gebhart/patrepeval huggingface dataset:
Patterning Indium Tin Oxide and Indium Zinc Oxide Using Microcontact Printing and Wet Etching (2001)

We report a procedure that uses microcontact printing and wet chemical etching to fabricate patterned films of indium tin oxide (ITO) and indium zinc oxide (IZO). The procedure consists of three steps: (1) inking a patterned elastomeric stamp with an alkanephosphonic acid; (2) microcontact printing to form a patterned multilayer film of alkanephosphonic acid on the surface of an ITO or IZO film; (3) etching the unprotected regions of the ITO or IZO film using 0.05 M oxalic acid as the etchant. We demonstrate this procedure by fabricating patterned ITO and IZO films with areas as large as 15 cm2 and minimum feature sizes of ∼2 μm. The key step in this procedure is applying the alkanephosphonic acid ink to the surface of the stamp. We present two different inking methods to illustrate the impact of stamp inking on the quality of printed and etched ITO and IZO films.
Development of a Magnetically Operated Artificial Urethral Sphincter (1993)

The artificial urethral sphincter (AUS) has been in clinical use for more than 20 years. Currently available AUS devices, however, are difficult to use and not entirely reliable. A magnetically operated AUS is currently under the development. Although the skin between the magnets will be compressed all day long, little information exists on the effects of chronic pressure on the skin structure and blood flow. In five miniature pigs, two internal magnets and one control metal disk were implanted subcutaneously at three different positions, and external magnets with differing magnetic forces were applied to the skin overlying the internal magnets for six weeks. In four pigs, the skin blood flow was measured by a laser Doppler flow meter applying different pressures. Compression of 10 mmHg preserved normal skin morphology in all but one animal where blood flow had not recovered 2 weeks after surgery. Compression of 20 mmHg for 6 weeks, however, produced pressure ulcers in all five cases (p < 0.05 vs. 10 mmHg group). The skin blood flow declined for pressures exceeding 20 mmHg (0 mmHg: 4.3 +/- 1.2, 10 mmHg: 4.3 +/- 3.3, 20 mmHg: 2.6 +/- 2.7 ml/min/100 g). We concluded that the magnetically operated AUS should use a magnetic coupling with a pressure less than 10 mmHg exerted on the interposing skin.
The calculation and synthesis of a template molecule (1993)

This paper discusses an algorithm to compute the geometric requirements for a template molecule. A Program called DESIGN is used to calculate templates by matching vectors from a database of carbon skeleta. Applications of the approach to an epitope of myoglobin and a fragment around the active site of the enzyme thioredoxin is examined. The synthesis of the template molecule 7 is described.
Th1-Th17 Cells Mediate Protective Adaptive Immunity against Staphylococcus aureus and Candida albicans Infection in Mice (2009)

We sought to define protective mechanisms of immunity to Staphylococcus aureus and Candida albicans bloodstream infections in mice immunized with the recombinant N-terminus of Als3p (rAls3p-N) vaccine plus aluminum hydroxide (Al(OH(3)) adjuvant, or adjuvant controls. Deficiency of IFN-gamma but not IL-17A enhanced susceptibility of control mice to both infections. However, vaccine-induced protective immunity against both infections required CD4+ T-cell-derived IFN-gamma and IL-17A, and functional phagocytic effectors. Vaccination primed Th1, Th17, and Th1/17 lymphocytes, which produced pro-inflammatory cytokines that enhanced phagocytic killing of both organisms. Vaccinated, infected mice had increased IFN-gamma, IL-17, and KC, increased neutrophil influx, and decreased organism burden in tissues. In summary, rAls3p-N vaccination induced a Th1/Th17 response, resulting in recruitment and activation of phagocytes at sites of infection, and more effective clearance of S. aureus and C. albicans from tissues. Thus, vaccine-mediated adaptive immunity can protect against both infections by targeting microbes for destruction by innate effectors.
Symptomatic Granular Cell Tumor Involving the Pituitary Gland in a Dog: A Case Report and Review of the Literature (2001)

A granular cell tumor involving the pituitary gland, optic chiasm and ventral pyriform lobes was discovered in a 12-year-old Labrador Retriever. Clinical signs included acute blindness, seizures, ataxia, weakness, and behavioral changes. The diagnosis was established by histopathologic and ultrastructural examination of neoplastic tissues collected at necropsy. Granular cell tumors involving the central nervous system are well documented in humans but rarely have been described in dogs. The location of the neoplasm and the clinical symptoms seen in this dog closely parallel those of a rare syndrome in humans commonly described as symptomatic parasellar or pituitary granular cell tumors. The cell of origin for these tumors is still highly debated, and attempts to characterize human granular cell tumors through immunohistochemistry have produced conflicting results. An immunohistochemical profile of this neoplasm revealed focal positive staining for vimentin with a lack of staining for neuron-specific enolase, glial fibrillary acidic protein, S-100, and synaptophysin. All neoplastic cells were strongly positive with the periodic acid-Schiff reaction.
Electrochemical Switching and Size Selection in Cucurbit[8]uril‐Mediated Dendrimer Self‐Assembly (2006)

A host of possibilities: Cucurbit[8]uril acts as a host to mediate in a highly effective way the formation of charge-transfer complexes between dendrimers containing accessible π-donor and π-acceptor units (see scheme). Redox switching of the self-assembly affords control over the size of the predominant dendrimer assemblies. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2006/z602220_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Differential Expression of Methanogenesis Genes of Methanothermobacter thermoautotrophicus (Formerly Methanobacterium thermoautotrophicum ) in Pure Culture and in Cocultures with Fatty Acid-Oxidizing Syntrophs (2002)

The expression of genes involved in methanogenesis in a thermophilic hydrogen-utilizing methanogen, Methanothermobacter thermoautotrophicus strain TM, was investigated both in a pure culture sufficiently supplied with H(2) plus CO(2) and in a coculture with an acetate-oxidizing hydrogen-producing bacterium, Thermacetogenium phaeum strain PB, in which hydrogen partial pressure was constantly kept very low (20 to 80 Pa). Northern blot analysis indicated that only the mcr gene, which encodes methyl coenzyme M reductase I (MRI), catalyzing the final step of methanogenesis, was expressed in the coculture, whereas mcr and mrt, which encodes methyl coenzyme M reductase II (MRII), the isofunctional enzyme of MRI, were expressed at the early to late stage of growth in the pure culture. In contrast to these two genes, two isofunctional genes (mtd and mth) for N(5),N(10)-methylene-tetrahydromethanopterin dehydrogenase, which catalyzes the fourth step of methanogenesis, and two hydrogenase genes (frh and mvh) were expressed both in a pure culture and in a coculture at the early and late stages of growth. The same expression pattern was observed for Methanothermobacter thermoautotrophicus strain DeltaH cocultured with a thermophilic butyrate-oxidizing syntroph, Syntrophothermus lipocalidus strain TGB-C1. Two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis of whole proteins of M. thermoautotrophicus strain TM obtained from a pure culture and a coculture with the acetate-oxidizing syntroph and subsequent N-terminal amino acid sequence analysis confirmed that MRI and MRII were produced in the pure culture, while only MRI was produced in the coculture. These results indicate that under syntrophic growth conditions, the methanogen preferentially utilizes MRI but not MRII. Considering that hydrogenotrophic methanogens are strictly dependent for growth on hydrogen-producing fermentative microbes in the natural environment and that the hydrogen supply occurs constantly at very low concentrations compared with the supply in pure cultures in the laboratory, the results suggest that MRI is an enzyme primarily functioning in natural methanogenic ecosystems.
ANDROPAUSE: A MISNOMER FOR A TRUE CLINICAL ENTITY (2000)

The onset of ADAM is unpredictable and its manifestations are subtle and variable, which has led to a paucity of interest in its diagnosis and treatment. Urological practice commonly includes a large proportion of men older than 50 years. Therefore, it is important for urologists to recognize the manifestations of and be familiar with evaluations necessary to document ADAM as well as its treatment and monitoring.
MRI alone simulation for conformal radiation therapy of prostate cancer: technical aspects (2006)

The value of MRI in defining target volumes and organs at risk is established. Numerous difficulties appear to stand in the way of using MRI alone in dose planning, with the result that this imaging modality is used in most cases in conjunction with computerized X-ray tomography (CT). The aim of this paper is to appreciate these difficulties: geometrical distortion, chemical shifts, dosimetric accuracy. Geometrical distortion measurements were carried out on two 1.5 T MR scanners and the effect of chemical shift and magnetic susceptibility were evaluated in volunteers. The effect on dosimetric calculations of uncertainty in determining electron densities was evaluated too. Geometrical distortion remained at small values: less than 2 mm and 3 mm for field of view of 20 cm and 45 cm. The chemical shift and magnetic susceptibility values obtained, ranging from 0.3 to 3 mm, were well below the theoretical values. The assignment of relative electron densities to only two structures in MR images seems to permit dose planning that is identical with that obtained with CT. None of the technical obstacles mentioned represents a stumbling block. The access to MRI facility could represent a persisting problem.
The Use of Mobile Devices in Aiding Dietary Assessment and Evaluation (2010)

There is a growing concern about chronic diseases and other health problems related to diet including obesity and cancer. The need to accurately measure diet (what foods a person consumes) becomes imperative. Dietary intake provides valuable insights for mounting intervention programs for prevention of chronic diseases. Measuring accurate dietary intake is considered to be an open research problem in the nutrition and health fields. In this paper, we describe a novel mobile telephone food record that will provide an accurate account of daily food and nutrient intake. Our approach includes the use of image analysis tools for identification and quantification of food that is consumed at a meal. Images obtained before and after foods are eaten are used to estimate the amount and type of food consumed. The mobile device provides a unique vehicle for collecting dietary information that reduces the burden on respondents that are obtained using more classical approaches for dietary assessment. We describe our approach to image analysis that includes the segmentation of food items, features used to identify foods, a method for automatic portion estimation, and our overall system architecture for collecting the food intake information.
Age-Related Alterations in the Circadian Rhythms of Pulsatile Luteinizing Hormone and Testosterone Secretion in Healthy Men (1988)

The effect of advancing age on the chronobiology of testosterone (T) and luteinizing hormone (LH) secretion in healthy men was investigated. Twenty young (average age 30.4 yrs) and 14 elderly (average age 70.4 yrs) men underwent 10 min blood sampling for 25 hrs to evaluate the circadian periodicity of LH, LH pulse frequency, and T. Using cosinor regression analysis, young men were found to have a significant (p less than .05) circadian variation in LH pulse frequency, with slowing of LH pulses during the night (maximum slowing at 2230 hr). There was also a tendency for LH pulse amplitude to increase at night (p = .06) in young men. However, no significant circadian pattern in LH pulse frequency or amplitude was detected in the elderly men. Mean LH by radioimmunoassay (RIA) and bioassay did not vary over the 24-hr period in either age group. Both young and elderly men had significant circadian rhythms in serum T, although the rhythm in elderly men was considerably blunted and was shifted in time compared to the young. These data provide evidence for age-related changes in the circadian rhythms of LH pulse frequency and T secretion and suggest that the LHRH pulse generator loses its circadian rhythmicity with normal aging in men.
Evolutionary engineering of a glycerol‐3‐phosphate dehydrogenase‐negative, acetate‐reducing S accharomyces cerevisiae strain enables anaerobic growth at high glucose concentrations (2013)

Glycerol production by Saccharomyces cerevisiae, which is required for redox-cofactor balancing in anaerobic cultures, causes yield reduction in industrial bioethanol production. Recently, glycerol formation in anaerobic S. cerevisiae cultures was eliminated by expressing Escherichia coli (acetylating) acetaldehyde dehydrogenase (encoded by mhpF) and simultaneously deleting the GPD1 and GPD2 genes encoding glycerol-3-phosphate dehydrogenase, thus coupling NADH reoxidation to reduction of acetate to ethanol. Gpd⁻ strains are, however, sensitive to high sugar concentrations, which complicates industrial implementation of this metabolic engineering concept. In this study, laboratory evolution was used to improve osmotolerance of a Gpd⁻ mhpF-expressing S. cerevisiae strain. Serial batch cultivation at increasing osmotic pressure enabled isolation of an evolved strain that grew anaerobically at 1 M glucose, at a specific growth rate of 0.12 h⁻¹. The evolved strain produced glycerol at low concentrations (0.64 ± 0.33 g l⁻¹). However, these glycerol concentrations were below 10% of those observed with a Gpd⁺ reference strain. Consequently, the ethanol yield on sugar increased from 79% of the theoretical maximum in the reference strain to 92% for the evolved strains. Genetic analysis indicated that osmotolerance under aerobic conditions required a single dominant chromosomal mutation, and one further mutation in the plasmid-borne mhpF gene for anaerobic growth.
Stereoisomeric Specificity of the Retinoid Cycle in the Vertebrate Retina (2000)

Understanding of the stereospecificity of enzymatic reactions that regenerate the universal chromophore required to sustain vision in vertebrates, 11-cis-retinal, is needed for an accurate molecular model of retinoid transformations. In rod outer segments (ROS), the redox reaction involves all-trans-retinal and pro-S-NADPH that results in the production of pro-R-all-trans-retinol. A recently identified all-trans-retinol dehydrogenase (photoreceptor retinol dehydrogenase) displays identical stereospecificity to that of the ROS enzyme(s). This result is unusual, because photoreceptor retinol dehydrogenase is a member of a short chain alcohol dehydrogenase family, which is often pro-S-specific toward their hydrophobic alcohol substrates. The second redox reaction occurring in retinal pigment epithelium, oxidation of 11-cis-retinol, which is largely catalyzed by abundantly expressed 11-cis-retinol dehydrogenase, is pro-S-specific to both 11-cis-retinol and NADH. However, there is notable presence of pro-R-specific activities. Therefore, multiple retinol dehydrogenases are involved in regeneration of 11-cis-retinal. Finally, the cellular retinaldehyde-binding protein-induced isomerization of all-trans-retinol to 11-cis-retinol proceeds with inversion of configuration at the C(15) carbon of retinol. Together, these results provide important additions to our understanding of retinoid transformations in the eye and a prelude for in vivo studies that ultimately may result in efficient pharmacological intervention to restore and prevent deterioration of vision in several inherited eye diseases.
Cutaneous vasodilation during dorsal column stimulation is mediated by dorsal roots and CGRP (1997)

Dorsal column stimulation (DCS) is used clinically to provide pain relief from peripheral vascular disease and has the benefit of increasing cutaneous blood flow to the affected lower extremities. The purpose of this study was to examine the role of dorsal roots, calcitonin gene-related peptide (CGRP), and substance P in the cutaneous vasodilation induced by DCS. Male rats were anesthetized with pentobarbital sodium (60 mg/kg ip). A unipolar ball electrode was placed unilaterally on the spinal cord at the L1-L2 spinal segment. Blood flow was recorded in each hindpaw foot pad with laser Doppler flowmeters. Blood flow responses were assessed during 1 min of DCS (either 0.2 mA subdural or 0.6 mA epidural at 50 Hz, 0.2-ms pulse duration). Dorsal rhizotomy of L3-L5 (n = 5) abolished the cutaneous vasodilation to subdural DCS, whereas removal of T10-T12 (n = 5) and T13-L2 dorsal roots (n = 5) did not attenuate the DCS-induced vasodilation. The CGRP antagonist, CGRP-(8-37) (2.6 mg/kg iv, n = 7), eliminated the epidural DCS-induced vasodilation, whereas the substance P receptor antagonist, CP-96345 (1 mg/kg iv, n = 6), had no effect. In summary, L3-L5 dorsal roots and CGRP are essential for the DCS-induced vasodilation. We propose that DCS antidromically activates afferent fibers in the dorsal roots, thus causing peripheral release of CGRP, which produces cutaneous vasodilation.
Spatio-temporal analysis of molecular delivery through the blood–brain barrier using focused ultrasound (2007)

The deposition of gadolinium through ultrasound-induced blood-brain barrier (BBB) openings in the murine hippocampus was investigated. First, wave propagation simulations through the intact mouse skull revealed minimal beam distortion while thermal deposition simulations, at the same sonication parameters used to induce BBB opening in vivo, revealed temperature increases lower than 0.5 degrees C. The simulation results were validated experimentally in ex vivo skulls (m = 6) and in vitro tissue specimens. Then, in vivo mice (n = 9) were injected with microbubbles (Optison; 25-50 microl) and sonicated (frequency: 1.525 MHz, pressure amplitudes: 0.5-1.1 MPa, burst duration: 20 ms, duty cycle: 20%, durations: 2-4 shots, 30 s per shot, 30 s interval) at the left hippocampus, through intact skin and skull. Sequential, high-resolution, T1-weighted MRI (9.4 Tesla, in-plane resolution: 75 microm, scan time: 45-180 min) with gadolinium (Omniscan; 0.5 ml) injected intraperitoneally revealed a threshold of the BBB opening at 0.67 MPa and BBB closing within 28 h from opening. The contrast-enhancement area and gadolinium deposition path were monitored over time and the influence of vessel density, size and location was determined. Sonicated arteries, or their immediate surroundings, depicted greater contrast enhancement than sonicated homogeneous brain tissue regions. In conclusion, gadolinium was delivered through a transiently opened BBB and contained to a specific brain region (i.e., the hippocampus) using a single-element focused ultrasound transducer. It was also found that the amount of gadolinium deposited in the hippocampal region increased with the acoustic pressure and that the spatial distribution of the BBB opening was determined not only by the ultrasound beam, but also by the vasculature of the targeted brain region.
Rat alveolar myofibroblasts acquire alpha-smooth muscle actin expression during bleomycin-induced pulmonary fibrosis. (1993)

The majority of fibroblasts in alveolar septa are characterized by the presence of cytoplasmic bundles of microfilaments that contain cytoplasmic actin isoforms; these cells have been named contractile interstitial cells or V-type myofibroblasts. In the rat, they express desmin as intermediate filament protein. In this study, we explored the possibility that modulation and replication of such septal fibroblasts result in the appearance of alpha-smooth muscle (alpha-SM) actin-positive myofibroblasts, typical of lung fibrosis. Experimental pulmonary fibrosis was produced by a unique intratracheal instillation of bleomycin to 28 rats. Eight additional rats used as controls received the equivalent volume of saline. Paraffin and frozen sections of lungs were examined at days 1, 3, 5 and 7 after treatment. Microfilaments and intermediate filaments were stained using antibodies against total actin, alpha-SM actin, desmin, vimentin, keratin, and SM myosin. Electron microscopic labeling of desmin and alpha-SM actin using immunogold technique was done on Lowicryl K4M resin-embedded specimens. alpha-SM actin appeared in desmin-positive alveolar fibroblasts as early as 24 hours after intratracheal bleomycin instillation; the modulation of alpha-SM actin in these cells was preceded by a lymphomonocytic infiltration of alveolar septa. Twenty-four hours to 3 days after bleomycin administration, a proliferation of alveolar myofibroblasts occurred. Fibrosis with laying down of collagen fibers took place after the above mentioned cellular modifications. Our results support the view that septal fibroblastic cells can modulate into typical alpha-SM actin-containing myofibroblasts during experimental bleomycin-induced pulmonary fibrosis. In such a modulation a possible role of cytokines, particularly of transforming growth factor-beta, is considered.
Local Injection of IFN-gamma Reduces the Number of Myofibroblasts and the Collagen Content in Palatal Wounds (2000)

Wound contraction and scar formation after cleft palate surgery impair maxillary growth and dentoalveolar development. Since myofibroblast numbers and scar formation are reduced by interferon-gamma (IFN-gamma) in the healing of dermal wounds, the hypothesis was tested that local administration of IFN-gamma reduces the numbers of myofibroblasts and the elevated amount of collagen during palatal mucoperiosteal wound healing. Standardized mucoperiosteal excision wounds were made in the palatal mucoperiosteum of young rats. Either IFN-gamma or vehicle alone (sham group) was repeatedly injected into the wound site between 4 and 29 days post-wounding. The results were compared with unmanipulated control wounds. Samples of wound tissue were prepared for biochemical and microscopic analysis. The hydroxyproline, sulfated glycosaminoglycan and DNA contents of the wound tissues were analyzed biochemically. The degree of re-epithelialization, tissue thickness, the numbers of myofibroblasts, and the amounts of elastin and collagen types I and III were evaluated on histological sections. Injection of vehicle alone affected almost all healing parameters, compared with the controls, and delayed the wound-healing process. IFN-gamma stimulated re-epithelialization and decreased the numbers of myofibroblasts when compared with vehicle-treated wounds. It also decreased the hydroxyproline and glycosaminoglycan contents of 60-day-old wound tissue, but the histological characteristics of scar tissue persisted. Therefore, IFN-gamma is able to reduce the numbers of myofibroblasts and the collagen content of scar tissue after palatal wound healing. It may be a promising pharmaceutical agent for the reduction of wound contraction and scarring after cleft palate surgery.