gebhart/patrepeval huggingface dataset:
Theory of infrared nanospectroscopy by photothermal induced resonance (2010)

We present a theoretical investigation of the physics involved in a recently developed spectromicroscopy technique, called photothermal induced resonance (PTIR). With this technique, one measures the local infrared absorption spectrum of a sample shined with a tunable infrared laser pulse, and detects the induced photothermal expansion with the tip of an atomic force microscope (AFM). Simple physical assumptions allow us to describe analytically the heating and expansion of the sample, the excitation of the vibration modes of the AFM cantilever, and the detected signal. We show that the signal depends on the thermal expansion velocity rather than on the absolute displacement of the tip, and we investigate the influence of the laser pulse length. Eventually, we express the PTIR signal in terms of relevant parameters, and prove its proportionality to the sample absorbance. This analytical approach complement our experimental results and validates the PTIR method as a technique of choice for infrared spectroscopy of nanoscopic samples, getting around optical artifacts like reflectance perturbation.
Trace element and vitamin concentrations and losses in critically ill patients treated with continuous venovenous hemofiltration (1999)

Objectives To measure the blood concentrations of a number of trace elements and vitamins in critically ill patients and examine their elimination by continuous venovenous hemofiltration (CVVH). Setting Intensive care unit of a tertiary institution. Design Prospective, controlled, clinical study. Patients Eight critically ill patients requiring renal replacement therapy, nine patients requiring intensive care treatment but not requiring renal replacement therapy, and nine healthy controls. Interventions Measurement of trace element and vitamin concentrations in blood and ultrafiltrate. Measurements and Main Results Compared with normal volunteers, critically ill patients requiring CVVH had significantly lower median blood concentrations of vitamin C, vitamin E, selenium, and zinc. During the first 24 hrs of CVVH, there were no changes in the trace element and vitamin concentrations in blood, nor were there differences between pre- and postfilter samples. Micronutrient losses in the ultrafiltrate were small or undetectable except for Vitamin C, chromium, and copper. Compared with normal volunteers, critically ill patients not requiring CVVH also had significantly lower median blood concentrations of vitamin C, vitamin E, selenium, and zinc. There were no differences between the two critically ill groups. Conclusions The clinical significance of the reductions in blood concentrations of selenium, zinc, vitamin C, and vitamin E in critically ill patients and the ultrafiltrate losses of Vitamin C, copper, and chromium remains unclear. (Crit Care Med 1999; 27:220-223)
Effect of Circulating Antigen on Immunoscintigraphy of Ovarian Cancer Patients Using Anti‐CA125 Monoclonal Antibody (1996)

The murine monoclonal antibody (mAb) 145-9 recognizes an epitope present on CA125 but different from the epitope defined by the mAb OC125. To evaluate the clinical usefulness of the 145-9 antibody, immunoscintigraphy was performed in ovarian cancer patients and the effect of circulating CA125 on tumor imaging was investigated. Two milligrams (74 MBq) of 111In-labeled 145-9 was injected intravenously into 11 patients with ovarian cancer. Pre-injection serum CA125 concentrations were between 166 U/ml and 7414 U/ml. Tumors were visualized in 10 of 11 patients. In two patients, lymph nodes that were not detected by other imaging modalities but were clinically suspected as metastases were visualized. There was no correlation between serum CA125 level and antibody uptake in the tumors. Immune complexes between the antibody and circulating antigen were observed in sera of all the patients, but the fraction of radioactivity in complex form did not correlate well with serum CA125 levels. The immune complexes survived in the circulation and the circulating radiolabel, including immune complexes, was still bound to solid-phase CA125. The plasma clearance rate and hepatic uptake of the antibody were not significantly affected by circulating CA125. In conclusion, the antibody 145-9 formed complexes with CA125 in vivo but this did not Compromise the outcome of antibody imaging. The antibody 145-9 can be used in immunoscintigraphy of ovarian cancer irrespective of serum CA125 level.
Rapid methods for the analysis of immunoglobulin gene hypermutation: application to transgenic and gene targeted mice (1997)

Hypermutation of immunoglobulin genes is a key process in antibody diversification. Little is known about the mechanism, but the availability of rapid facile assays for monitoring immunoglobulin hypermutation would greatly aid the development of culture systems for hypermutating B cells as well as the screening for individuals deficient in the process. Here we describe two such assays. The first exploits the non-randomness of hypermutation. The existence of a mutational hotspot in the Ser31 codon of a transgenic immunoglobulin V gene allowed us to use PCR to detect transgene hypermutation and identify cell populations in which this mutation had occurred. For animals that do not carry immunoglobulin transgenes, we exploited the fact that hypermutation extends into the region flanking the 3'-side of the rearranged J segments. We show that PCR amplification of the 3'-flank of VDJH rearrangements that involve members of the abundantly-used VHJ558 family provides a large database of mutations where the germline counterpart is unequivocally known. This assay was particularly useful for analysing endogenous immunoglobulin gene hypermutation in several mouse strains. As a rapid assay for monitoring mutation in the JH flanking region, we show that one can exploit the fact that, following denaturation/renaturation, the PCR amplified JH flanking region DNA from germinal centre B cells yields mismatched heteroduplexes which can be quantified in a filter binding assay using the bacterial mismatch repair protein MutS -Wagner et al. (1995) Nucleic Acids Res. 23, 3944-3948-. Such assays enabled us, by example, to show that antibody hypermutation proceeds in the absence of the p53 tumour suppressor gene product.
Ground penetrating radar of northern lacustrine deltas (1991)

Ground penetrating radar (GPR) was used in several selected deltaic sedimentary environments to better understand subsurface stratigraphy and reconstruct former depositional environments. The profiles provide high-resolution, continuous subsurface data on facies thickness and depths, orientation of major sedimentary structures, postdepositional failure planes, and depth of peat deposits.Field experiments were carried out on six river deltas. Records from four of the deltas exhibit sedimentary facies; a record from one delta shows a possible slump; and records from another delta reveal the thickness and stratigraphic relationships of peat deposits. The delta types are (i) sandy, wave influenced; (ii) sandy, immature wave influenced (steeper middle and lower shoreface); (iii) sandy braided; and (iv) gravelly, fan–foreset.In areas of limited subsurface control (stratigraphic logs from drill core, cutbank exposure, or geophysical logs), radar profiles can provide ''big picture'' perspectives of the subsurface, a view only available in laterally extensive exposures. High-resolution profiles of subsurface stratigraphy and sedimentary facies from GPR provide an opportunity for geomorphologists and sedimentologists to further advance field research. Although GPR has limited success in silt and clay, results from sand and gravel deposits often reveal detailed facies assemblages.
PISA: Performance models for Index Structures with and without Aggregated data (2003)

Different models to estimate the performance of tree-based index structures exist. Materialized aggregates in the inner nodes of such index structures are used to speed up range queries on aggregates. This is achieved by avoiding traversing the index tree down to the leaves through aggregates precomputed in the inner nodes. None of the existing models deals with these aggregated data. In this paper, we extend the existing models to take account of aggregated data. Our main contribution is a new generic performance model to estimate the Performance of Index Structures with and without Aggregated data (PISA) that covers both aspects. In addition, the PISA model is adaptable to the distribution of the data and to the location of the query boxes (e.g. uniform, normal and skewed distributions). Experiments confirm that, in most cases, the PISA model is more accurate than other models.
Effect of the Nature of the 3β-Substitution in Manoyl Oxides on the Thermotropic Behavior of DPPC Lipid Bilayer and on DPPC Liposomes (2007)

Functionalized manoyl oxide derivatives have been proved over the years to evoke several biological responses. Among them, 3beta-hydroxy-manoyl oxide (1) and 3beta-acetoxy-manoyl oxide (2) have been shown to exhibit in vitro antimicrobial and cytotoxic activity, while N-imidazole-3 beta-thiocarbonyl ester of manoyl oxide (3) was found to exhibit potent cytotoxic effect. Their partitioning into phospholipid bilayers may lead to membrane structure modifications that are crucial in liposome development as they may influence their maintenance and integrity. DSC was used to study the modifications induced in DPPC bilayers by incorporating increasing concentrations of the three manoyl oxide derivatives. All derivatives were found to strongly affect the bilayer structural organization in terms of a decrease of the cooperativity, the fluidization and partially destabilization of the gel phase and the induction of a lateral phase separation in clustering domains. Derivatives 1 and 3 were incorporated into DPPC liposomes and their physicochemical stability was monitored at 4 degrees C. The stability of liposomes was strongly influenced by the presence of 1 and 3 at any molar ratio studied. DPPC/1 liposomes were found to retain its stability for 48 h at low concentration of 10% mol, while at higher concentrations up to 30% mol they collapsed into aggregated material. In all cases DPPC/3 liposomes were found unstable and sticky aggregated structures precipitated from the bulk suspension.
Surface energy induced patterning of polymer nanostructures for cancer diagnosis and therapy (2007)

We have developed a new simple method to pattern discrete polymer micro and nanostructures. A Si template is patterned by lithography and selective surface treatment to have spatially different surface energies that induce microfluidic self-patterning of a spincoated polymer layer. Biocompatible diblock co-polymer and SU8 are patterned using this method to form monodisperse and shape specific microstructures. After patterning, these particles are lifted off the template surface into aqueous solution. The template is then cleaned and re-used. These freestanding polymer particles with uniform and precise spherical morphology can be used as carriers for drug and imaging agents for biomedical applications.
Bromomaleimides: new reagents for the selective and reversible modification of cysteine (2009)

Bromomaleimides react rapidly and selectively with cysteine to afford thiomaleimides which can be cleaved with a phosphine to regenerate the cysteine or treated with a base to afford dehydroalanine.
Development of genetic vaccines for pathogenic genes (1997)

The vif variants developed in this study exhibited non-productive phenotypes, yet were capable of inducing specific immune responses against HIV-1. These constructs could be used as part of a DNA vaccine strategy for HIV-1. This vaccine adaptation strategy could be used for the development of immunogens for any pathogen resulting in cross-reactive immunity and attenuated gene pathogenesis.
Identification of a heparin-releasable lipoprotein lipase binding protein from endothelial cells. (1992)

Triglycerides in circulating plasma lipoproteins are hydrolyzed by lipoprotein lipase (LPL) which is thought to bind to proteoglycans on the luminal endothelial cell surface. Previous studies from this laboratory using LPL-Sepharose affinity chromatography identified a 220-kDa LPL binding proteoglycan. Using ligand blotting with 125I-LPL, we now report a 116-kDa LPL binding protein in plasma membrane preparations of endothelial cells. 125I-LPL binding to this protein was abolished by addition of unlabeled LPL. When the cell surface of endothelial cells was labeled with biotin, a 116-kDa protein was biotinylated. Furthermore, the biotinylated 116-kDa protein bound to LPL-Sepharose and eluted with 0.4 M NaCl suggesting that the 116-kDa LPL binding protein is present on the cell surface. When detergent extracts of endothelial cells were applied to LPL-Sepharose in the presence of 0.15 M NaCl, the 116-kDa, but not the 220-kDa, protein still bound to LPL-Sepharose. The 116-kDa protein was not labeled with 35SO4 and eluted from DEAE-cellulose prior to proteoglycans, suggesting that it is not a proteoglycan. However, a 116-kDa endothelial cell surface protein was metabolically labeled with [35S]methionine. This protein was dissociated from the cell surface by incubating cells with heparin (50 units/ml)-containing buffer. After heparin treatment of endothelial cells, LPL binding to and internalization by the cells decreased greater than 70% compared to control cells. These results suggest that endothelial cells synthesize a heparin-releasable, high affinity 116-kDa LPL binding protein. We postulate that this protein is associated with proteoglycans on luminal endothelial surfaces and mediates LPL binding, internalization, and recycling. We name this protein hrp (heparin-releasable protein)-116.
Resynthesizing facial animation through 3D model-based tracking (1999)

Given video footage of a person's face, we present new techniques to automatically recover the face position and the facial expression from each frame in the video sequence. A 3D face model is fitted to each frame using a continuous optimization technique. Our model is based on a set of 3D face models that are linearly combined using 3D morphing. Our method has the advantages over previous techniques of fitting directly a realistic 3-dimensional face model and of recovering parameters that can be used directly in an animation system. We also explore many applications, including performance-driven animation (applying the recovered position and expression of the face to a synthetic character to produce an animation that mimics the input video), relighting the face, varying the camera position, and adding facial ornaments such as tattoos and scars.
A discriminative classification-based approach to information state updates for a multi-domain dialog system (2012)

We propose a discriminative classification approach for updating the current information state of a multi-domain dialog system based on user responses. Our method uses a set of lexical and domain independent features to compare the spoken language understanding (SLU) output for the current user turn with the previous information state. We then update the information state accordingly, employing a discriminative machine learning approach. Using a data set collected from our conversational interaction system, we investigate the impact of features based on context dependent and context independent SLU tagging schemas. We show that the proposed approach outperforms two non-trivial baselines, one based on manually crafted rules and the other on classification with lexical features alone. Furthermore, such an approach allows the addition of new domains to the dialog manager in a seamless way.
Local DNA hypomethylation activates genes in rice endosperm (2010)

Cytosine methylation silences transposable elements in plants, vertebrates, and fungi but also regulates gene expression. Plant methylation is catalyzed by three families of enzymes, each with a preferred sequence context: CG, CHG (H = A, C, or T), and CHH, with CHH methylation targeted by the RNAi pathway. Arabidopsis thaliana endosperm, a placenta-like tissue that nourishes the embryo, is globally hypomethylated in the CG context while retaining high non-CG methylation. Global methylation dynamics in seeds of cereal crops that provide the bulk of human nutrition remain unknown. Here, we show that rice endosperm DNA is hypomethylated in all sequence contexts. Non-CG methylation is reduced evenly across the genome, whereas CG hypomethylation is localized. CHH methylation of small transposable elements is increased in embryos, suggesting that endosperm demethylation enhances transposon silencing. Genes preferentially expressed in endosperm, including those coding for major storage proteins and starch synthesizing enzymes, are frequently hypomethylated in endosperm, indicating that DNA methylation is a crucial regulator of rice endosperm biogenesis. Our data show that genome-wide reshaping of seed DNA methylation is conserved among angiosperms and has a profound effect on gene expression in cereal crops.
Nucleotide sequence of a cloned structural gene coding for a precursor of pancreatic somatostatin. (1980)

We have constructed and cloned, in bacteria, recombinant plasmids containing DNA complementary to mRNA coding for a pancreatic pre-prosomatostatin, a product of the cell-free translation of pancreatic islet mRNAs shown previously by immunoprecipitation to be a precursor of somatostatin. A clone containing a nearly full-length cDNA insert of 550 base pairs was identified and appeared to contain the entire coding sequence for the somatostatin precursor in addition to portions of the 5' and 3' untranslated regions. mRNA coding for the pre-prosomatostatin is 600-630 bases long as determined by agarose gel electrophoresis and hybridization with labeled cDNA. Analyses of the nucleotide sequence of the cDNA revealed a protein of 119 amino acid beginning with methionine followed by a typical leader sequence containing 18 hydrophobic amino acids. The tetradecapeptide somatostatin, identical in sequence to mammalian hypothalamic somatostatin, is located at the carboxy terminus followed immediately by a stop codon. An ARg-Lys sequence immediately preceding the sequence of somatostatin is typical of a prohormone cleavage site. A sequence Ala-Pro-Arg-Glu preceding the Arg-Lys cleavage site is identical to that found in porcine prosomatostatin. The evolutionary conservation of the identical amino acid sequence of the somatostatin tetradecapeptide from fish to mammals is remarkable. In addition, similar conservation, in fish and mammals, of the sequence Ala-Pro-Arg-Glu-Arg-Lys preceding the coding region for somatostatin suggets that this particular sequence may have biologic importance in cellular processing of the somatostatin precursor.
Diagnostics of the heating system and lining of coke ovens (2014)

Problems arising in the reconstruction of coke battery 1 at Isfahan steel plant are considered. The construction of coke battery 1 (coke-oven capacity 27.3 m3) with a PVR-51 dust-free coke-discharge system and bottom heating-gas supply is described. The losses of unprocessed coke-oven gas are calculated after coke-battery startup and after the elimination of leaks at seams in the refractory lining. Introduction of a method of detecting leaks at lining seams in the coke-oven walls reduces the losses of unprocessed coke-oven gas from 1738.73 to 44.6 m3/h.
Widely dispersed p53 mutation in respiratory epithelium. A novel mechanism for field carcinogenesis. (1997)

Individuals with one aerodigestive tract malignancy have a high incidence of second primary aerodigestive tumors. The mechanism for this field effect has not been determined. We studied an individual with widespread dysplastic changes in the respiratory epithelium but no overt carcinoma. The entire tracheobronchial tree obtained at autopsy was embedded in paraffin, and bronchial epithelial cells were isolated by microdissection. DNA extracted from the microdissected cells was analyzed for point mutations in the p53 tumor suppressor gene. A single, identical point mutation consisting of a G:C to T:A transversion in codon 245 was identified in bronchial epithelium from 7 of 10 sites in both lungs. Epithelium at sites containing the p53 mutation was morphologically abnormal, exhibiting squamous metaplasia and mild to moderate atypia. No invasive tumor was found in the tracheobronchial tree or any other location. Cells from peripheral blood, kidney, liver, and lymph node exhibited no abnormality in the p53 gene. The widespread presence of a single somatic p53 point mutation in the bronchi of a smoker suggests that a single progenitor bronchial epithelial clone may expand to populate broad areas of the bronchial mucosa-a novel mechanism for field carcinogenesis in the respiratory epithelium that may be of importance in assessing individuals for risk of a second primary tumor as well as in devising effective strategies for chemoprevention of lung cancer.
MODIFICATION OF A DNA EXTRACTION TECHNIQUE FROM WHITE HUMAN BLOOD CELLS (2012)

Introducción: Las técnicas modificadas de extracción de ADN a partir de glóbulos blancos, permiten obtener un buen rendimiento en cantidad y pureza de ADN extraído.&amp;nbsp;Objetivo: Modificar la técnica de extracción de ADN para economizar tiempo y reactivos utilizados.&amp;nbsp;Materiales y Métodos: Fueron modificados los pasos de la técnica de extracción de Gustafson (1987). La cantidad de ADN producida fue calculada por espectrofotometría. La pureza del ADN extraído fue evaluada mediante amplificación con PCR y comprobación en geles de agarosa. Resultados: Las modificaciones que proponemos al método de Gustafson (1987) representan un ahorro económico del 70% y en tiempo de 6 horas aproximadamente.&amp;nbsp; Conclusión: El método que se propone en el presente trabajo es más económico en tiempo y dinero para la extracción de ADN de glóbulos blancos. Además, el rendimiento en cuanto a la cantidad de ADN producida es superior.
Characterisation of a Novel Series of Aprotinin-derived Anticoagulants (1995)

Upon vascular damage platelet activation and blood coagulation are initiated. Interference at the initial level of the activation of the coagulation cascade can result in effective inhibition of thrombus formation. The in vivo antithrombotic properties of a series of bovine pancreatic trypsin inhibitor mutants (BPTI, aprotinin) 4C2, 7L22, 5L15, 5L15-PEG, 6L15 and 5L84, as described in the accompanying paper, with a combined inhibitory activity on factor Xa, factor VIIa-tissue factor complex, factor XIa and plasma kallikrein were compared to rTAP, r-hirudin, heparin and enoxaparin in a platelet rich thrombosis model in hamsters. Platelet dependent thrombus deposition was quantified by dedicated image analysis after transillumination of the femoral vein to which a standardised vascular trauma was applied. After increasing intravenous bolus injections all tested agents, except for aprotinin, induced a dose dependent decrease of thrombus formation and a concomitant prolongation of the aPTT. From the linear correlation between these two parameters it was found that 5 out of the 6 tested aprotinin analogues, rTAP and r-hirudin completely inhibited thrombus formation at a therapeutical (2- to 3-fold) aPTT prolongation while 4C2, heparin and enoxaparin only inhibited thrombus formation for 40 to 50 percent at a 2-fold aPTT prolongation. Based on the calculated IC50 values for thrombus formation rTAP was found to be the most active compound in this model. It is concluded that acceptable interference at the initial level of the blood coagulation, e.g. within a therapeutical aPTT prolongation, can significantly inhibit platelet deposition at a site of vascular injury.