gebhart/patrepeval huggingface dataset:
Ultra-Fast and Sensitive Detection of Non-Typhoidal Salmonella Using Microwave-Accelerated Metal-Enhanced Fluorescence (“MAMEF”) (2011)

Certain serovars of Salmonella enterica subsp. enterica cause invasive disease (e.g., enteric fever, bacteremia, septicemia, meningitis, etc.) in humans and constitute a global public health problem. A rapid, sensitive diagnostic test is needed to allow prompt initiation of therapy in individual patients and for measuring disease burden at the population level. An innovative and promising new rapid diagnostic technique is microwave-accelerated metal-enhanced fluorescence (MAMEF). We have adapted this assay platform to detect the chromosomal oriC locus common to all Salmonella enterica subsp. enterica serovars. We have shown efficient lysis of biologically relevant concentrations of Salmonella spp. suspended in bacteriological media using microwave-induced lysis. Following lysis and DNA release, as little as 1 CFU of Salmonella in 1 ml of medium can be detected in <30 seconds. Furthermore the assay is sensitive and specific: it can detect oriC from Salmonella serovars Typhi, Paratyphi A, Paratyphi B, Paratyphi C, Typhimurium, Enteritidis and Choleraesuis but does not detect Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae, Streptococcus pneumoniae, Haemophilus influenzae or Acinetobacter baumanii. We have also performed preliminary experiments using a synthetic Salmonella oriC oligonucleotide suspended in whole human blood and observed rapid detection when the sample was diluted 1:1 with PBS. These pre-clinical data encourage progress to the next step to detect Salmonella in blood (and other ordinarily sterile, clinically relevant body fluids).
Hair growth modulation by topical immunophilin ligands: induction of anagen, inhibition of massive catagen development, and relative protection from chemotherapy-induced alopecia. (1997)

Selected immunophilin ligands (IPLs) are not only potent immunosuppressants but also modulate hair growth. Their considerable side effects, however, justify at best topical applications of these drugs for the management of clinical hair growth disorders. Therefore, we have explored hair growth manipulation by topical cyclosporin A (CsA) and FK 506 in previously established murine models that mimic premature hair follicle regression (catagen) or chemotherapy-induced alopecia, two major pathomechanisms underlying human hair loss. We confirm that topical CsA and FK 506 induce active hair growth (anagen) in the back skin of C57BL/6 mice with all follicles in the resting stage (telogen) and show that both IPLs also inhibit massive, dexamethasone-induced, premature catagen development in these mice. Furthermore, we demonstrate that CsA and FK 506 provide relative protection from alopecia and follicle dystrophy induced by cyclophosphamide, possibly by favoring the dystrophic anagen pathway of follicle response to chemical damage. Although it remains to be established whether these IPLs exert the same effects on human hair follicles, our study provides proof of the principle that topical IPLs can act as potent manipulators of clinically relevant hair-cycling pathomechanisms. This strongly encourages one to explore the use of topical IPLs in the management of human hair growth disorders.
Control of yeast gene expression by transposable elements: maximum expression requires a functional Ty activator sequence and a defective Ty promoter. (1988)

Integration of a transposable element adjacent to a gene frequently results in an alteration in expression of the nearby gene. The purpose of our experiments was to identify cis-acting sequences within a yeast transposon (Ty) that are important for expression of the adjacent gene. The role of these sequences in Ty transcription was also analyzed in order to examine the relationship between Ty and adjacent gene expression. Three naturally occurring Ty elements located at the HIS4 locus were examined. These Ty elements differed by multiple sequence changes and had different effects on HIS4 expression. To determine which sequences were important to Ty and HIS4 expression, Ty::lacZ and Ty::HIS4::lacZ fusion genes were constructed and analyzed. Results of these experiments indicated that a sequence element is present in the Ty epsilon region that is necessary for HIS4 expression but which has only a modest effect on Ty transcription. Additionally, a mutation in the Ty promoter region decreased Ty transcription and increased HIS4 expression. The opposite effects of this mutation on Ty and adjacent gene expression were probably caused by promoter competition.
Vascular changes in neuroblastoma of mice following x-irradiation. (1974)

Vascular changes in a transplantable neuroblastoma of A/J mice following X-irradiation were studied. X-irradiation with doses lower than 500 rads in a single exposure caused a slight increase in the functional intravascular volume, as measured with 51Cr-labeled red cells 1 day after the irradiation, and a gradual decrease thereafter. X-irradiation with 1000 and 2000 rads, in contrast, induced a decrease in the vascular volume at 1 day postirradiation and a further gradual decrease thereafter. The extravasation of plasma protein, as measured with 125I-labeled plasma protein, increased soon after irradiation with doses of 250 to 2000 rads, and then decreased. Histopathological studies of tumors irradiated with 2000 rads revealed a progressive crowding or condensation of the vascular bed as the tumor cell population became reduced or tumor lobules receded. Direct irradiation-induced damage to the vessels and the disorganization of the architecture of vascular networks following irradiation appear to cause vascular occlusion and interfere with the blood flow in the tumors.
Mass Transport of Macromolecules within an In Vitro Model of Supragingival Plaque (2003)

The aim of this study was to examine the diffusion of macromolecules through an in vitro biofilm model of supragingival plaque. Polyspecies biofilms containing Actinomyces naeslundii, Fusobacterium nucleatum, Streptococcus oralis, Streptococcus sobrinus, Veillonella dispar, and Candida albicans were formed on sintered hydroxyapatite disks and then incubated at room temperature for defined periods with fluorescent markers with molecular weights ranging from 3,000 to 900,000. Subsequent examination by confocal laser scanning microscopy revealed that the mean square penetration depths for all tested macromolecules except immunoglobulin M increased linearly with time, diffusion coefficients being linearly proportional to the cube roots of the molecular weights of the probes (range, 10,000 to 240,000). Compared to diffusion in bulk water, diffusion in the biofilms was markedly slower. The rate of diffusion for each probe appeared to be constant and not a function of biofilm depth. Analysis of diffusion phenomena through the biofilms suggested tortuosity as the most probable explanation for retarded diffusion. Selective binding of probes to receptors present in the biofilms could not explain the observed extent of retardation of diffusion. These results are relevant to oral health, as selective attenuated diffusion of fermentable carbohydrates and acids produced within dental plaque is thought to be essential for the development of carious lesions.
Sensitive assay for measurement of antibodies to Clostridium botulinum neurotoxins A, B, and E: use of hapten-labeled-antibody elution to isolate specific complexes (1997)

The measurement of chicken and human antibodies to Clostridium botulinum neurotoxins A, B, and E was accomplished by affinity isolation of complexes containing these antibodies. By this approach, a mixture of toxin with the test antibody, fluoresceinated antibody, and enzyme (Russell's viper venom factor X activator)-labeled antibody is allowed to form a complex in solution phase. This complex is then bound to a matrix containing antifluorescein antibody. All components not bound to the matrix are washed off, and the complex is isolated intact by elution with fluorescein, which competes with the complex for binding to the antifluorescein matrix. The eluted complex is then bound to a matrix which specifically binds the test antibody (anti-chicken immunoglobulin Y [IgY] or anti-human IgG), and the bound complex is measured by using the enzyme label. Using this approach, we were able to measure as little as 1 ng of specific antibody per ml from affinity-isolated, monospecific chicken antibody preparations and to measure antibody specifically from IgY fractions of monospecific chicken antibody preparations. Human antibodies from subjects immunized with pentavalent toxoid preparations were detectable at dilutions as great as 24,300-fold, and undiluted serum from most control subjects showed no measurable antibody. Antibody was also measured in 65 subjects who were receiving preparations of neurotoxin A (BOTOX) for the treatment of spastic disorders. Eighteen of them had toxin-specific antibody reactive with toxin B, and two of them had toxin-specific antibody reactive with toxin A. The two patients having antibody to toxin A were refractory to treatment with this toxin. This approach of isolation of hapten-labeled immune complexes under nondenaturing conditions with hapten is broadly applicable to the specific measurement of antibodies present at very low concentrations in serum.
Solubilization of polyaniline in water by interpolymer complexation (1995)

Abstract Water solubility of electro‐active polymers in their doped state may provide a possibility for environmentally feasible manufacturing processes. Because previous results in this direction require expensive modifications or impractical template polymerization methods, we created a simple method of mixing components with a large molecular weight difference. The polymer which acts as an acidic dopant and provides water solubility, has to have the higher molecular weight. The formed complex resembles a block copolymer but in this case the polyaniline block is attached to the sulfonated polystyrene chain by strong physical interactions instead of chemical end‐to‐end linkage.
Unique patterns of CpG island methylation in inflammatory bowel disease-associated colorectal cancers (2011)

Cancer-specific CGI hypermethylation and age-associated CGI hypermethylation are diminished in IBD-CRCs relative to S-CRCs, while the KRAS mutation rate is comparable between these cancers. CGI hypermethylation appears to play only a minor role in IBD-associated carcinogenesis. We speculate that aging, rather than inflammation per se, promotes CIMP(+) CRCs in IBD patients.
Specific Enzymatic Amplification of DNA In Vitro: The Polymerase Chain Reaction (1986)

The discovery of specific restriction endonucleases (Smith and Wilcox 1970) made possible the isolation of discrete molecular fragments of naturally occurring DNA for the first time. This capability was crucial to the development of molecular cloning (Cohen et al. 1973); and the combination of molecular cloning and endonuclease restriction allowed the synthesis and isolation of any naturally occurring DNA sequence that could be cloned into a useful vector and, on the basis of flanking restriction sites, excised from it. The availability of a large variety of restriction enzymes (Roberts 1985) has significantly extended the utility of these methods.
Discovery of an Orally Efficacious Inhibitor of Coagulation Factor Xa Which Incorporates a Neutral P1Ligand (2003)

The discovery and SAR of ketopiperazino methylazaindole factor Xa inhibitors are described. Structure-activity data suggesting that this class of inhibitors does not bind in the canonical mode were confirmed by an X-ray crystal structure showing the neutral haloaromatic bound in the S(1) subsite. The most potent azaindole, 33 (RPR209685), is selective against related serine proteases and attains higher levels of exposure upon oral dosing than comparable benzamidines and benzamidine isosteres. Compound 33 was efficacious in the canine AV model of thrombosis.
Methyl groups in carcinogenesis: effects on DNA methylation and gene expression. (1992)

Lipotrope-deficient (methyl-deficient) diets cause fatty livers and increased liver-cell turnover and promote carcinogenesis in rodents. In rats prolonged intake of methyl-deficient diets results in liver tumor development. The mechanisms responsible for the cancer-promoting and carcinogenic properties of this deficiency remain unclear. The results of the experiments described here lend support to the hypothesis that intake of such a diet, by causing depletion of S-adenosylmethionine pools, results in DNA hypomethylation, which in turn leads to changes in expression of genes that may have key roles in regulation of growth. In livers of rats fed a severely methyl-deficient diet (MDD), lowered pools of S-adenosylmethionine and hypomethylated DNA were observed within 1 week. The extent of DNA hypomethylation increased when MDD was fed for longer periods. The decreases in overall levels of DNA methylation were accompanied by simultaneous alterations in gene expression, yielding patterns that closely resembled those reported to occur in livers of animals exposed to cancer-promoting chemicals and in hepatomas. Northern blot analysis of polyadenylated RNAs from livers of rats fed control or deficient diets showed that, after 1 week of MDD intake, there were large increases in levels of mRNAs for the c-myc and c-fos oncogenes, somewhat smaller increases in c-Ha-ras mRNA, and virtually no change in levels of c-Ki-ras mRNA. In contrast, mRNAs for epidermal growth factor receptor decreased significantly. The elevated levels of expression of the c-myc, c-fos, and c-Ha-ras genes were accompanied by selective changes in patterns of methylation within the sequences specifying these genes. Changes in DNA methylation and in gene expression induced in livers of rats fed MDD for 1 month were gradually reversed after restoration of an adequate diet. In hepatomas induced by prolonged dietary methyl deficiency, methylation patterns of c-Ki-ras and c-Ha-ras were abnormal. Although human diets are unlikely to be as severely methyl deficient as those used in these experiments, in some parts of the world intake of diets that are low in methionine and choline and contaminated with mycotoxins, such as aflatoxin, are common. Even in industrialized nations, deficiencies of folic acid and vitamin B12 are not uncommon and are exacerbated by some therapeutic agents and by substance abuse. Thus, it seems possible that interactions of diet and contaminants or drugs, by inducing changes in DNA methylation and aberrant gene expression, may contribute to cancer causation in humans.
Threshold dependence of laser-induced optical breakdown on pulse duration (1995)

A model for optical breakdown is presented, that takes the effects of avalanche ionization, electron–ion recombination, and electron diffusion into account. By assuming a rectangular temporal shape of the laser pulse, an analytical solution of the threshold parameters can be given. Especially, a square root dependence of the energy density on the pulse duration is found for pulse duration values between roughly 4 ps and 8 μs. The theory explains the results of several previous experiments investigating threshold parameters for a variety of target materials.
A network architecture solution for efficient IOT WSN backhauling: challenges and opportunities (2014)

At present, Sensor Networks and the emerging Internet of Things paradigm are playing a key role in the industry and in academic research. In this article we outline a common scenario, currently arising standards, and other emerging technologies having a direct impact on network architecture. In particular we introduce a novel network architecture based on an M2M Gateway and discuss it in relation to smart building applications. The proposed network architecture will improve services for users and will offer new opportunities for both service providers and network operators.
Modeling System Dynamics in a MEMS-Based Stirling Cooler (2011)

Micro-scale devices based on the Stirling cycle are an attractive choice for chip- and board-level electronics. A new Stirling cycle micro-refrigeration system composed of arrays of silicon MEMS cooling elements has been designed. COMSOL is used to evaluate the thermal performance of the system. Simulation of compressible flow and heat transfer with a large deformed mesh has been successfully implemented and is used to determine the cooling capacity and coefficient of performance, COP. Future work will focus on modeling the coupling of the thermal fluid phenomena with electrostatics.
Contactins (2009)

Contactins are a subgroup of molecules belonging to the immunoglobulin superfamily that are expressed exclusively in the nervous system. The subgroup consists of six members: contactin, TAG-1, BIG-1, BIG-2, NB-2 and NB-3. Since their identification in the late 1980s, contactin and TAG-1 have been studied extensively. Axonal expression and the neurite extension activity of contactin and TAG-1 attracted researchers to study the function of these molecules in axon guidance during development. After the exciting discovery of the molecular function of contactin and TAG-1 in myelination earlier this decade, these two molecules have come to be known as the principal molecules in the function and maintenance of myelinated neurons. In contrast, the function of the other four members of this subgroup remained unknown until recently. Here, we will give an overview of contactin function, including recent progress on BIG-2, NB-2 and NB-3.
Defocus Magnification (2007)

Abstract A blurry background due to shallow depth of field is often desired for photographs such as portraits, but, unfortunately, small point‐and‐shoot cameras do not permit enough defocus because of the small diameter of their lenses. We present an image‐processing technique that increases the defocus in an image to simulate the shallow depth of field of a lens with a larger aperture. Our technique estimates the spatially‐varying amount of blur over the image, and then uses a simple image‐based technique to increase defocus. We first estimate the size of the blur kernel at edges and then propagate this defocus measure over the image. Using our defocus map, we magnify the existing blurriness, which means that we blur blurry regions and keep sharp regions sharp. In contrast to more difficult problems such as depth from defocus, we do not require precise depth estimation and do not need to disambiguate textureless regions.
Altered Pituitary Growth Hormone (GH) Regulation in Streptozotocin-Diabetic Rats: A Combined Defect of Hypothalamic Somatostatin and GH-Releasing Factor* (1990)

Diabetes mellitus in the rat is associated with loss of pulsatile GH secretion. An interplay between hypothalamic GH-releasing factor (GRF) and inhibitory factor [somatostatin (SRIF)] secretion is thought to account for episodic pituitary GH release. An increase in SRIF tone/action or a decrease in GRF release/response in diabetic rats could account for the suppressed GH levels. Pituitaries from streptozotocin-diabetic rats contained less GH than controls (15.9 +/- 2.5 vs. 29.5 +/- 4.6 micrograms/mg; P less than 0.05) despite normal somatotrope representation, as demonstrated using immunofluorescence studies. Basal GH secretion from monolayer culture of dispersed anterior pituitary (AP) cells from diabetic rats was proportionately decreased (150 +/- 10 vs. 103 +/- 10 ng/10(5) cells; P less than 0.005). GRF (10(-11)-10(-8) M)-induced release of GH from AP cells was decreased in diabetic rats (maximum response to 10(-8) M GRF, 401 +/- 60 vs. 618 +/- 41 ng/10(5) cells; P less than 0.01); however, sensitivity to GRF was unchanged (EC50, 79 +/- 41 vs. 128 +/- 67 pM). By contrast, SRIF (10(-7)-10(-10)-induced inhibition of GRF (10(-8) M)-mediated GH release was impaired in AP cells of diabetic rats compared to that in controls (IC50, 112 +/- 33 vs. 55 +/- 31 pM; P less than 0.05) associated with a decrease in AP plasma membrane SRIF receptor concentration (63.4 +/- 15.6 vs. 160.3 +/- 13.7 fmol/mg protein; P less than 0.05), with no change in affinity. These findings are consistent with chronic exposure to increased hypothalamic SRIF influence. GH synthesis has been shown to be independent of SRIF regulation; however, insulin-like growth factor-I and GRF inhibit and stimulate GH synthesis, respectively. In diabetic rats insulin-like growth factor-I levels were decreased, appropriate to low GH status, in serum (290 +/- 66 vs. 1662 +/- 92 ng/ml; P less than 0.001) and hypothalamus (6.8 +/- 1.0 vs. 13.0 +/- 0.4 pg/mg wet wt; P less than 0.001) and, thus, did not seem to account for the low AP GH content. Hypothalamic GRF content in diabetic rats (1.11 +/- 0.10 ng/hypothalamus) did not differ from that in controls (1.16 +/- 0.17 ng/hypothalamus). GRF mRNA levels, however, were reduced by 80% in diabetic rats compared to controls. Taken together these data support a combined role for decreased hypothalamic GRF and increased SRIF in mediating alterations of GH synthesis and secretion in streptozotocin-induced diabetes.
A 3.5–6.8-GHz Wide-Bandwidth DTC-Assisted Fractional-N All-Digital PLL With a MASH $\Delta \Sigma $ -TDC for Low In-Band Phase Noise (2017)

This paper proposes a digital-to-time converter (DTC)-assisted fractional-N wide-bandwidth all-digital phaselocked loop (ADPLL) with a fine-resolution time-to-digital converter (TDC). The TDC employs a two-channel time-interleaved time-domain register with an implicit adder/subtractor realizing an error-feedback topology. Such an error-feedback unit of a first-order ΔΣ-TDC can be cascaded as a multi-stage noise shaping configuration to achieve higher-order noise-shaping and, thereby, low in-band phase noise (PN) of the ADPLL. A digitally controlled oscillator with a transformer and a pair of cross-coupled NMOS amplifiers exploits magnetic and capacitive coupling to achieve nearly an octave frequency coverage, i.e., 1.73-3.38 GHz (after a ÷2 division). Fabricated in 40-nm CMOS, the ADPLL achieves better than -110-dBc/Hz in-band PN and occupies an active area of 0.5 mm2. With a 50-MHz reference clock, a 2-GHz output RF clock, and a loop bandwidth of 800 kHz, this prototype achieves 420-fsrms jitter, integrated from 1-kHz to 30-MHz offset, while drawing 10.7 mW.
Bending Properties of Single Functionalized Graphene Sheets Probed by Atomic Force Microscopy (2008)

We probe the bending characteristics of functionalized graphene sheets with the tip of an atomic force microscope. Individual sheets are transformed from a flat into a folded configuration. Sheets can be reversibly folded and unfolded multiple times, and the folding always occurs at the same location. This observation suggests that the folding and bending behavior of the sheets is dominated by pre-existing kink (or even fault) lines consisting of defects and/or functional groups.