gebhart/patrepeval huggingface dataset:
Rational pattern design for in vitro cellular networks using surface photochemistry (1994)

The ability to create patterns of specific silane monolayers by deep ultraviolet lithography has been previously demonstrated, and preliminary attempts have been made to use these patterns to control adhesion and outgrowth of neurons and other types of mammalian cells. Here we report characterization of the mechanisms involved in these photoinitiated processes and their utility in various strategies for creating patterns for biologically relevant systems. We have divided the mechanisms into three general classes. The first is surface photolysis of the silane monolayer, which appears to proceed by a purely photochemical mechanism. The second mechanism involves direct photochemical conversion of a terminal functional group on a silane monolayer into a species with altered properties, e.g., the conversion of a thiol to a more oxidized form that inhibits the subsequent adhesion of proteins. The third is a photolytic degradation of the monolayer. The mechanisms have been probed by x-ray photoelectron spectroscopy, ellipsometry, and wettability measurements. One result of these investigations has been the development of better strategies to create patterns. Controlled growth of hippocampal neurons on high resolution patterns is presented as demonstration of the efficacy of these strategies in spatially dictating cell adhesion. These results have important implications in designing in vitro culture systems to study well-oriented neuronal systems.
Increased hepcidin in transferrin-treated thalassemic mice correlates with increased liver BMP2 expression and decreased hepatocyte ERK activation (2015)

Iron overload results in significant morbidity and mortality in β-thalassemic patients. Insufficient hepcidin is implicated in parenchymal iron overload in β-thalassemia and approaches to increase hepcidin have therapeutic potential. We have previously shown that exogenous apo-transferrin markedly ameliorates ineffective erythropoiesis and increases hepcidin expression in Hbb(th1/th1) (thalassemic) mice. We utilize in vivo and in vitro systems to investigate effects of exogenous apo-transferrin on Smad and ERK1/2 signaling, pathways that participate in hepcidin regulation. Our results demonstrate that apo-transferrin increases hepcidin expression in vivo despite decreased circulating and parenchymal iron concentrations and unchanged liver Bmp6 mRNA expression in thalassemic mice. Hepatocytes from apo-transferrin-treated mice demonstrate decreased ERK1/2 pathway and increased serum BMP2 concentration and hepatocyte BMP2 expression. Furthermore, hepatocyte ERK1/2 phosphorylation is enhanced by neutralizing anti-BMP2/4 antibodies and suppressed in vitro in a dose-dependent manner by BMP2, resulting in converse effects on hepcidin expression, and hepatocytes treated with MEK/ERK1/2 inhibitor U0126 in combination with BMP2 exhibit an additive increase in hepcidin expression. Lastly, bone marrow erythroferrone expression is normalized in apo-transferrin treated thalassemic mice but increased in apo-transferrin injected wild-type mice. These findings suggest that increased hepcidin expression after exogenous apo-transferrin is in part independent of erythroferrone and support a model in which apo-transferrin treatment in thalassemic mice increases BMP2 expression in the liver and other organs, decreases hepatocellular ERK1/2 activation, and increases nuclear Smad to increase hepcidin expression in hepatocytes.
Gender Specific Pelvic Pain Severity in Neurogenic Cystitis (2011)

These data suggest that pelvic pain in mice with murine neurogenic cystitis is mediated by gender specific responsiveness to mast cells while pelvic pain severity is modulated by genetic factors.
Bioconjugation protocols : strategies and methods (2004)

Contemporary approaches to the synthesis of chemically modified proteins not only require efficient means to control conjugation and the specific site of attachment of the conjugated moiety, but also the effective use of recent developments in microarray technologies and nanobiotechnology. In Bioconjugation Protocols: Strategies and Methods, expert laboratorians update the classic methods and introduce valuable new approaches that go beyond basic conjugation techniques to include elements from advanced organic synthesis, molecular biology, and materials science. These readily reproducible methods cover the preparation of protein conjugates using covalent and noncovalent conjugation, the synthesis of nucleic acid conjugates using a variety of labeling techniques, and approaches to semisynthetic conjugates of proteins. Additional chapters address the biofunctionalization of inorganic surfaces, including the on-chip synthesis of peptide nucleic acids to generate microarrays for the high-throughput analysis of RNA and DNA, gold nanoparticles, and carbon nanotube probes for atomic force microscopy. All the protocols follow the successful Methods in Molecular Biology™ series format, each one offering step-by-step laboratory instructions, an introduction outlining the principle behind the technique, lists of the necessary equipment and reagents, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and highly practical, Bioconjugation Protocols: Strategies and Methods offers both novice and experienced researchers access to the broad array of techniques needed to master the semisynthesis of functional biomolecular reagents for a wide variety of applications-ranging from novel biomedical diagnostics, to powerful new therapeutics, to advanced biomaterials
Obese gene expression: reduction by fasting and stimulation by insulin and glucose in lean mice, and persistent elevation in acquired (diet-induced) and genetic (yellow agouti) obesity. (1996)

Mutations in the obese (ob) gene lead to obesity. This gene has been recently cloned, but the factors regulating its expression have not been elucidated. To address the regulation of the ob gene with regard to body weight and nutritional factors, Northern blot analysis was used to assess ob mRNA in adipose tissue from mice [lean, obese due to diet, or genetically (yellow agouti) obese] under different nutritional conditions. ob mRNA was elevated in both forms of obesity, compared to lean controls, correlated with elevations in plasma insulin and body weight, but not plasma glucose. In lean C57BL/6J mice, but not in mice with diet-induced obesity, ob mRNA decreased after a 48-hr fast. Similarly, in lean C57BL/6J controls, but not in obese yellow mice, i.p. glucose injection significantly increased ob mRNA. For up to 30 min after glucose injection, ob mRNA in lean mice significantly correlated with plasma glucose, but not with plasma insulin. In a separate study with only lean mice, ob mRNA was inhibited >90% by fasting, and elevated approximately 2-fold 30 min after i.p. injection of either glucose or insulin. These results suggest that in lean animals glucose and insulin enhance ob gene expression. In contrast to our results in lean mice, in obese animals ob mRNA is elevated and relatively insensitive to nutritional state, possibly due to chronic exposure to elevated plasma insulin and/or glucose.
The vascular theory of migraine—a great story wrecked by the facts (2008)

The vascular theory of migraine
Multiple Mechanisms for the Carcinogenic Effects of Asbestos and Other Mineral Fibers (1989)

Asbestos and other mineral fibers are carcinogenic to humans and animals but differ from many carcinogens in that they do not induce gene mutations. An understanding of these interesting human carcinogens, therefore, is an important problem in cancer research. Asbestos and other fibers induce predominantly two types of cancers: mesotheliomas and bronchogenic carcinomas. Fiber size is an important factor in the carcinogenic activity of these substances as has been shown for mesothelioma induction. For bronchogenic carcinomas, but not for mesotheliomas, a synergistic effect of asbestos exposure and cigarette smoke has been observed in humans. The mechanisms by which fibers alone versus fibers in concert with other carcinogens induce cancers are probably distinct. In addition to fiber dimensions, fiber durability and surface properties of fibers are important properties affecting carcinogenicity. Evidence exists that asbestos is a complete carcinogen, an initiator and a promoter. Multiple mechanisms must be operative to explain the diverse effects of mineral fibers. Although asbestos is inactive as a gene mutagen, there is now clear evidence that it induces chromosomal mutations (aneuploidy and aberrations) in a wide variety of mammalian cells including mesothelial cells. Asbestos also induces transformation of cells in culture including mesothelial cells and fibroblasts. A mechanism for cell transformation, which is dependent on fiber dimension, has been proposed. The fibers are phagocytized by the cells and accumulate in the perinuclear region of the cells. When the cell undergoes mitosis, the physical presence of the fibers interferes with chromosome segregation and results in anaphase abnormalities. The transformed cells show aneuploidy and other chromosome abnormalities.(ABSTRACT TRUNCATED AT 250 WORDS)
&lt;i&gt;In Vitro&lt;/i&gt; Characterization of the Efficacy and Safety Profile of a Proprietary Ajuga Turkestanica Extract (2012)

Ajuga Turkestanica, an herbaceous flowering species in the mint family, has been traditionally used in Turkeyand Uzbekistan for heart disease, muscle aches and stomach problems. Due to its high levels of phytoecdysteroids (particularly the characteristic C-11-hydroxylated Turkesterone), anabolic properties have also been reported. The aim of our study was to screen for early signs of efficacy and safety of a proprietary Ajuga turkestanica extract (ATE) using in vitro models. C2C12 mouse myotube cell line was used to study potential effects on viability and gene modulation. Cell viability was evaluated with different concentrations [0.2 - 200 ppm (mg/L)] of ATE. Gene modulation was assessed by quantitative polymerase chain reaction (qRT-PCR) after 6h incubation (ATE vs. the androgenic anabolic steroid methandrostenolone). Total androgenic activity was measured using the A-SCREEN bioassay. Ultra-high performance liquid chromatography analysis showed good correlation between the phytochemical profile of the native plant and our ATE. C2C12 mouse myotube cells treated with ATE experienced no significant loss of viability (concentrations 0.2 - 200 ppm, 1 - 24 hs, p > 0.05). qRT-PCR array analysis showed significant (p regulation of Caspase-3 (2-fold) and Myostatin (4-fold). The extract showed no androgenic activity within the dose range used. Our results indicate the potential for an ATE to support muscle mass without typical androgenic side effects of synthetic anabolic drugs.
Saturated Fatty Acids Promote Endoplasmic Reticulum Stress and Liver Injury in Rats with Hepatic Steatosis (2005)

Nonalcoholic fatty liver disease is a relatively new hepatic sequela of obesity and type 2 diabetes. The pathogenesis of liver injury and disease progression in nonalcoholic fatty liver disease, however, is poorly understood. The present study examined the hypothesis that the composition of fatty acids in the steatotic liver promotes liver injury. Using dietary models of hepatic steatosis characterized by similar accumulation of total triglyceride but different composition of fatty acids, we show that hepatic steatosis characterized by increased saturated fatty acids is associated with increased liver injury and markers of endoplasmic reticulum stress (e.g. X-box binding protein-1 mRNA splicing and glucose-regulated protein 78 expression). These changes preceded and/or occurred independently of obesity and differences in leptin, TNFalpha, insulin action, and mitochondrial function. In addition, hepatic steatosis characterized by increased saturated fatty acids reduced proliferative capacity in response to partial hepatectomy and increased liver injury in response to lipopolysaccharide. These data suggest that the composition of fatty acids in the steatotic liver is an important determinant of susceptibility to liver injury.
Waking up from the DREAM of preventing diabetes with drugs (2007)

The current epidemic of diabetes makes a drug to prevent it attractive. But despite promotion of recent research evidence, <b>Victor Montori</b>, <b>William Isley</b>, and <b>Gordon Guyatt </b>argue that we are not there yet
A new galvanometric scanner for rapid tuning of CO/sub 2/ lasers (2002)

A device for rapidly tuning both CW (continuous-wave) and TEA (transversely excited atmospheric) CO/sub 2/ lasers is presented. This galvanometer-driven unit is of considerable importance over that previously reported in that it can attain at least 200 Hz tuning without the need for additional equipment or algorithms. Tuning a TEA laser at repetition rates of 200 Hz has been demonstrated for even the widest excursions, corresponding to tuning over the entire CO/sub 2/ spectrum. No amplitude-dependent adjustments were needed for even the weakest available transitions. CW laser tuning was also demonstrated to approximate this limit, and it was shown that this type of galvanometer is also suitable for heterodyne detection lidar tuning.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Characterization of Electron Traps in Aluminum-Implanted SiO2 (1978)

Johnson, Johnson, and Lampert have studied the effect of Al implantation on the trapping behavior of SiO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> . The large fluence that they used (1 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">14</sup> Al/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ) and the low annealing temperatures (up to 600°C) resulted in a trapping efficiency of 1 and made it impossible to characterize the traps. In the present study a lower fluence and higher annealing temperatures to reduce the trapping efficiency are used to permit characterization of the traps. The predominant trap cross sections are 1.26 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">−16</sup> and 1.40 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">−17</sup> cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . In a companion paper by DiMaria, Young, Hunter, and Serrano the location of the trapped charge is discussed.
Glucagon-like peptide-1(7-36) amide (GLP-1) enhances insulin-stimulated glucose metabolism in 3T3-L1 adipocytes: one of several potential extrapancreatic sites of GLP-1 action (1994)

We investigated the effects of glucagon-like peptide-1(7-36) amide, GLP-1, on glucose metabolism in 3T3-L1 adipocytes and we used polymerase chain reaction to search for the presence of GLP-1 receptors in various rat tissues. GLP-1 at 1 nM significantly increased insulin-mediated 2-deoxyglucose uptake by 40% while having no effect on basal uptake. In conjunction with the elevated uptake, the insulin-dependent incorporation of 14C-glucose into fatty acids was also increased. Moreover, neither glycogen synthesis nor insulin binding to its receptor were affected by GLP-1. In addition to the presence of GLP-1 receptor in pancreas we found messenger RNA for this receptor in brain, kidney, heart, fat, skeletal muscle, liver, and intestine. This study indicates that GLP-1, in addition to its well known effect of stimulating insulin secretion, may improve insulin responsiveness by promoting fatty acid synthesis in adipose cells and possibly modulating insulin signaling in other insulin sensitive tissues.
THE EXPRESSION PATTERN OF WILMS' TUMOUR GENE (WT1) PRODUCT IN NORMAL TISSUES AND PAEDIATRIC RENAL TUMOURS (1996)

WT1, the Wilms' tumour suppressor gene located at chromosome 11p13, plays an important role in the development of the kidney. It is mutated in 10 per cent of Wilms' tumours (WTs) and their putative precursors called nephrogenic rests (NRs). A sensitive immunohistochemical technique was established to localize the WT1 gene product in archival normal tissues and paediatric renal tumour samples. Strong nuclear signal was seen in the various sites such as the kidneys, gonads, and decidua. Nuclear immunoreactivity of variable intensity was also seen in the skeletal muscle, smooth muscle of urinary bladder, ureter, and arteries. All 28 WTs (including the anaplastic variant) showed the WT1 gene product in a varying proportion of the blastema, epithelium, and stroma. The anaplastic nuclei in six WTs showed an intensity of staining comparable to their adjacent favourable histology counterparts. All the intralobar and perilobar types of NR demonstrated the WT1 gene product. All three malignant rhabdoid tumours were positive, while three of four mesoblastic nephromas and a clear cell sarcoma were negative. These findings provide an insight into the interrelationships of these renal tumours.
Tuning complex event processing rules using the prediction-correction paradigm (2009)

There is a growing need for the use of active systems, systems that act automatically based on events. In many cases, providing such active functionality requires materializing (inferring) the occurrence of relevant events. A widespread paradigm for enabling such materialization is Complex Event Processing (CEP), a rule based paradigm, which currently relies on domain experts to fully define the relevant rules. These experts need to provide the set of basic events which serves as input to the rule, their inter-relationships, and the parameters of the events for determining a new event materialization. While it is reasonable to expect that domain experts will be able to provide a partial rules specification, providing all the required details is a hard task, even for domain experts. Moreover, in many active systems, rules may change over time, due to the dynamic nature of the domain. Such changes complicate even further the specification task, as the expert must constantly update the rules. As a result, we seek additional support to the definition of rules, beyond expert opinion. This work presents a mechanism for automating both the initial definition of rules and the update of rules over time. This mechanism combines partial information provided by the domain expert with machine learning techniques, and is aimed at improving the accuracy of event specification and materialization. The proposed mechanism consists of two main repetitive stages, namely rule parameter prediction and rule parameter correction. The former is performed by updating the parameters using an available expert knowledge regarding the future changes of parameters. The latter stage utilizes expert feedback regarding the actual past occurrence of events and the events materialized by the CEP framework to tune rule parameters. We also include possible implementations for both stages, based on a statistical estimator and evaluate our outcome using a case study from the intrusion detection domain.
Tunable SIW Structures: Antennas, VCOs, and Filters (2015)

Due to their high quality factor (hundreds), high power handling, and good isolation, SIW structures are excellent candidates for a variety of microwave devices, including filters, antennas, VCOs, and isolators. However, their use has been hindered due to their narrow BW and high sensitivity to the fabrication process. Tuning the SIW-based microwave structures has the advantages of covering more bands, the possibility of post-fabrication fine-tuning, and less crosstalk sensitivity. However, the conventional tuning methods applicable to regular microwave structures are not effective for SIWs. Finding a way to tune these structures over a wide tuning range while maintaining their high Q seems to be very appealing and, at the same time, very challenging. To address all these points in more detail, the main focus of this article was on frequency-tunable/ reconfigurable SIW structures. The reported tuning methods applied to SIW structures so far are studied, and their pros and cons are discussed in detail. Also, separate libraries for SIW-based tunable filters, antennas, and VCOs are provided.
Mechanism of prolonged electromechanical delay in late activated myocardium during left bundle branch block (2011)

During left bundle branch block (LBBB), electromechanical delay (EMD), defined as time from regional electrical activation (REA) to onset shortening, is prolonged in the late-activated left ventricular lateral wall compared with the septum. This leads to greater mechanical relative to electrical dyssynchrony. The aim of this study was to determine the mechanism of the prolonged EMD. We investigated this phenomenon in an experimental LBBB dog model (n = 7), in patients (n = 9) with biventricular pacing devices, in an in vitro papillary muscle study (n = 6), and a mathematical simulation model. Pressures, myocardial deformation, and REA were assessed. In the dogs, there was a greater mechanical than electrical delay (82 ± 12 vs. 54 ± 8 ms, P = 0.002) due to prolonged EMD in the lateral wall vs. septum (39 ± 8 vs.11 ± 9 ms, P = 0.002). The prolonged EMD in later activated myocardium could not be explained by increased excitation-contraction coupling time or increased pressure at the time of REA but was strongly related to dP/dt at the time of REA (r = 0.88). Results in humans were consistent with experimental findings. The papillary muscle study and mathematical model showed that EMD was prolonged at higher dP/dt because it took longer for the segment to generate active force at a rate superior to the load rise, which is a requirement for shortening. We conclude that, during LBBB, prolonged EMD in late-activated myocardium is caused by a higher dP/dt at the time of activation, resulting in aggravated mechanical relative to electrical dyssynchrony. These findings suggest that LV contractility may modify mechanical dyssynchrony.
Towards Better Analysis of Deep Convolutional Neural Networks (2016)

Deep convolutional neural networks (CNNs) have achieved breakthrough performance in many pattern recognition tasks such as image classification. However, the development of high-quality deep models typically relies on a substantial amount of trial-and-error, as there is still no clear understanding of when and why a deep model works. In this paper, we present a visual analytics approach for better understanding, diagnosing, and refining deep CNNs. We formulate a deep CNN as a directed acyclic graph. Based on this formulation, a hybrid visualization is developed to disclose the multiple facets of each neuron and the interactions between them. In particular, we introduce a hierarchical rectangle packing algorithm and a matrix reordering algorithm to show the derived features of a neuron cluster. We also propose a biclustering-based edge bundling method to reduce visual clutter caused by a large number of connections between neurons. We evaluated our method on a set of CNNs and the results are generally favorable.