gebhart/patrepeval huggingface dataset:
Comparison and Validation of Some ITS Primer Pairs Useful for Fungal Metabarcoding Studies (2014)

Current metabarcoding studies aiming to characterize microbial communities generally rely on the amplification and sequencing of relatively short DNA regions. For fungi, the internal transcribed spacer (ITS) region in the ribosomal RNA (rRNA) operon has been accepted as the formal fungal barcode. Despite an increasing number of fungal metabarcoding studies, the amplification efficiency of primers is generally not tested prior to their application in metabarcoding studies. Some of the challenges that metabarcoding primers should overcome efficiently are the amplification of target DNA strands in samples rich in non-target DNA and environmental pollutants, such as humic acids, that may have been co-extracted with DNA. In the current study, three selected primer pairs were tested for their suitability as fungal metabarcoding primers. The selected primer pairs include two primer pairs that have been frequently used in fungal metabarcoding studies (ITS1F/ITS2 and ITS3/ITS4) and a primer pair (ITS86F/ITS4) that has been shown to efficiently amplify the ITS2 region of a broad range of fungal taxa in environmental soil samples. The selected primer pairs were evaluated in a 454 amplicon pyrosequencing experiment, real-time PCR (qPCR) experiments and in silico analyses. Results indicate that experimental evaluation of primers provides valuable information that could aid in the selection of suitable primers for fungal metabarcoding studies. Furthermore, we show that the ITS86F/ITS4 primer pair outperforms other primer pairs tested in terms of in silico primer efficiency, PCR efficiency, coverage, number of reads and number of species-level operational taxonomic units (OTUs) obtained. These traits push the ITS86F/ITS4 primer pair forward as highly suitable for studying fungal diversity and community structures using DNA metabarcoding.
Expansion of Human Regulatory T-Cells From Patients With Type 1 Diabetes (2008)

The results support the feasibility of isolating Tregs for in vitro expansion. Based on expansion capacity, FOXP3 stability, and functional properties, the CD4+CD127(lo/-)CD25+ T-cells represent a viable cell population for cellular therapy in this autoimmune disease.
Targeting duplex DNA with DNA‐PNA chimeras? Physico‐chemical characterization of a triplex DNA‐PNA/DNA/DNA (2004)

Targeting double-stranded DNA with homopyrimidine PNAs results in strand displacement complexes PNA/DNA/PNA rather than PNA/DNA/DNA triplex structures. Not much is known about the binding properties of DNA-PNA chimeras. A 16-mer 5'-DNA-3'-p-(N)PNA(C) has been investigated for its ability to hybridize a complementary duplex DNA by DSC, CD, and molecular modeling studies. The obtained results showed the formation of a triplex structure having similar, if not slightly higher, stability compared to the same all-DNA complex.
Synthesis of Sulfated Colominic Acids and Their Interaction with Fibroblast Growth Factors (2000)

Colominic acid, an alpha (2-->8)-linked poly(sialic acid), was sulfated and characterized by NMR spectroscopy. During sulfation, the secondary hydroxyl group at C-4 had almost the same reactivity as the primary hydroxyl group at C-9, while the secondary hydroxyl group at C-7 was hardly substituted. Analysis by molecular modeling suggested that the lack of substitution at C-7 was due to a steric hindrance. A mobility shift assay indicated that FGF-2 bound to the sulfated colominic acid. Synthetic sulfated colominic acid potentiated the mitogenic activity of FGFs for fibroblasts in the same manner as heparin. Sulfated colominic acid with a low degree of sulfation was able to potentiate FGF activity. Regardless of the degree of sulfation, sulfated colominic acid-induced cytotoxicity was not observed. It was suggested that the carboxyl groups in sulfated colominic acid cooperate with the sulfate groups to reinforce the interaction with FGFs and to reduce the cytotoxicity of sulfated colominic acids.
Molecular mimicry of a carbohydrate epitope on a major surface glycoprotein of Trypanosoma cruzi by using anti-idiotypic antibodies. (1985)

The use of anti-idiotypic antibodies (Ab2) to induce anti-microbial immunity might be particularly advantageous with respect to responses directed against carbohydrate determinants, because it may not be feasible to reproduce these epitopes by recombinant DNA technology. In the present studies, rabbit Ab2 were produced against a recurrent BALB/c idiotype defined by a monoclonal antibody (WIC 29.26) with specificity for a carbohydrate epitope of a major surface glycoprotein of Trypanosoma cruzi. The Ab2 induced specific antibodies in mice, rabbits, and guinea pigs, and reacted with parasite-induced anti-T. cruzi antibodies from mice and rabbits as well as humans. The behavior of this Ab2 is therefore consistent with that of the antigen itself, and suggests that molecular mimicry of carbohydrate epitopes can be easily achieved.
Homogeneous Detection of Nucleic Acids Based upon the Light Scattering Properties of Silver-Coated Nanoparticle Probes (2007)

Herein we report the development of a simple, rapid, homogeneous, and sensitive detection system for DNA based on the scattering properties of silver-amplified gold nanoparticle probes. The assay uses DNA-functionalized magnetic particle probes that act as scavengers for target DNA, which can be collected via a magnetic field. Once the DNA targets are isolated from the initial sample, they are sandwiched via hybridization by a second set of probes. The latter probes are 13-nm gold nanoparticles modified with a different target complementary DNA. Excess probes are removed through repetitive washing steps. The gold particles are dispersed in solution by dehybridization, corresponding to an assumed 1:1 ratio with the target DNA. Electroless deposition of silver on the surface of the gold probes results in particle growth, which increases their scattering efficiency with time. The scattering efficiency and the extinction signatures of the particle sizes are monitored as a function of time and correlated with target concentration. The limit of detection for this novel assay was determined to be 10 fM.
Qué opinan los futuros docentes acerca de su ortografía (2003)

La ortografia es una disciplina arida, dificil por su contenido y poco atractiva por la metodologia empleada tradicionalmente para ensenarla. Todo esto provoca que la sola mencion de su nombre haga cambiar el gesto de los alumnos y no precisamente para bien, presentando, desde el primer contacto con ella, una actitud poco abierta hacia su aprendizaje. Es en si ?o, mejor dicho, la hemos convertido en ? una materia nada motivadora pero en la que toda persona con una instruccion mas que basica piensa que no tiene problemas. Este articulo presenta una investigacion realizada con estudiantes de Magisterio para comprobar su conciencia ortografica y su actitud ante esta disciplina, sobre todo teniendo en cuenta la profesion que desempenaran en un futuro.
Characterizing diffusion dynamics of a membrane protein associated with nanolipoproteins using fluorescence correlation spectroscopy (2010)

Nanolipoprotein particles (NLPs) represent a unique nanometer-sized scaffold for supporting membrane proteins (MP). Characterization of their dynamic shape and association with MP in solution remains a challenge. Here, we present a rapid method of analysis by fluorescence correlation spectroscopy (FCS) to characterize bacteriorhodopsin (bR), a membrane protein capable of forming a NLP complex. By selectively labeling individual components of NLPs during cell-free synthesis, FCS enabled us to measure specific NLP diffusion times and infer size information for different NLP species. The resulting bR-loaded NLPs were shown to be dynamically discoidal in solution with a mean diameter of 7.8 nm. The insertion rate of bR in the complex was ∼55% based on a fit model incorporating two separate diffusion properties to best approximate the FCS data. More importantly, based on these data, we infer that membrane protein associated NLPs are thermodynamically constrained as discs in solution, while empty NLPs appear to be less constrained and dynamically spherical.
HIV-1 Nef protein is secreted into vesicles that can fuse with target cells and virions. (2008)

HIV-1 Nef is a major determinant in HIV-1 pathogenicity. However, its properties have mainly been associated with its biochemical activities within the producer cell. Nef is also secreted from infected and transfected cells. Our primary objective was to determine the nature of secreted Nef protein and its effect on target cells. We determined that HIV-1 Nef is secreted in the form of exosome-like vesicles. Nef protein present in these vesicles is largely protected from protease digestion, which suggests that most of the protein is present on the lumenal side of the vesicles. We observed that HEK293 cells, transfected with a Nef-GFP expression vector, can secrete vesicles containing Nef-GFP fusion protein into the extracellular medium. When the conditioned medium was used to treat Jurkat cells, we found that the cells can take up the Nef fusion protein. The pattern of distribution of the Nef-GFP fusion protein within the target cells is mainly cytoplasmic and results in a punctate staining pattern. We also observed that Nef (-) virions treated with Nef-conditioned medium have their infectivity restored to near wild-type levels. This implies that the Nef contained within vesicles has the ability to fuse with HIV-1 virions and deliver functional Nef to these virions. It also demonstrates that Nef protein delivered in trans can restore infectivity even after virion maturation has occurred. These studies suggest that secreted Nef could play a role in HIV-1 pathogenesis by inducing effects in noninfected bystander cells.
Dystrophin Expression in Muscles of mdx Mice After Adenovirus-Mediated In Vivo Gene Transfer (1996)

We have generated high-titer adenoviral recombinants (AVR) expressing a 6.3-kb partial dystrophin cDNA insert under the control of either the Rous sarcoma virus (RSV) or cytomegalovirus (CMV) promoter. These AVR preparations were free of both E1-containing AVR and AVR with a nonfunctional dystrophin expression cassette. With these optimal AVR preparations, we have obtained a high degree of short-term (10 days) expression of a truncated (approximately 200 kD) dystrophin in dystrophin-deficient mdx muscles injected in the neonatal period; a lesser degree of expression of dystrophin was found in muscles injected in the young adult age and in old animals. Microscopic indices of muscle damage revealed that the truncated dystrophin provided a significant protection of the transduced muscle fibers. However, by 60 days post-injection, a substantial reduction of the number of dystrophin-positive fibers was noted, even in the neonatally injected muscles, and near-total elimination of dystrophin-positive fibers occurred in muscles injected in the adult age. These effects appeared to be brought about by the activity of CD8+ cytotoxic lymphocytes directed against the transduced cells, leading to their eventual elimination. In severe combined immunodeficiency (SCID) mice, lacking both humoral and cellular immune competence, muscles transduced (either in the neonatal or adult age) by AVR containing a CMV-LacZ expression cassette maintained the early (10 day) transduction level up to 30 days post-injection. Systemic administration of AVR (i.e., into the left ventricle of the heart) led in 5 days to a high number of dystrophin-positive fibers in heart, diaphragm, and intercostal muscles but not in limb muscles.
Contaminant‐induced current decline in capillary array electrophoresis (2005)

High-throughput capillary array electrophoresis (CAE) instruments for DNA sequencing suffer to varying degrees from read length degradation associated with electrophoretic current decline and inhibition or delay in the arrival of fragments at the detector. This effect is known to be associated with residual amounts of large, slow-moving fragments of template or genomic DNA carried through from sample preparation and sequencing reactions. Here, we investigate the creation and expansion of an ionic depletion region induced by overloading the capillary with low-mobility DNA fragments, and the effect of growth of this region on electrophoresis run failure. Slow-moving fragments are analytically and experimentally shown to reduce the ionic concentration of the downstream electrolyte. With injection of large fragments beyond a threshold quantity, the anode-side boundary of the nascent depletion region begins to propagate toward the anode at a rate faster than the contaminant DNA migration. Under such conditions, the depletion region expands, the capillary current declines dramatically, and the electrophoresis run yields a short read length or fails completely.
Rotation invariant spherical harmonic representation of 3D shape descriptors (2003)

One of the challenges in 3D shape matching arises from the fact that in many applications, models should be considered to be the same if they differ by a rotation. Consequently, when comparing two models, a similarity metric implicitly provides the measure of similarity at the optimal alignment. Explicitly solving for the optimal alignment is usually impractical. So, two general methods have been proposed for addressing this issue: (1) Every model is represented using rotation invariant descriptors. (2) Every model is described by a rotation dependent descriptor that is aligned into a canonical coordinate system defined by the model. In this paper, we describe the limitations of canonical alignment and discuss an alternate method, based on spherical harmonics, for obtaining rotation invariant representations. We describe the properties of this tool and show how it can be applied to a number of existing, orientation dependent descriptors to improve their matching performance. The advantages of this tool are two-fold: First, it improves the matching performance of many descriptors. Second, it reduces the dimensionality of the descriptor, providing a more compact representation, which in turn makes comparing two models more efficient.
Purification and partial characterization of the capsular polymer of Haemophilus pleuropneumoniae serotype 5 (1987)

The capsular polymer (CP) of Haemophilus pleuropneumoniae serotype 5 was purified, and its chemical composition was analyzed. Radioimmunoassay experiments showed that the maximum amount of CP could be obtained from broth cultures of bacteria in the late stationary phase, rather than from bacteria washed off agar plates. The CP was precipitated from culture supernatant with 5 mM hexadecyltrimethylammonium bromide (Cetavlon) and solubilized with 0.4 M NaCl. Ninety percent of the CP in the culture supernatant was precipitated with Cetavlon, although some material remained insoluble after NaCl extraction. The CP was further purified by phenol extraction, ultracentrifugation, and Sepharose CL-4B gel filtration. The Kav of the CP from Sepharose CL-4B chromatography was 0.33. The CP preparation contained 85% hexosamine, 12% hexose, 3% phosphate, 0.17% protein, 0.20% nucleic acid, and 0.01% endotoxin. Thin-layer chromatography, an amino acid analyzer, and a glucose oxidase colorimetric kit were used to identify the sugar components of the hydrolyzed CP as glucosamine and glucose. Analysis of the native CP by 13C nuclear magnetic resonance indicated that amino, N-acetyl, and carboxyl groups were present and that the CP was a disaccharide.
Video browsing by direct manipulation (2008)

We present a method for browsing videos by directly dragging their content. This method brings the benefits of direct manipulation to an activity typically mediated by widgets. We support this new type of interactivity by: 1) automatically extracting motion data from videos; and 2) a new technique called relative flow dragging that lets users control video playback by moving objects of interest along their visual trajectory. We show that this method can outperform the traditional seeker bar in video browsing tasks that focus on visual content rather than time.
Insertional mutagenesis and illegitimate recombination in mycobacteria. (1991)

Mycobacteria, particularly Mycobacterium tuberculosis, Mycobacterium leprae, and Mycobacterium avium, are major pathogens of man. Although insertional mutagenesis has been an invaluable genetic tool for analyzing the mechanisms of microbial pathogenesis, it has not yet been possible to apply it to the mycobacteria. To overcome intrinsic difficulties in directly manipulating the genetics of slow-growing mycobacteria, including M. tuberculosis and bacille Calmette-Guérin (BCG) vaccine strains, we developed a system for random shuttle mutagenesis. A genomic library of Mycobacterium smegmatis was subjected to transposon mutagenesis with Tn5 seq1, a derivative of Tn5, in Escherichia coli and these transposon-containing recombinant plasmids were reintroduced into mycobacterial chromosomes by homologous recombination. This system has allowed us to isolate several random auxotrophic mutants of M. smegmatis. To extend this strategy to M. tuberculosis and BCG, targeted mutagenesis was performed using a cloned BCG methionine gene that was subjected to Tn5 seq1 mutagenesis in E. coli and reintroduced into the mycobacteria. Surprisingly for prokaryotes, both BCG and M. tuberculosis were found to incorporate linear DNA fragments into illegitimate sites throughout the mycobacterial genomes at a frequency of 10(-5) to 10(-4) relative to the number of transformants obtained with autonomously replicating vectors. Thus the efficient illegitimate recombination of linear DNA fragments provides the basis for an insertional mutagenesis system for M. tuberculosis and BCG.
Role of sympathetic nervous system and neuropeptides in obesity hypertension (2000)

Obesity is the most common cause of human essential hypertension in most industrialized countries. Although the precise mechanisms of obesity hypertension are not fully understood, considerable evidence suggests that excess renal sodium reabsorption and a hypertensive shift of pressure natriuresis play a major role. Sympathetic activation appears to mediate at least part of the obesity-induced sodium retention and hypertension since adrenergic blockade or renal denervation markedly attenuates these changes. Recent observations suggest that leptin and its multiple interactions with neuropeptides in the hypothalamus may link excess weight gain with increased sympathetic activity. Leptin is produced mainly in adipocytes and is believed to regulate energy balance by acting on the hypothalamus to reduce food intake and to increase energy expenditure via sympathetic activation. Short-term administration of leptin into the cerebral ventricles increases renal sympathetic activity, and long-term leptin infusion at rates that mimic plasma concentrations found in obesity raises arterial pressure and heart rate via adrenergic activation in non-obese rodents. Transgenic mice overexpressing leptin also develop hypertension. Acute studies suggest that the renal sympathetic effects of leptin may depend on interactions with other neurochemical pathways in the hypothalamus, including the melanocortin-4 receptor (MC4-R). However, the role of this pathway in mediating the long-term effects of leptin on blood pressure is unclear. Also, it is uncertain whether there is resistance to the chronic renal sympathetic and blood pressure effects of leptin in obese subjects. In addition, leptin also has other cardiovascular and renal actions, such as stimulation of nitric oxide formation and improvement of insulin sensitivity, which may tend to reduce blood pressure in some conditions. Although the role of these mechanisms in human obesity has not been elucidated, this remains a fruitful area for further investigation, especially in view of the current "epidemic" of obesity in most industrialized countries.
Successful Treatment of a Large Soft Tissue Sarcoma With Irreversible Electroporation (2011)

Irreversible electroporation (IRE) is a promising technique for the focal treatment of pathologic tissues that involves placing minimally invasive electrodes within the targeted region. A series of short, intense electric pulses are then applied to destabilize the cell membrane, presumably by creating nanopores,¹ inducing cell death in a nonthermal manner.² The unique therapeutic mechanism of IRE does not rely on tissue temperature changes, as with hyperthermic or cryoablative procedures.³,⁴ Therefore, IRE preserves the extracellular matrix, major tissue vasculature, and other sensitive structures.⁵⁻⁷ Treated regions resolve rapidly,⁵ with submillimeter resolution between treated and unaffected cells,⁸ and are predictable with numerical modeling.⁹ Treatments promote an immune response,⁵,¹⁰,¹¹ are unaltered by blood flow, can be administered quickly (approximately 5 minutes), and can be visualized in real time.¹⁰,¹²
Dynamic NMR microscopy of chromatographic columns (1998)

Abstract Pulsed magnetic field gradients encoded a discrete spatial and temporal motion of the molecules of a fluid percolating through the packed bed of a dynamic radial compression column for liquid chromatography. Two packing materials of porous, chemically bonded C18 silica were used: large irregularly shaped particles (55 – 105 μm) and small spherical particles (6 μm). By combining pulsed field gradient NMR and NMR imaging the distribution of the fluid dynamic displacement probability was determined quantitatively at each point of the static image space. The local axial dispersion coefficient, fluid velocity, and external porosity of the bed were also estimated. The resolution achieved was 250 μm × 250 μm × 2,500 μm per voxel, corresponding to a 250 μm × 250 μm pixel in a 2.5‐mm‐thick slice. Irregularly shaped particles showed slight external porosity heterogeneities over the column cross section, causing a dramatic loss of performance. Spherically shaped particles offered a nearly planar distribution of the transport characteristics across the packed bed, making radial compression of the bed enhance the performance.
Mathematical model of sarcoidosis (2014)

Sarcoidosis is a disease involving abnormal collection of inflammatory cells forming nodules, called granulomas. Such granulomas occur in the lung and the mediastinal lymph nodes, in the heart, and in other vital and nonvital organs. The origin of the disease is unknown, and there are only limited clinical data on lung tissue of patients. No current model of sarcoidosis exists. In this paper we develop a mathematical model on the dynamics of the disease in the lung and use patients' lung tissue data to validate the model. The model is used to explore potential treatments.
Prodrug Approaches of Nucleotides and Oligonucleotides (2006)

The main threshold for the therapeutic applications of nucleotides and oligonucleotides is their ionic structure which implies poor cellular uptake and unfavorable pharmacokinetic parameters. To circumvent these problems, the anionic phosphate moieties may be temporarily masked with enzymolabile protecting groups to form neutral pronucleotides or pro-oligonucleotides. In cells, enzymes cleave the protecting groups and release the parent drug. Several prodrug strategies have been developed, but the kinetics and mechanisms of the deprotection of potential prodrug candidates are still often poorly known. The purpose of the present review is to summarize the current knowledge on the chemical aspects of alternative prodrug strategies at nucleotide and oligonucleotide level.