gebhart/patrepeval huggingface dataset:
Adeno-Associated Virus Vectors and Stem Cells: Friends or Foes? (2017)

The infusion of healthy stem cells into a patient-termed "stem-cell therapy"-has shown great promise for the treatment of genetic and non-genetic diseases, including mucopolysaccharidosis type 1, Parkinson's disease, multiple sclerosis, numerous immunodeficiency disorders, and aplastic anemia. Stem cells for cell therapy can be collected from the patient (autologous) or collected from another "healthy" individual (allogeneic). The use of allogenic stem cells is accompanied with the potentially fatal risk that the transplanted donor T cells will reject the patient's cells-a process termed "graft-versus-host disease." Therefore, the use of autologous stem cells is preferred, at least from the immunological perspective. However, an obvious drawback is that inherently as "self," they contain the disease mutation. As such, autologous cells for use in cell therapies often require genetic "correction" (i.e., gene addition or editing) prior to cell infusion and therefore the requirement for some form of nucleic acid delivery, which sets the stage for the AAV controversy discussed herein. Despite being the most clinically applied gene delivery context to date, unlike other more concerning integrating and non-integrating vectors such as retroviruses and adenovirus, those based on adeno-associated virus (AAV) have not been employed in the clinic. Furthermore, published data regarding AAV vector transduction of stem cells are inconsistent in regards to vector transduction efficiency, while the pendulum swings far in the other direction with demonstrations of AAV vector-induced toxicity in undifferentiated cells. The variation present in the literature examining the transduction efficiency of AAV vectors in stem cells may be due to numerous factors, including inconsistencies in stem-cell collection, cell culture, vector preparation, and/or transduction conditions. This review summarizes the controversy surrounding AAV vector transduction of stem cells, hopefully setting the stage for future elucidation and eventual therapeutic applications.
Vaccine design : the role of cytokine networks (1997)

The Role of Cytokines in the Action of Immunological Adjuvants A.C. Allison. The Role of Tumour Necrosis Factor in Lymphoid Tissue Formation and Function M. Pasparakis, et al. Dendritic Cells and Cytokines J.M. Austyn. Control of HIV Entry and Transcription, as a Possible Mechanism of the Antiviral Effects of T Lymphocytes in HIV Infection J.-L. Virelizier, et al. Development of an Influenza-IscomTM Vaccine J. Cox, et al. Development of Parainfluenza Virus and Respiratory Syncytial Virus Subunit Vaccines M. Ewasyshyn, et al. Mucosal Vaccines: Perspectives on the Development of Anti-H.Pylori. Vaccines P. Ghiara. A Single Treatment with Adjuvant Stimulates Thl-like Cytokines and Downregulates Th2-Mediated Primary and Secondary Allergic Responses D.E. Scott, B. Golding. Induction of IL-12 Secretion and Enhanced Surface Expression of B7.1/B7.2 and ICAM-1 in Human Monocytes Activated by the Vaccine Carrier Brucella Abortus: Correlaton with in Vivo Generation of Cellular Immune Responses H. Golding, et al. The Potential use of Different Vaccination Protocols to Tailor Cytokine Profiles E. Comoy, et al. Modulation of Cytokine Responses by Iscoms and Iscom-Matrix M. Villacres-Eriksson, et al. Vaccines and Vaccine Delivery Systems: Experience with HSV, Influenza and Mucosal Routes of Immunisation R. Jennings, et al. 7 Additional Articles. Index.
STED imaging of nitrogen vacancy centers in diamond (2013)

Because of its optical property of photostability, Nitrogen-Vacancy center (NV center) is desired to be applied for biomedical staining for super-resolution microscopy. In this paper, we report the sub-diffraction imaging of NV centers in nano-diamond and bulk materials. The resolution of ~65nm is achieved in the FND sample with our home built CW STED system.
Intravenous iron in inflammatory bowel diseases (2012)

Oral iron is not an ideal option for treating anemia and iron deficiency in IBD. i.v. iron should be preferred at least in five scenarios: intolerance to oral iron, severe anemia, failure of oral therapy, need for a quick recovery, and use of erythropoietin. Direct evidence in IBD patients not only confirms the effectiveness of i.v. iron, but also demonstrates that new, more convenient preparations probably will become the standard in the near future.
Multicellular spheroids grown directly from human tumour material (1984)

Human tumour cells from surgical material were grown as multicellular spheroids. In 16 out of 20 cultures spheroids with a diameter of more than 250 microns could be observed. In 6 out of 20 cultures more than 30 spheroids with a diameter of at least 300 microns were obtained, i.e. 30% of the cultures fulfilled the criterion for a possible chemosensitivity test on primary cell spheroids. A study of stained sections from the spheroids and the respective tumours, showed that the morphology of the spheroid was very similar that of the tumour from which the cells were derived. Samples from 9 malignant melanomas, 4 bladder carcinomas, 2 renal-cell carcinomas, 2 ovarian carcinomas, 1 lymphoma, 1 colon carcinoma, and 1 schwannoma were tested for spheroid growth. Spheroids were obtained from at least one representative of all these tumour types. However, investigations involving larger numbers of tumours are needed to find out which tumour types are most suitable for further biological characterization of primary cell spheroids and tests for therapy response.
THE SPECTRUM OF 67-kD LAMININ RECEPTOR EXPRESSION IN BREAST CARCINOMA PROGRESSION (1997)

Laminin is a glycoprotein of the basement membrane (BM), involved in a variety of normal and pathological cellular events including tumour invasion and metastasis. Cells bind laminin through different types of receptor. The 67-kD laminin receptor (67LR) is a cell-surface protein which binds laminin with high affinity. 67LR expression has been shown to increase in neoplastic cells, compared with normal tissues, and 67LR seems to play an important role during the first steps of neoplastic progression. In this study, 67LR expression was analysed during the morphological phases of breast cancer progression from normal tissue to invasive carcinoma. A total of 506 formalin-fixed, paraffin-embedded normal breast structures and lesions were stained by immunohistochemistry usign the MLuC5 monoclonal antibody, which is specific for 67LR. The results show that in normal breast and in any kind of breast lesion, myoepithelial and endothelial cells express 67LR. While 67LR is not seen in the epithelium of normal breast, cysts, adenosis, and benign tumours, it is expressed in the epithelial cells of several hyperplasias and carcinomas in situ, both ductal and lobular, as well as in all invasive carcinomas. The 67LR-positive cell subpopulation expands from hyperplastic lesions to invasive carcinoma, suggesting that 67LR could be related to the induction and progression of breast cancer.
The Role of Soil Microorganisms in Plant Mineral Nutrition—Current Knowledge and Future Directions (2017)

In their natural environment, plants are part of a rich ecosystem including numerous and diverse microorganisms in the soil. It has been long recognized that some of these microbes, such as mycorrhizal fungi or nitrogen fixing symbiotic bacteria, play important roles in plant performance by improving mineral nutrition. However, the full range of microbes associated with plants and their potential to replace synthetic agricultural inputs has only recently started to be uncovered. In the last few years, a great progress has been made in the knowledge on composition of rhizospheric microbiomes and their dynamics. There is clear evidence that plants shape microbiome structures, most probably by root exudates, and also that bacteria have developed various adaptations to thrive in the rhizospheric niche. The mechanisms of these interactions and the processes driving the alterations in microbiomes are, however, largely unknown. In this review, we focus on the interaction of plants and root associated bacteria enhancing plant mineral nutrition, summarizing the current knowledge in several research fields that can converge to improve our understanding of the molecular mechanisms underpinning this phenomenon.
Genetic variants of insulin receptor substrate‐1 (IRS‐1) in syndromes of severe insulin resistance. Functional analysis of Ala513Pro and Gly1158Glu IRS‐1 (2002)

While subtle effects of these variants cannot be excluded in this system, it is unlikely that these variants are responsible for the extreme insulin resistance seen in the subjects harbouring them. Although IRS proteins play a central role in insulin signalling, functionally significant mutations in the IRS-1 gene are a rare cause of human syndromes of severe insulin resistance.
A prenylated protein-specific endoprotease in rat liver microsomes that produces a carboxyl-terminal tripeptide (1993)

The maturation of proteins that contain the C-terminal sequence Cys-Ali-Ali-Xaa (where Ali is usually an aliphatic amino acid and Xaa is a number of different amino acids) involves the attachment of a farnesyl or geranylgeranyl group to the cysteine residue, proteolytic removal of the C-terminal three amino acids, and methylation of the prenylated cysteine alpha-carboxyl group. Two prenylated and radiolabeled peptides were prepared in order to detect the proteolysis step(s) in a cell-free system and to determine the reaction products. These peptides are ECB-NPFRQRRFFC(S-geranylgeranyl)AI[3H]L and ECB-C(S-farnesyl)VI[3H]S (ECB is an extended-chain biotin group) which are patterned after the C-termini of geranylgeranylated and farnesylated G protein gamma-subunits. Incubation of these peptides with rat liver microsomes, but not cytosol, results in the production of radiolabeled dipeptides (I[3H]L and I[3H]S) and tripeptides (AI[3H]L and VI[3H]S) as the major products and smaller amounts of amino acids ([3H]L and [3H]S). A multitude of independent experiments shows that the dipeptides are produced from the tripeptides by secondary proteolysis. Although a portion of the [3H]S produced comes directly from ECB-C(S-farnesyl)VI[3H]S, the KM of > 30 microM for this reaction is significantly higher than the KM of 1.1 microM for the production of VI[3H]S from the farnesylated peptide. This suggests that the carboxypeptidase is not part of the pathway for the maturation of prenylated proteins. Nonprenylated peptides at concentrations of 10-100-fold higher than those of the prenylated substrates did not reduce the amount of tripeptide produced.(ABSTRACT TRUNCATED AT 250 WORDS)
Facile Fabrication of Superhydrophobic Surface via SiO<sub>2</sub>/Fluoro-Containing Polymer Composite Particles (2013)

SiO2/fluoro-containing polymer (SiO2/PFS) composite particles consisting of a vinyl-functional silica core with grafted mixed block copolymer were prepared by emulsion polymerization with styrene and 1H,1H,2H,2H-perfluorooctyl methacrylate as the reaction monomers. Vinyl-functional silica spheres and SiO2/PFS composite particles were characterized by SEM, FT-IR spectroscopy, TEM and XPS. The results indicate that fluoro-containing polymer has been successfully grafted onto the surface of vinyl-functional silica sphere and SiO2/PFS particle has a core-shell structure. The SiO2/PFS coating possesses a micro/nano-scale hierarchical structure and low surface free energy, which are prerequisite surface properties for obtaining superhydrophobicity. The static water contact angle on the SiO2/PFS coating has as high as 171° and water droplet can easily roll off the coated substrate.
Neutralization of the Chemokine CXCL10 Reduces Inflammatory Cell Invasion and Demyelination and Improves Neurological Function in a Viral Model of Multiple Sclerosis (2001)

Intracerebral infection of mice with mouse hepatitis virus (MHV) results in an acute encephalomyelitis followed by a chronic demyelinating disease with clinical and histological similarities with the human demyelinating disease multiple sclerosis (MS). Following MHV infection, chemokines including CXC chemokine ligand (CXCL)10 (IFN inducible protein 10 kDa), CXCL9 (monokine induced by IFN-gamma), and CC chemokine ligand 5 (RANTES) are expressed during both acute and chronic stages of disease suggesting a role for these molecules in disease exacerbation. Previous studies have shown that during the acute phase of infection, T lymphocytes are recruited into the CNS by the chemokines CXCL10 and CXCL9. In the present study, MHV-infected mice with established demyelination were treated with antisera against these two chemokines, and disease severity was assessed. Treatment with anti-CXCL10 reduced CD4+ T lymphocyte and macrophage invasion, diminished expression of IFN-gamma and CC chemokine ligand 5, inhibited progression of demyelination, and increased remyelination. Anti-CXCL10 treatment also resulted in an impediment of clinical disease progression that was characterized by a dramatic improvement in neurological function. Treatment with antisera against CXCL9 was without effect, demonstrating a critical role for CXCL10 in inflammatory demyelination in this model. These findings document a novel therapeutic strategy using Ab-mediated neutralization of a key chemokine as a possible treatment for chronic human inflammatory demyelinating diseases such as MS.
USAID and agricultural research - review of USAID support for agricultural research 1952-1996 (1997)

Metadata only record
Chimeric Nucleases Stimulate Gene Targeting in Human Cells (2003)

Correction of gene defects in human somatic cells by targeting as has been used in murine embryonic stem cells (1, 2) has been precluded by the low spontaneous rate of gene targeting (3). However, creation of a DNA double-stranded break (DSB) in the genomic target (DSB-GT) can stimulate homologous recombination by over 1000-fold (4). &#13;\n&#13;\nWe can rapidly and quantitatively measure gene targeting by correcting a mutation in a green fluorescent protein (GFP) gene that has been stably integrated into the genome (5) (fig. S1). With an optimized GFP gene targeting system, the introduction of a DSB by I–Sce I (Sce) stimulated GT &gt;40,000-fold and the absolute rate of gene targeting reached 3 to 5% (fig. S2). Such a system, however, depends on the prior introduction of a Sce binding site into the target gene and cannot be used for endogenous genes. Chimeric nucleases (CNs) have the potential to create sequence-specific DSBs (6). CNs—fusions between zinc finger binding DNA binding domains and the endonuclease domain of Fok I—can sitespecifically cleave naked DNA in vitro (6), extrachromosomal DNA in Xenopus oocytes (7), and chromosomal DNA in Drosophila (8). CNs work as dimers, and their efficiency depends on the spacing and orientation of the zinc finger binding sites with respect to the length of the amino acid linker between the DNA binding and endonuclease domains (7, 9). &#13;\n&#13;\nQQR is an artificial zinc finger DNA binding domain that recognizes the sequence 5′-GGGGAAGAA-3′ with nanomolar affinity (10). We modified QQR chimeric nucleases (QQR-CNs) (7, 9) (Fig. 1A) and tested whether they stimulated gene targeting (Fig. 1B). The background rate of gene targeting was 0.71 events per million transfected cells (fig. S1C). QQRL18-CN stimulated gene targeting 17-fold on target QQR6 and 260-fold on target QQR8 (Fig. 1B). QQRL0-CN did not stimulate gene targeting on target QQR8, but it was as efficient as Sce in stimulating gene targeting by over 2000-fold on target QQR6 (Fig. 1B). QQRL18-CN showed some preference for an 8–base pair (bp) spacing between binding sites whereas QQRL0-CN preferred 6-bp spacing. Thus, removing the linker between the zinc spacfinger and the nuclease domains increased the activity and specificity of the fusion protein in mammalian cells. As controls, we showed that the CNs did not stimulate gene targeting if (i) they lacked a nuclear localization signal, (ii) there was a single binding site rather than an inverted repeat binding site in the target, and (iii) the cognate binding site was changed. Thus, homodimers of CNs are potent stimulators of gene targeting in human somatic cells.
Erogress Toward a Potentially Implantable, Enzyme-Based Glucose Sensor (1982)

Our efforts toward the development of a potentially implantable, enzyme-based glucose sensor have concentrated on understanding in sufficient detail the most important component, the enzyme-containing membrane. We describe here some features that this membrane must have to operate as a constituent of a chronically implanted sensor. A model of reaction and diffusion within the membrane is outlined and methods of membrane characterization are reviewed.
The SHINE Clade of AP2 Domain Transcription Factors Activates Wax Biosynthesis, Alters Cuticle Properties, and Confers Drought Tolerance when Overexpressed in Arabidopsis[W] (2004)

The interface between plants and the environment plays a dual role as a protective barrier as well as a medium for the exchange of gases, water, and nutrients. The primary aerial plant surfaces are covered by a cuticle, acting as the essential permeability barrier toward the atmosphere. It is a heterogeneous layer composed mainly of lipids, namely cutin and intracuticular wax with epicuticular waxes deposited on the surface. We identified an Arabidopsis thaliana activation tag gain-of-function mutant shine (shn) that displayed a brilliant, shiny green leaf surface with increased cuticular wax compared with the leaves of wild-type plants. The gene responsible for the phenotype encodes one member of a clade of three proteins of undisclosed function, belonging to the plant-specific family of AP2/EREBP transcription factors. Overexpression of all three SHN clade genes conferred a phenotype similar to that of the original shn mutant. Biochemically, such plants were altered in wax composition (very long fatty acid derivatives). Total cuticular wax levels were increased sixfold in shn compared with the wild type, mainly because of a ninefold increase in alkanes that comprised approximately half of the total waxes in the mutant. Chlorophyll leaching assays and fresh weight loss experiments indicated that overexpression of the SHN genes increased cuticle permeability, probably because of changes in its ultrastructure. Likewise, SHN gene overexpression altered leaf and petal epidermal cell structure, trichome number, and branching as well as the stomatal index. Interestingly, SHN overexpressors displayed significant drought tolerance and recovery, probably related to the reduced stomatal density. Expression analysis using promoter-beta-glucuronidase fusions of the SHN genes provides evidence for the role of the SHN clade in plant protective layers, such as those formed during abscission, dehiscence, wounding, tissue strengthening, and the cuticle. We propose that these diverse functions are mediated by regulating metabolism of lipid and/or cell wall components.
Accuracy and Stability of Numerical Algorithms (2002)

From the Publisher:
What is the most accurate way to sum floating point numbers? What are the advantages of IEEE arithmetic? How accurate is Gaussian elimination and what were the key breakthroughs in the development of error analysis for the method? The answers to these and many related questions are included here. 
This book gives a thorough, up-to-date treatment of the behavior of numerical algorithms in finite precision arithmetic. It combines algorithmic derivations, perturbation theory, and rounding error analysis. Software practicalities are emphasized throughout, with particular reference to LAPACK and MATLAB. The best available error bounds, some of them new, are presented in a unified format with a minimum of jargon. Because of its central role in revealing problem sensitivity and providing error bounds, perturbation theory is treated in detail. 
Historical perspective and insight are given, with particular reference to the fundamental work of Wilkinson and Turing, and the many quotations provide further information in an accessible format. 
The book is unique in that algorithmic developments and motivations are given succinctly and implementation details minimized, so that attention can be concentrated on accuracy and stability results. Here, in one place and in a unified notation, is error analysis for most of the standard algorithms in matrix computations. Not since Wilkinson's Rounding Errors in Algebraic Processes (1963) and The Algebraic Eigenvalue Problem (1965) has any volume treated this subject in such depth. A number of topics are treated that are not usually covered in numerical analysis textbooks, including floating point summation, block LU factorization, condition number estimation, the Sylvester equation, powers of matrices, finite precision behavior of stationary iterative methods, Vandermonde systems, and fast matrix multiplication. 
Although not designed specifically as a textbook, this volume is a suitable reference for an advanced course, and could be used by instructors at all levels as a supplementary text from which to draw examples, historical perspective, statements of results, and exercises (many of which have never before appeared in textbooks). The book is designed to be a comprehensive reference and its bibliography contains more than 1100 references from the research literature. 
Audience 
Specialists in numerical analysis as well as computational scientists and engineers concerned about the accuracy of their results will benefit from this book. Much of the book can be understood with only a basic grounding in numerical analysis and linear algebra. 
About the Author 
Nicholas J. Higham is a Professor of Applied Mathematics at the University of Manchester, England. He is the author of more than 40 publications and is a member of the editorial boards of the SIAM Journal on Matrix Analysis and Applications and the IMA Journal of Numerical Analysis. His book Handbook of Writing for the Mathematical Sciences was published by SIAM in 1993.
Continuous Blood Pressure Monitoring using Pulse Wave Transit Time (2005)

In this paper, we describe the method of non-invasive blood pressure measurement using pulse wave transit time(PWTT). PWTT is a new parameter involved with a vascular that can indicate the change of BP. PWTT is measured by continuous monitoring of ECG and pulse wave. No additional sensors or modules are required. In many cases, the change of PWTT correlates with the change of BP. We measure pulse wave using the photo plethysmograph(PPG) sensor in an earlo be and we measure ECG using the ECG monitoring device our made in the chest. The measurement device for detecting pulse wave consists of infrared LED for transmitted light illumination, pin photodiode as light detector, amplifier and filter. We composed 0. 5Hz high pass, 60Hz notch and 10Hz low pass filter. ECG measurement device consists of multiplexer, amplifier, filter, micro-controller and RF module. After amplification and filtering, ECG signal and pulse wave is fed through micro-controller. We performe d the initial work towards the development of ambulatory BP monitoring system using PWTT. An earlobe is suitable place to measure PPG signal without the restraint in daily work. From the results, we can know that the dependence of PWTT on BP is almost linear and it is possible to monitoring an individual BP continuously after the individual calibration.
The Fluoride Cleavable 2-(Cyanoethoxy)Methyl (CEM) Group as Reversible 3′-O-Terminator for DNA Sequencing-by-Synthesis—Synthesis, Incorporation, and Cleavage (2007)

A new and promising sequencing technology called sequencing-by-synthesis (SBS) enables fast determination of DNA sequences. 2'-Deoxynucleotides containing the (2-cyanoethoxy)methyl (CEM) group at the 3'-O-position are potential reversible terminators for the SBS technology. Herein we describe the synthesis, the incorporation by several polymerases, and the cleavage of this 3'-O-blocking group using 3'-O-CEM-thymidinyl-5'-O-triphosphate 7 as an example.