Think of the world without the color. Color can turn everything, even the unsightly, into a visual pleasure. Properly used, color creates atmosphere, defines space and proportion, establishes order and exudes emotion. To perceive all these one has to have the so-called color sense. (i.e. the ability to make the right color choice). Colored restoration or prostheses should impart the translucency and fluorescence of natural dentition, and reproduce the opacity and vitality of natural tooth structure. The practicing dentist apparently accommodates to the environmental influences of light and color in his surroundings to the extent that he is able to correct the color of the restoration or prosthesis to his own satisfaction and to that of his patients. In esthetic dentistry, the focus is on merging function and beauty with the values and the individual needs of the patient. The color of a restoration or prosthesis to surrounding teeth may be the only parameter of treatment with which the patient is concerned. It is often media driven and can result in a desire for excessively white and bright natural teeth that enhance the face, but do not attract unwarranted attention.
Preclinical In Vivo Evaluation of the Safety of a Multi-shRNA-based Gene Therapy Against HIV-1 (2013)

Highly active antiretroviral therapy (HAART) has significantly improved the quality of life and the life expectancy of HIV-infected individuals. Still, drug-induced side effects and emergence of drug-resistant viral variants remain important issues that justify the exploration of alternative therapeutic options. One strategy consists of a gene therapy based on RNA interference to induce the sequence-specific degradation of the HIV-1 RNA genome. We have selected four potent short hairpin RNA (shRNA) candidates targeting the viral capside, integrase, protease and tat/rev open-reading frames and screened the safety of them during human hematopoietic cell development, both in vitro and in vivo. Although the four shRNA candidates appeared to be safe in vitro, one shRNA candidate impaired the in vivo development of the human immune system in Balb/c Rag2(-/-)IL-2Rγc(-/-) (BRG) mice. The three remaining shRNA candidates were combined into one single lentiviral vector (LV), and safety of the shRNA combination during human hematopoietic cell development was confirmed. Overall, we demonstrate here the preclinical in vivo safety of a LV expressing three shRNAs against HIV-1, which is proposed for a future Phase I clinical trial.Molecular Therapy-Nucleic Acids (2013) 2, e120; doi:10.1038/mtna.2013.48; published online 3 September 2013.
Case Study - Assessing Spatial Distribution of Web Resources for Navigation Services (2004)

We present the results of a case study assessing the suitability of the World Wide Web in its current state of the art to provide supporting information for an automated pedestrian urban navigation service. Our experiment simulates an application providing a navigator with navigation aids---routemarks and landmarks---along a path generated by a web service. The instructions generated by this service are tested in human subject testing and evaluated. We conclude that automated, agent based systems could profit of the current state of Internet content to provide enhanced navigation services using landmarks. Further enhancements will be possible with the advent of the Semantic Web.
A New Optical Distortion Model for Multi-camera Calibration (2009)

A new optical distortion model is proposed, to recover the ideal rectified image for camera calibration. This method is applied as a preprocessing step of a vanishing point calibration procedure that is proved to get a sufficient level of precision for video surveillance applications. Some experimental results are referred in the paper to demonstrate the possibility of 3D model projection from multiple camera views as well as integration of different optical sensors (planar lens and fish eye panoramic cameras). Performance criteria are defined in terms of direct and inverse transformations between the image plane and the 3D reference system in the scene, by using 3D model projection.
Generation, Release, and Uptake of the NAD Precursor Nicotinic Acid Riboside by Human Cells (2015)

NAD is essential for cellular metabolism and has a key role in various signaling pathways in human cells. To ensure proper control of vital reactions, NAD must be permanently resynthesized. Nicotinamide and nicotinic acid as well as nicotinamide riboside (NR) and nicotinic acid riboside (NAR) are the major precursors for NAD biosynthesis in humans. In this study, we explored whether the ribosides NR and NAR can be generated in human cells. We demonstrate that purified, recombinant human cytosolic 5'-nucleotidases (5'-NTs) CN-II and CN-III, but not CN-IA, can dephosphorylate the mononucleotides nicotinamide mononucleotide and nicotinic acid mononucleotide (NAMN) and thus catalyze NR and NAR formation in vitro. Similar to their counterpart from yeast, Sdt1, the human 5'-NTs require high (millimolar) concentrations of nicotinamide mononucleotide or NAMN for efficient catalysis. Overexpression of FLAG-tagged CN-II and CN-III in HEK293 and HepG2 cells resulted in the formation and release of NAR. However, NAR accumulation in the culture medium of these cells was only detectable under conditions that led to increased NAMN production from nicotinic acid. The amount of NAR released from cells engineered for increased NAMN production was sufficient to maintain viability of surrounding cells unable to use any other NAD precursor. Moreover, we found that untransfected HeLa cells produce and release sufficient amounts of NAR and NR under normal culture conditions. Collectively, our results indicate that cytosolic 5'-NTs participate in the conversion of NAD precursors and establish NR and NAR as integral constituents of human NAD metabolism. In addition, they point to the possibility that different cell types might facilitate each other's NAD supply by providing alternative precursors.
DNA microarray gene expression analysis technology and its application to neurological disorders (2001)

DNA microarray technology is currently an area of great interest. Also called "genechip" technology, it incorporates molecular genetics and computer science on a massive scale. This technology can rapidly provide a detailed view of the simultaneous expression of entire genomes and provide new insights into gene function, disease pathophysiology, disease classification, and drug development. In this review, the author discusses the basic theory behind genechip and the other biologic chip technologies, their limitations given the current state of biologic knowledge and computational abilities, and their potential applications to the understanding of neurologic disorders.
Tumoritropic and lymphotropic principles of macromolecular drugs. (1989)

The advantages and disadvantages of macromolecular drugs, particularly on synthetic polymer-protein conjugates, are described in this article. Improvements in protein drugs, after tailoring with polymers, are as follows: increased plasma half-life, loss of antigenecity, lymphotropism, and, especially, preferred tumor-targeting efficiency and long-term retention in the tumor tissues. Hydrophobic character can make a drug also possible for oily formulation. Explained are the rationales of macromolecular drugs to preferential delivery to the tumor and lymphatic tissues based on our finding on pathological/anatomical differences of the blood and lymphatic vasculatures. Enhanced vascular permeability, which facilitates the macromolecular drug-leakage out of the blood vessel, is discussed. A model compound, which is discussed in detail, is smancs--styrene-co-maleic acid conjugated neocarzinostatin (MW 16 K). Some data on polymer-conjugated enzymes as potential therapeutic agents are described as well.
Magnetic resonance tracking of transplanted bone marrow and embryonic stem cells labeled by iron oxide nanoparticles in rat brain and spinal cord (2004)

Nuclear magnetic resonance (MR) imaging provides a noninvasive method for studying the fate of transplanted cells in vivo. We studied, in animals with a cortical photochemical lesion or with a balloon-induced spinal cord compression lesion, the fate of implanted rat bone marrow stromal cells (MSCs) and mouse embryonic stem cells (ESCs) labeled with superparamagnetic iron oxide nanoparticles (Endorem). MSCs were colabeled with bromodeoxyuridine (BrdU), and ESCs were transfected with pEGFP-C1 (eGFP ESCs). Cells were either grafted intracerebrally into the contralateral hemisphere of the adult rat brain or injected intravenously. In vivo MR imaging was used to track their fate; Prussian blue staining and electron microscopy confirmed the presence of iron oxide nanoparticles inside the cells. During the first week postimplantation, grafted cells migrated to the lesion site and populated the border zone of the lesion. Less than 3% of MSCs differentiated into neurons and none into astrocytes; 5% of eGFP ESCs differentiated into neurons, whereas 70% of eGFP ESCs became astrocytes. The implanted cells were visible on MR images as a hypointense area at the injection site, in the corpus callosum and in the lesion. The hypointense signal persisted for more than 50 days. The presence of GFP-positive or BrdU-positive and nanoparticle-labeled cells was confirmed by histological staining. Our study demonstrates that both grafted MSCs and eGFP ESCs labeled with a contrast agent based on iron oxide nanoparticles migrate into the injured CNS. Iron oxide nanoparticles can therefore be used as a marker for the long-term noninvasive MR tracking of implanted stem cells.
Regulation of in vitro Calcium Phosphate Mineralization by Combinatorially Selected Hydroxyapatite-Binding Peptides (2008)

We report selection and characterization of hydroxyapatite-binding heptapeptides from a peptide-phage library and demonstrate the effects of two peptides, with different binding affinities and structural properties, on the mineralization of calcium phosphate mineral. In vitro mineralization studies carried out using one strong- and one weak-binding peptide, HABP1 and HABP2, respectively, revealed that the former exhibited a drastic outcome on mineralization kinetics and particle morphology. Strong-binding peptide yielded significantly larger crystals, as observed by electron microscopy, in comparison to those formed in the presence of a weak-binding peptide or in the negative control. Molecular structural studies carried out by circular dichroism revealed that HABP1 and HABP2 differed in their secondary structure and conformational stability. The results indicate that sequence, structure, and molecular stability strongly influence the mineralization activity of these peptides. The implication of the research is that the combinatorially selected short-sequence peptides may be used in the restoration or regeneration of hard tissues through their control over of the formation of calcium phosphate biominerals.
Exploitation of nanoparticle–protein corona for emerging therapeutic and diagnostic applications (2016)

Exposure of nanoparticles (NPs) to biological fluids (e.g., plasma, interstitial fluid, and cytoplasm) leads to the absorption of proteins on the NP surface, forming a protein corona (PC) that drastically influences the NP physicochemical properties. Herein, we highlight the emerging applications of PC towards its use in therapeutics and diagnostics. In particular, special emphasis is given to the exploitation of PC for targeted delivery of nanomaterials and early cancer detection. By highlighting such recent applications of PC, we hope to demonstrate that this bio-entity has the potential to determine the success of NPs in biomedicine beyond their currently envisioned purposes.
Myocardial infarction: diagnosis and vital status prediction using neural networks (2002)

Neural networks (NNs) have been found useful in many biomedical applications. The authors' purpose is to apply NNs to two specific problems in cardiology, namely, diagnosis of echocardiograms for myocardial infarction and prediction of vital status of patients that suffered such. The authors used NNs to discriminate between normal and infarcted myocardium, by looking at intensity changes. The intensities of selected regions are used for training and testing. In predicting the vital status of patients that have suffered acute myocardial infarction, the authors used a large database (MIDAS) with follow-ups. The NN in this case has two hidden layers with 18 patient variables from the MIDAS dataset as inputs. The NN was again trained with the feedback algorithm ALOPEX and tested with unknown data.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Consumer attitudes towards Internet advertising (1997)

Advertising on the Internet can be viewed as a social contract between advertisers and Internet users. The attributes comprising this contract are: access to advertisements, placement of advertisements, message, influence on fee, and information collection. Examines empirically the tradeoffs consumers make among the attributes in the social contract using an online survey analysed through conjoint analysis. The findings indicate that consumer attitudes towards Internet advertising differ from many predictions about this new media.
Imaging in real-time with FRET the redox response of tumorigenic cells to glutathione perturbations in a microscale flow (2010)

Despite the potential benefits of selective redox-modulating strategies for cancer therapy, an efficacious methodology for testing therapies remains elusive because of the difficulty in measuring intracellular redox potentials over time. In this report, we have incorporated a new FRET-based biosensor to follow in real time redox-sensitive processes in cells transformed to be tumorigenic and cultured in a microfluidic channel. A microfluidic network was used to control micro-scale flow near the cells and at the same time deliver drugs exogenously. Subsequently, the response of a redox homeostasis circuit was tested, namely reduced glutathione (GSH)/oxidized glutathione(GSSG), to diamide, a thiol oxidant, and two drugs used for cancer therapies: BSO (L-buthionine-[SR]-sulfoximine) and BCNU (carmustine). The main outcome from these experiments is a comparison of the temporal depletion and recovery of GSH in single living cells in real-time. These data demonstrate that mammalian cells are capable of restoring a reduced intracellular redox environment in minutes after an acute oxidative insult is removed. This recovery is significantly delayed by (i) the inhibition of GSH biosynthesis by BSO; (ii) the inactivation of glutathione reductase by BCNU; and (iii) in tumorigenic cells relative to an isogenic non-tumorigenic control cell line.