gebhart/patrepeval huggingface dataset:
Impact dynamics and rebound of water droplets on superhydrophobic carbon nanotube arrays (2007)

The authors report the impact response of water droplets impinging on superhydrophobic carbon nanotube arrays and observe that arrays with different wetting properties display significantly different responses. For an array with a static contact angle of 163°, the droplet bounces off the surface several times, while for an array with a reduced contact angle of 140°, the droplet does not rebound and remains pinned. The contact angle hysteresis and contact line pinning for the 140° array suggest that the momentum of the droplet during the initial impact enables it to penetrate and displace the air pockets that are responsible for the superhydrophobicity of the array under static conditions.
Adjusting batch effects in microarray expression data using empirical Bayes methods (2006)

Non-biological experimental variation or "batch effects" are commonly observed across multiple batches of microarray experiments, often rendering the task of combining data from these batches difficult. The ability to combine microarray data sets is advantageous to researchers to increase statistical power to detect biological phenomena from studies where logistical considerations restrict sample size or in studies that require the sequential hybridization of arrays. In general, it is inappropriate to combine data sets without adjusting for batch effects. Methods have been proposed to filter batch effects from data, but these are often complicated and require large batch sizes ( > 25) to implement. Because the majority of microarray studies are conducted using much smaller sample sizes, existing methods are not sufficient. We propose parametric and non-parametric empirical Bayes frameworks for adjusting data for batch effects that is robust to outliers in small sample sizes and performs comparable to existing methods for large samples. We illustrate our methods using two example data sets and show that our methods are justifiable, easy to apply, and useful in practice. Software for our method is freely available at: http://biosun1.harvard.edu/complab/batch/.
Metabolic Analysis of <i>Corynebacterium glutamicum</i> during Lactate and Succinate Productions under Oxygen Deprivation Conditions (2004)

Lactate and succinate were produced from glucose by Corynebacterium glutamicum under oxygen deprivation conditions without growth. Addition of bicarbonate to the reaction mixture led not only to a 3.6-fold increase in succinate production rate, but also to a 2.3- and 2.5-fold increase, respectively, of the rates of lactate production and glucose consumption, compared to the control. Furthermore, when small amounts of pyruvate were added to the reaction mixture, acid production rates and the glucose consumption rate were multiplied by a factor ranging from 2 to 3. These phenomena were paralleled by an increase in the NAD(+)/NADH ratio, thus corroborating the view that the efficient regeneration of NAD(+) could be triggered by the addition of either bicarbonate or pyruvate. To investigate the global metabolism of corynebacteria under oxygen deprivation conditions, we engineered several strains where the genes coding for key metabolic enzymes had been inactivated by gene disruption and replacement. A lactate dehydrogenase (LDH)-deficient mutant was not able to produce lactate, suggesting this enzyme has no other isozyme. Although a pyruvate carboxylase (pyc) mutant exhibited similar behavior to that of the wild type, phosphoenolpyruvate carboxylase (ppc) mutants were characterized by a dramatic decrease in succinate production, which was concomitant to decreased lactate production and glucose consumption rates. This set of observations corroborates the view that in coryneform bacteria under oxygen deprivation conditions the major anaplerotic reaction is driven by the ppc gene product rather than by the pyc gene product. Moreover, intracellular NADH concentrations in C. glutamicum were observed to correlate to oxygen-deprived metabolic flows.
Next generation 15 µm terahertz antennas:  mesa-structuring of  InGaAs/InAlAs photoconductive layers (2010)

Mesa-structuring of InGaAs/InAlAs photoconductive layers is performed employing a chemical assisted ion beam etching (CAIBE) process. Terahertz photoconductive antennas for 1.5 microm operation are fabricated and evaluated in a time domain spectrometer. Order-of-magnitude improvements versus planar antennas are demonstrated in terms of emitter power, dark current and receiver sensitivity.
Comparative genomic hybridization analysis of human oocytes and polar bodies (2006)

The results presented in this study more than double the quantity of CGH data from female gametes currently available. Abnormalities caused by whole chromosome non-disjunction, unbalanced chromatid predivision and chromosome breakage were reliably identified using the CGH protocol. Analysis of the data revealed a preferential participation of chromosome X and the smaller autosomes in aneuploidy and provided further evidence for the existence of age-independent factors in female aneuploidy.
Localization of Upper Airway Collapse during Sleep in Patients with Obstructive Sleep Apnea (1990)

The present study was conducted to determine the effects of body position and sleep state, as well as the effect of uvulopalatopharyngoplasty (UPPP) on the regions over which the upper airway (UA) collapses during sleep. To accomplish this goal, 18 male patients with obstructive sleep apnea (OSA) underwent overnight polysomnography with simultaneous monitoring of pressures in the posterior nasopharynx, oropharynx, hypopharynx, and esophagus. From the profile of pressures recorded in the UA and esophagus, the regions over which the UA collapses during apneas could be determined. The patients were 54 +/- 14 y of age and were grossly obese with a body mass index of 37 +/- 2 kg/m2. They had moderately severe OSA with a mean apnea plus hypopnea index of 62 +/- 8 per hour. During NREM sleep, 10 of the 18 (56%) patients had collapse confined to the velopharyngeal or retropalatal segment of the upper airway. The remaining 44% of the patients demonstrated collapse of the retroglossal segment of the oropharynx located caudal to the inferior margin of the soft palate. Upper airway collapse at the level of the hyoid bone was not observed during NREM sleep. Observations made during REM sleep in nine patients demonstrated that collapse occurred in a more caudal segment of the UA in seven patients during REM than during NREM sleep. The effect of sleep position was evaluated in 10 patients and found to have little affect on the extent over which the UA collapsed during sleep independent of sleep state. The effects of UPPP on regional UA collapse were evaluated in a small group of six patients.(ABSTRACT TRUNCATED AT 250 WORDS)
Discovering statistically significant pathways in expression profiling studies (2005)

Accurate and rapid identification of perturbed pathways through the analysis of genome-wide expression profiles facilitates the generation of biological hypotheses. We propose a statistical framework for determining whether a specified group of genes for a pathway has a coordinated association with a phenotype of interest. Several issues on proper hypothesis-testing procedures are clarified. In particular, it is shown that the differences in the correlation structure of each set of genes can lead to a biased comparison among gene sets unless a normalization procedure is applied. We propose statistical tests for two important but different aspects of association for each group of genes. This approach has more statistical power than currently available methods and can result in the discovery of statistically significant pathways that are not detected by other methods. This method is applied to data sets involving diabetes, inflammatory myopathies, and Alzheimer's disease, using gene sets we compiled from various public databases. In the case of inflammatory myopathies, we have correctly identified the known cytotoxic T lymphocyte-mediated autoimmunity in inclusion body myositis. Furthermore, we predicted the presence of dendritic cells in inclusion body myositis and of an IFN-alpha/beta response in dermatomyositis, neither of which was previously described. These predictions have been subsequently corroborated by immunohistochemistry.
Bladder Smooth Muscle Cells in Culture: I. Identification and Characterization (1993)

This report documents the growth and culture characteristics of human and fetal bovine bladder smooth muscle cells in vitro. Bladder smooth muscle cell strains have been identified by their spindle shaped morphology, noncontact inhibited growth characteristics and the expression of smooth muscle cell specific alpha-actin. Extracellular matrix protein biosynthesis by these cells in vitro has been characterized by metabolic labeling of proteins with [14C] radiolabeled proline and analysis by SDS gel electrophoresis. These studies demonstrate that bladder smooth muscle cells synthesize predominantly types I and III collagen, and fibronectin. In addition type III collagen exists in both a partially processed (pN alpha 1[III]) form and processed form. Complementary immunohistochemical studies show localization of type I, III, and IV collagens, and fibronectin to bladder smooth muscle cell extracellular matrix. We conclude that both fetal bovine and human smooth muscle bladder cells are capable of secreting the classic components of the surrounding connective tissue.
Spatial light modulation based on photoinduced change in the complex refractive index of bacteriorhodopsin (1996)

Bacteriorhodopsin exhibits photoinduced changes in both absorption and refractive index at 633 nm. To explore the possibility of exploiting this property in constructing a photoaddressed spatial light modulator, we investigated the transmission property of a Fabry-Perot interferometer containing a bacteriorhodopsin thin film. Film was formed that had a phase shift of π/4 and sufficient interference fringe contrast for spatial light modulation. This establishes the possibility of constructing a spatial light modulator that features nonlinear input-output characteristics and can operate at moderate light intensities of the order of tens of milliwatts per centimeter square.
A single disulfide bond restores thermodynamic and proteolytic stability to an extensively mutated protein (2000)

The potential for engineering stable proteins with multiple amino acid substitutions was explored. Eleven lysine, five methionine, two tryptophan, one glycine, and three threonine substitutions were simultaneously made in barley chymotrypsin inhibitor-2 (CI-2) to substantially improve the essential amino acid content of the protein. These substitutions were chosen based on the three-dimensional structure of CI-2 and an alignment of homologous sequences. The initial engineered protein folded into a wild-type-like structure, but had a free energy of unfolding of only 2.2 kcal/mol, considerably less than the wild-type value of 7.5 kcal/mol. Restoration of the lysine mutation at position 67 to the wild-type arginine increased the free energy of unfolding to 3.1 kcal/mol. Subsequent cysteine substitutions at positions 22 and 82 resulted in disulfide bond formation and a protein with nearly wild-type thermodynamic stability (7.0 kcal/mol). None of the engineered proteins retained inhibitory activity against chymotrypsin or elastase, and all had substantially reduced inhibitory activity against subtilisin. The proteolytic stabilities of the proteins correlated with their thermodynamic stabilities. Reduction of the disulfide bond resulted in substantial loss of both thermodynamic and proteolytic stabilities, confirming that the disulfide bond, and not merely the cysteine substitutions, was responsible for the increased stability. We conclude that it is possible to replace over a third of the residues in CI-2 with minimal disruption of stability and structural integrity.
The current biology of resistin (2004)

Obesity and noninsulin-dependent diabetes mellitus are globally epidemic. Insulin resistance is a major contributor to the pathogenesis of type II diabetes and plays a role in numerous other metabolic disorders including hypertension, dyslipidaemia and atherosclerosis. Obesity, in particular visceral adiposity, is positively correlated with insulin resistance. Although this correlation between adiposity and insulin resistance is well established in human beings as well as in rodent models, the mechanisms involved in obesity-related insulin resistance are not fully defined. One mechanism is that factors secreted from adipocytes can affect peripheral insulin resistance. One candidate for such a factor is resistin, an adipocyte-secreted hormone that impairs glucose homeostasis and insulin action in the mouse. This review will summarize our current understanding of resistin and will attempt to provide a framework for future study of its role in rodent and human physiology.
Enzymatic basis for the accumulation of glycolipids with X and dimeric X determinants in human lung cancer cells (NCI-H69). (1985)

Many human carcinomas accumulate a large quantity of glycolipids having X (Gal beta 1----4[Fuc alpha 1----3] GlcNAc) as well as di- or trimeric X determinant (Gal beta 1----4 [Fuc alpha 1----3] GlcNAc beta 1----3Gal beta 1----4 [Fuc alpha 1----3]GlcNAc beta 1----3Gal) (e.g. Hakomori, S., Nudelman, E., Levery, S. B., and Kannagi, R. (1984) J. Biol. Chem. 259, 4672-4680). The enzymatic basis of this phenomenon has been investigated with human small cell lung carcinoma NCI-H69 cells, in which a series of these structures has been found to accumulate. An alpha 1----3 fucosyltransferase solubilized from the membrane fraction with Triton X-100 catalyzed not only the transfer of a fucosyl residue from GDP-fucose to the penultimate GlcNAc residue of lactoneotetraosylceramide (nLc4) and lactonorhexaosylceramide (nLc6), but also to the internal GlcNAc residue (III-GlcNAc) of y2 glycolipid (V3FucnLc6) and that of sialosyl2----6lactonorhexaosylceramide (VI6NeuAcnLc6). No transfer of fucose to the internal GlcNAc (III-GlcNAc) of lactonorhexaosylceramide occurred, unless the above substitutions (V3Fuc or VI6NeuAc) were present. Fucosylation at V-GlcNAc and III-GlcNAc of nLc6 could be catalyzed by the same enzyme, based on the following observations: (i) fucosylation at both III- and V-GlcNAc was competitively inhibited by V3FucnLc6 and III3V3Fuc2nLc6; (ii) the same conditions (pH, bivalent cation, detergent) were optimal for fucosylation at both III- and V-GlcNAc; (iii) the Km values of the enzyme for nLc4, nLc6, and V3FucnLc6 were approximately the same; and (iv) the activity of the enzyme catalyzing fucosylation at both III- and V-GlcNAc was adsorbed on GDP-hexanolamine-Sepharose and was not inhibited by N-ethylmaleimide. The enzyme preferentially transferred fucose to the penultimate VGlcNAc, followed by transfer to the internal III-GlcNAc of nLc6. Thus, the pathway for synthesis of dimeric X proceeds as follows: nLc6----V3FucnLc6----III3V3Fuc2nLc6. No mechanism was found to operate for chain elongation of the X hapten structure through addition of GlcNAc residues to the terminal Gal of the X hapten.
Semiconductor Silicon as a Selective Emitter (2003)

Silicon operating in a vacuum is a good candidate thermal emitter since it has a high melting point (1680 K). The semiconductor bandgap, which can provide selective emission, adds to the potential for high operating temperature and, therefore, high radiated power. We present the detailed emitter theory, along with both theoretical and experimental results for spectral emittance of thin (∼1 μm) silicon films on sapphire substrates with a platinum backing. These results show the importance of temperature and film thickness in determining the selective spectral emittance and, with the proper material parameters, can be readily extended to other materials and systems.
Production of germline chimeric chickens, with high transmission rate of donor‐derived gametes, produced by transfer of primordial germ cells (1994)

Germline chimeric chickens were produced by transfer of primordial germ cells from White Leghorn to Barred Plymouth Rock, and vice versa. Blood was collected from stage 13-15 embryos and primordial germ cells were concentrated by Ficoll density gradient centrifugation. Approximately 200 primordial germ cells were injected into the bloodstream through the dorsal aorta of stage 14-15 recipient embryos from which blood had been drawn via the dorsal aorta prior to the injection. Intact embryos were also prepared as recipients for White Leghorns only. The manipulated embryos were cultured in recipient eggshells until hatching. Germline chimerism of the chickens reaching maturity was examined by mating them with Barred Plymouth Rocks and donor-derived offspring were identified based on their feather color. The efficiency of production of germline chimeras was 95% (19/20). When primordial germ cells were transferred from White Leghorn to Barred Plymouth Rock, the average frequency of donor-derived offspring was 81% for three male chimeras (96% for one female chimera), and it was approximately 3.5 times higher for transfer in the opposite direction (23% for 6 male chimeras). Removing blood from recipient embryos prior to primordial germ cell injection enhanced the frequency of donor-derived offspring by 10% in resulting male chimeras. Male chimeras produced donor-derived offspring more frequently (approximately 3.8 times) than female chimeras. Increases, decreases, or no changes were observed in the frequency of donor-derived offspring from the germline chimeras with increasing age.(ABSTRACT TRUNCATED AT 250 WORDS)
Marinobufagenin Stimulates Fibroblast Collagen Production and Causes Fibrosis in Experimental Uremic Cardiomyopathy (2006)

We have observed recently that experimental renal failure in the rat is accompanied by increases in circulating concentrations of the cardiotonic steroid, marinobufagenin (MBG), and substantial cardiac fibrosis. We performed the following studies to examine whether MBG might directly stimulate cardiac fibroblast collagen production. In vivo studies were performed using the 5/6th nephrectomy model of experimental renal failure (PNx), MBG infusion (MBG), PNx after immunization against MBG, and concomitant PNx and adrenalectomy. Physiological measurements with a Millar catheter and immunohistochemistry were performed. In vitro studies were then pursued with cultured isolated cardiac fibroblasts. We observed that PNx and MBG increased MBG levels, blood pressure, heart size, impaired diastolic function, and caused cardiac fibrosis. PNx after immunization against MBG and concomitant PNx and adrenalectomy had similar blood pressure as PNx but less cardiac hypertrophy, diastolic dysfunction, and cardiac fibrosis. MBG induced increases in procollagen-1 expression by cultured cardiac fibroblasts at 1 nM concentration. These increases in procollagen expression were accompanied by increases in collagen translation and increases in procollagen-1 mRNA without any demonstrable increase in procollagen-1 protein stability. The stimulation of fibroblasts with MBG could be prevented by administration of inhibitors of tyrosine phosphorylation, Src activation, epidermal growth factor receptor transactivation, and N-acetyl cysteine. Based on these findings, we propose that MBG directly induces increases in collagen expression by fibroblasts, and we suggest that this may be important in the cardiac fibrosis seen with experimental renal failure.
Development and Comparison of Four Real-Time Polymerase Chain Reaction Systems for Specific Detection and Quantification of Zea mays L. (2004)

Four real-time polymerase chain reaction systems aiming at the specific detection and quantification of maize DNA are described. They have been developed in four independent laboratories targeting different maize sequences, i.e., alcohol dehydrogenase (Adh1), high mobility group protein (hmga), invertase A (ivr1), and zein, respectively. They were all fully specific, showing a very similar quantification accuracy along a number of distantly related maize cultivars and being either single or low copy number genes. They were highly sensitive and exhibited limits of quantification below 100 maize genomic copies. In consequence, they are considered suitable for use as maize specific endogenous reference genes in DNA analyses, including GMO quantitative tests.
CMOS RF circuits for integrated wireless systems (2002)

There is increasing interest in the use of CMOS circuits for highly integrated high frequency wireless telecommunications systems. This paper presents the results of on-going work into the development of a cell library that includes many of the circuit elements required for the high frequency sub-system of a communications integrated circuit. The cells were fabricated using standard CMOS processes and measurement results are presented. No post processing was used with the circuits described.
Disaccharide uptake and priming in animal cells: inhibition of sialyl Lewis X by acetylated Gal beta 1-->4GlcNAc beta-O-naphthalenemethanol. (1995)

Inhibitors of glycosylation provide a tool for studying the biology of glycoconjugates. One class of inhibitors consists of glycosides that block glycoconjugate synthesis by acting as primers of free oligosaccharide chains. A typical primer contains one sugar linked to a hydrophobic aglycone. In this report, we describe a way to use disaccharides as primers. Chinese hamster ovary cells readily take up glycosides containing a pentose linked to naphthol, but they take up hexosides less efficiently and disaccharides not at all. Linking phenanthrol to a hexose improves its uptake dramatically but has no effect on disaccharides. To circumvent this problem, analogs of Xyl beta 1-->6Gal beta-O-2-naphthol were tested as primers of glycosaminoglycan chains. The unmodified disaccharide did not prime, but methylated derivatives had activity in the order Xyl beta 1-->6Gal(Me)3-beta-O-2-naphthol > Xyl beta 1-->6Gal (Me)2 beta-O-2-naphthol >> Xyl beta 1-->6Gal(Me)beta-O-2-naphthol. Acetylated Xyl beta 1-->6Gal beta-O-2-naphthol also primed glycosaminoglycans efficiently, suggesting that the terminal xylose residue was exposed by removing the acetyl groups. The general utility of using acetyl groups to create disaccharide primers was shown by the priming of oligosaccharides on peracetylated Gal beta 1-->4GlcNAc beta-O-naphthalenemethanol. This disaccharide inhibited sialyl Lewis X expression on HL-60 cells.
In Medication‐Overuse Headache, fMRI Shows Long‐Lasting Dysfunction in Midbrain Areas (2012)

Our study showed that MOH patients present dysfunctions in the mesocorticolimbic dopamine circuit, in particular in the ventromedial prefrontal cortex and in the substantia nigra/ventral tegmental area complex. The ventromedial prefrontal cortex dysfunctions seem to be reversible and attributable to the acute/chronic headache, whereas the substantia nigra/ventral tegmental area complex dysfunctions are persistent and possibly related to medication overuse. These dysfunctions might be the expression of long-lasting neuroadaptations related to the overuse of medications and/or a pre-existing neurophysiological condition leading to vulnerability to medication overuse. The observed persistent dysfunctions in the midbrain dopamine suggest that MOH may share some neurophysiological features with addiction.