gebhart/patrepeval huggingface dataset:
In silico identification of breast cancer genes by combined multiple high throughput analyses (2005)

Publicly available human genomic sequence data provide an unprecedented opportunity for researchers to decode the functionality of human genome. Such information is extremely valuable in cancer prevention diagnosis and treatment. Cancer Genome Anatomy Project (CGAP) and Gene Expression Omnibus (GEO) are two bioinformatic infrastructures for studying functional genomics. The goal of this study is to explore the feasibility of incorporating the Internet-available bioinformatic databases to discover human breast cancer-related genes. Several tools including the Gene Finder, Virtual Northern (vNorthern) and SAGE digital gene expression displayer (DGED) were used to analyze differential gene expression between benign and malignant breast tissues. A pilot study was performed using both EST and SAGE vNorthern to analyze the expression of a panel of known genes, including high abundance genes beta-actin and G3PDH, low abundance genes BRCA1 and p53, tissue-specific genes CEA and PSA and two breast cancer-related genes Her2/neu and MUC1. We found a high expression of beta-actin and G3PDH and a low expression of BRCA1 and p53 across different types of tissues as well as a tissue-specific expression of CEA in colon and PSA in prostate. A further analysis of 30 known breast cancer-related genes in breast cancer tissues by vNorthern demonstrated a high expression of oncogenes and low expression of tumor suppressor genes. An open-end analysis of two pools of breast cancer and benign breast tissue libraries by SAGE DGED produced 53 differentially expressed genes according to the screening criteria of a >five-fold difference and p<0.01. Further analysis by EST vNorthern and virtual microarray analysis reduced the candidate genes to six, with four down-regulated genes, ANXA1, CAV1, KRT5 and MMP7, and two up-regulated genes, ERBB2 and G1P3 in breast cancer. These findings were validated by a real-time RT-PCR analysis in eight paired human breast cancer tissue samples. We conclude that the combined multiple high throughput analyses is an effective data mining strategy in cancer gene identification. This approach may improve the usage of public available genomic data through strategic data mining of high throughput analysis.
Supplementary Table S1 from Platelet-Derived Growth Factor-AA Is an Essential and Autocrine Regulator of Vascular Endothelial Growth Factor Expression in Non–Small Cell Lung Carcinomas (2023)

Supplementary Table S1 from Platelet-Derived Growth Factor-AA Is an Essential and Autocrine Regulator of Vascular Endothelial Growth Factor Expression in Non–Small Cell Lung Carcinomas
Determining Cursive or Printed Nature of Handwritten Samples (2011)

Abstract. Forensic document examiners tend to compare documents to one another only when they are both cursive or both hand printed documents. Thus, for an automated system to process writer identification or verification, it is desirable to determine whether a sample of handwritten text is of a hand printed or cursive nature. We identify a feature based upon the number of segmented words and number of connected components which are identified as single characters. We evaluate the performance of this feature by using all 4,701 documents present CEDAR letter dataset and find that using this feature identifies documents as hand printed correctly 95 % of the time and identifies them as cursive 91 % of the time. 1.
On detection of gapped code clones using gap locations (2002)

It is generally accepted that a code clone is one factor making software maintenance difficult. A code clone is a code portion in source files that is identical or similar to another. Clones are introduced because of various reasons such as reusing code by 'copy-and-paste' and so on. Since developers usually modify the copied-and-pasted code portions, there are gaps between them and the original code portion. We call such code portions including gaps gapped code clones. Several code clone detection methods, which consider such gaps, have been proposed. However, it is costly to detect all gapped code clones. This paper proposes a new method to visualize gapped code clones as if they were actually detected, based on the detection results of conventional code clones. Using the proposed method, the developer can specify target clones efficiently. Moreover, we implement the proposed method in the maintenance support environment and conduct an experimental evaluation.
SOME CONTEMPORARY ACCOUNTS OF RENAISSANCE PRINTING METHODS (1936)

SOME CONTEMPORARY ACCOUNTS OF RENAISSANCE PRINTING METHODS Get access DON CAMERON ALLEN DON CAMERON ALLEN 1 This paper was written while the author was a Fellow of the American Council of Learned Societies Search for other works by this author on: Oxford Academic Google Scholar The Library, Volume s4-XVII, Issue 2, September 1936, Pages 167–171, https://doi.org/10.1093/library/s4-XVII.2.167 Published: 01 September 1936
光緒年間的粵曲唱片 : 「謀得利」和「愛迪生」唱片公司的灌錄製作 (2000)

1 99720-24(2) ' () ' 1998 4 2-4 (3)"Music and Technology: Recording Cantonese and Peking Opera at the Turn of the Century,"paper presented at the international symposium "From the Late Ming to the Late Qing:
Hierarchical G1 smooth surface interpolation with local control (2005)

No abstract available.
Mechanical properties of ultrathin gold nanowires from first principles: Interdependencies between size, morphology, and twin boundaries (2020)

The mechanical behavior of $\ensuremath{\langle}111\ensuremath{\rangle}$ ultrathin gold nanowires (NWs) and their dependence on the correlated parameters of size (i.e., diameter $\ensuremath{\sim}1--1.6$ nm), morphology (rectangular and hexagonal prism), and ultrahigh density twin boundaries was investigated using density functional theory calculations. The parameters of size, morphology, and the presence of twins all significantly influence the mechanical behavior of Au NWs, and their effects are interdependent. Importantly, an ultrahigh density of twins in NWs enhances their strength in both morphologies, and across all sizes studied. Our calculations reveal a remarkable range of Young's modulus (60--158 GPa) and ultimate tensile strengths (3.7--14.0 GPa), suggesting that the scatter observed in experimental research involving ultrathin gold nanowires is a feature of intrinsic complexity. In particular, a ``wrinkling'' of the atomic planes along the wire axis due to a combination of anisotropic surface stresses and wire core response, is demonstrated to be largely suppressed by the presence of high-density twins. The high tensile strengths of the studied nanowires with twins is attributed to a combination of the suppression of this anisotropic phenomena and slip plane disruption. This work demonstrates that precise control of these parameters is required during synthesis to achieve target mechanical behaviour in industrial device applications. Moreover, the work demonstrates that this system has the potential to be tuned for access to a vast range of materials design space.
Chiral 2,2-disubstituted cyclohexanones; annulation via Claisen rearrangement products (1990)

The methyl enol ether of 2-methylcyclohexanone reacts regiospecifically with the optically active forms of but-3-yn-2-ol and but-3-en-2-ol. (R)-But-3-yn-2-ol yields an approximately 4 : 1 mixture of (R)-2-methyl-2-(R-buta-1,2-dienyl)cyclohexanone and the corresponding SR compound. By contrast the but-3-en-2-ol reaction is ca. 96% enantioselective; (R)-but-3-en-2-ol gives (R)-2-(trans-but-2-enyl)-2-methylcyclohexanone and (S)-but-3-en-2-ol gives the corresponding (S)-cyclohexanone. These Claisen rearrangement products have been transformed into Robinson-type annulated ketones. Cleavage of some highly hindered esters has been carried out efficiently by sodium methylsulphinyl-methanide in dimethyl sulphoxide.
Drosophila fabp is a retinoid-inducible gene required for Rhodopsin-1 homeostasis and photoreceptor survival (2021)

Abstract Retinoids act as chromophore co-factors for light-detecting rhodopsin proteins. In vertebrates, retinoids also actively regulate gene expression. Whether retinoids regulate gene expression in Drosophila for a specific biological function remains unclear. Here, we report that Drosophila fatty acid binding protein ( fabp ) is a retinoid-inducible gene required for Rhodopsin-1 (Rh1) protein homeostasis and photoreceptor survival. Specifically, we performed a photoreceptor-specific gene expression profiling study in flies bearing a misfolding-prone Rhodopsin-1 (Rh1) mutant, ninaE G69D , which serves as a Drosophila model for Retinitis Pigmentosa. ninaE G69D photoreceptors showed increased expression of genes that control Rh1 protein levels, along with a poorly characterized gene, fabp . We found that in vivo fabp expression was reduced when the retinoids were deprived through independent methods. Conversely, fabp mRNA was induced when we challenged cultured Drosophila cells with retinoic acid. In flies reared under light, loss of fabp caused an accumulation of Rh1 proteins in cytoplasmic vesicles. fabp mutants exhibited light-dependent retinal degeneration, a phenotype also found in other mutants that block light-activated Rh1 degradation. These observations indicate that a retinoid-inducible gene expression program regulates fabp that is required for Rh1 proteostasis and photoreceptor survival. Author Summary Rhodopsins are light-detecting proteins that use retinoids as chromophore co-factors. In vertebrates, retinoids also actively regulate gene expression. Whether retinoids regulate Rhodopsin function aside from its role as a chromophore remains unclear. Here, we report that Drosophila fatty acid binding protein ( fabp ) is a retinoid-inducible gene required for Rhodopsin-1 (Rh1) protein homeostasis and photoreceptor survival. Specifically, we found that fabp is among the genes induced by a misfolding-prone Rhodopsin-1 (Rh1) mutant, ninaE G69D , which serves as a Drosophila model for Retinitis Pigmentosa. We further found that fabp induction in ninaE G69D photoreceptors required retinoids. fabp was required in photoreceptors to help degrade light-activated Rh1. In the absence of fabp , Rh1 accumulated in cytoplasmic vesicles in a light-dependent manner, and exhibited light-dependent retinal degeneration. These observations indicate that a retinoid-inducible gene expression program regulates fabp that is required for Rh1 proteostasis and photoreceptor survival.
Computational processing and analysis of ear images (2010)

Tese de mestrado. Engenharia Biomédica. Faculdade de Engenharia. Universidade do Porto. 2011
A New Rat Model of Thrombotic Focal Cerebral Ischemia (1997)

We developed a fibrin-rich thrombotic focal cerebral ischemic model with reproducible and predictable infarct volume in rats. In male Wistar rats (n = 77), a thrombus was induced at the origin of the middle cerebral artery (MCA) by injection of thrombin via an intraluminal catheter placed in the intracranial segment of the internal carotid artery (ICA). Thrombus induction and consequent ischemic cell damage were examined by histopathological analysis and neurological deficit scoring, and by measuring changes in cerebral blood flow (CBF) using laser-Doppler flowmetery (LDF), perfusion-weighted imaging (PWI), and by diffusion weighted imaging (DWI). Histopathology revealed that a fibrin-rich thrombus localized to the origin of the right MCA. Regional cerebral blood flow (rCBF) in the right parietal cortex was reduced by 34-58% of preinjection levels after injection of thrombin in rats administered 30 U of thrombin (n = 10). Magnetic resonance imaging (MRI) showed a reduction in CBF and a hyperintensity DWI encompassing the territory supplied by the right MCA. The infarct volume in rats administered 80 U of thrombin was 31.29 +/- 12.9% of the contralateral hemisphere at 24 h (n = 13), and 34.7 +/- 16.4% of the contralateral hemisphere at 168 h (n = 6). Rats administered 30 U of thrombin exhibited a hemispheric infarct volume of 34.0 +/- 14.5% (n = 9) at 24 h and 29.7 +/- 13.9% (n = 8) at 168 h. In addition, thrombotic rats (n = 3) treated with recombinant tissue plasminogen activator (rt-PA) (10 mg/kg) 2 h after thrombosis showed that CBF rapidly returned towards preischemic values as measured by PWI. This model of thrombotic ischemia is relevant to thromboembolic stroke in humans and may be useful in documenting the safety and efficacy of thrombolytic intervention as well as for investigating therapies complementary to antithrombotic therapy.
Nanobonding Technology Toward Electronic, Fluidic, and Photonic Systems Integration (2010)

In this paper, a review of surface-activation-based nanobonding technology for packaging and integration is presented. In this paper, the focus will be on nanobonding technology for electronic, photonic, and fluidic devices for miniaturized biomedical and environmental-sensing systems. We describe four different nanobonding techniques that have been developed and successfully implemented in a wide range of materials that include metals, semiconductors, flexible laminations, and ionic materials. Nanobonding technologies are particularly attractive because they offer void-free, strong, and nanoscale bonding at room temperature or at low temperature (<;200°C), and without the need for chemicals, adhesives, and high external pressure. Therefore, there are significant potential and opportunities for nanobonding technologies in the development of low cost, low loss, and high-speed miniaturized emerging systems based on a combination of electronic, fluidic, and photonic devices.
Transformation of Chick-Embryo Fibroblasts by Wild-Type and Temperature-Sensitive Rous Sarcoma Virus Alters Adenylate Cyclase Activity (1973)

The activity of the enzyme adenylate cyclase, a component of the plasma membrane, has been determined in chick-embryo fibroblasts and in cells transformed by either Bryan high-titer strain of Rous sarcoma virus (RSV-BH) or a temperature-sensitive mutant of this virus (RSV-BH-Ta). Adenylate cyclase activity is reduced in cells transformed by the wild-type virus and also by the temperature-sensitive mutant when the cells are grown at the permissive temperature (37 degrees ). Transformation results in an altered affinity (K(m)) for the substrate (Mg ATP). The apparent K(m) ATP is 0.23 mM in normal cells and 1.1 mM in cells transformed with wild-type virus. The K(m) ATP of the cells infected with RSV-BH-Ta is 0.67-1.0 mM at 37 degrees and 0.28 mM at 42 degrees . The enzyme from normal cells appears to have two binding sites for Mg(++), one at the catalytic site and a second at a regulatory site. Transformation by RSV-BH or RSV-BH-Ta (37 degrees ) apparently alters this second Mg(++) site. A decrease in adenylate cyclase activity occurs within 10 min after cells infected with RSV-BH-Ta are shifted from 42 degrees to 37 degrees ; the activity falls to one-half that of normal cells 30 min after the temperature shift. Our observations indicate that a viral function lowers cyclic AMP content by lowering the activity of adenylate cyclase, probably through some modification of the plasma membrane.
Low frequency of cigarette smoking and the risk of head and neck cancer in the INHANCE consortium pooled analysis (2015)

Our results suggest a public health message that low frequency of cigarette consumption contributes to the development of HNC. However, smoking duration seems to play at least an equal or a stronger role in the development of HNC.
A Nationwide Enumeration of Operations Performed for Pediatric Patients in Ghana (2020)

Ghana has a large unmet need for pediatric surgical care. Pediatric-specific benchmarking is needed to guide surgical capacity efforts in low- and middle-income country healthcare systems.
VR-based Batter Training System with Motion Sensing and Performance Visualization (2019)

This paper aims to establish a novel VR system for evaluating the performance of baseball batters. Existing VR systems for sports have been utilized as a tool for image training. In order to move such VR systems to the next stage, we introduce functions that sense the users' reaction to the VR stimulus. Our VR system has three features; (a) it synthesizes highly realistic VR video from the data captured in actual games, (b) it estimates the reaction of the user to the VR stimulus by capturing the 3D positions of full body parts, and (c) it consists of off-the-shelf devices and is easy to use. Our demonstration provides users with a chance to experience our VR system and give them some quick feedback by visualizing the estimated 3D positions of their body parts.
Glycogen Synthase Kinase-3β Phosphorylates Protein Tau and Rescues the Axonopathy in the Central Nervous System of Human Four-repeat Tau Transgenic Mice (2000)

Protein tau filaments in brain of patients suffering from Alzheimer's disease, frontotemporal dementia, and other tauopathies consist of protein tau that is hyperphosphorylated. The responsible kinases operating in vivo in neurons still need to be identified. Here we demonstrate that glycogen synthase kinase-3beta (GSK-3beta) is an effective kinase for protein tau in cerebral neurons in vivo in adult GSK-3beta and GSK-3beta x human tau40 transgenic mice. Phosphorylated protein tau migrates slower during electrophoretic separation and is revealed by phosphorylation-dependent anti-tau antibodies in Western blot analysis. In addition, its capacity to bind to re-assembled paclitaxel (Taxol((R)))-stabilized microtubules is reduced, compared with protein tau isolated from mice not overexpressing GSK-3beta. Co-expression of GSK-3beta reduces the number of axonal dilations and alleviates the motoric impairment that was typical for single htau40 transgenic animals (Spittaels, K., Van den Haute, C., Van Dorpe, J., Bruynseels, K., Vandezande, K., Laenen, I., Geerts, H., Mercken, M., Sciot, R., Van Lommel, A., Loos, R., and Van Leuven, F. (1999) Am. J. Pathol. 155, 2153-2165). Although more hyperphosphorylated protein tau is available, neither an increase in insoluble protein tau aggregates nor the presence of paired helical filaments or tangles was observed. These findings could have therapeutic implications in the field of neurodegeneration, as discussed.
Cylindrical dielectric cavity antenna loaded by a beam forming ring (2003)

A technique for improving the radiation characteristics of a resonant cylindrical dielectric cavity antenna by using a circular conducting ring is proposed. The ring is assumed to be residing on the top surface of the dielectric material. The effect of the thickness and diameter of the ring on the E- and H-plane radiation patterns as well as the cross-polarized field of the dielectric cavity antennas of various geometrical dimensions and dielectric constants are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Epicardial activation and repolarization patterns in patients with right ventricular hypertrophy. (1991)

To map global epicardial repolarization patterns and test the "SI" model of T wave generation, the patterns of epicardial activation and repolarization in patients with chronic pulmonary thromboembolism and right ventricular hypertrophy were studied by computerized mapping techniques and monophasic action potential (MAP) recording. The ventricular activation patterns were characterized by delayed right ventricular activation and the absence of normal early epicardial ventricular breakthrough in some cases. The repolarization patterns were characterized by nonuniform distribution of T wave morphologies. The T waves were predominantly positive over the left ventricular epicardium and negative or biphasic over the right ventricular epicardium. The activation-recovery (A-R) intervals were measured from the local activation to the maximal dV/dt of the upstroke of the T waves (Wyatt method). The difference between the A-R intervals and the MAP from onset of activation to 90% repolarization (MAP90) varies according to T wave morphology and could be as high as 96 msec with positive T waves, despite significant correlations (r = 0.56-0.90) between MAP90 and A-R intervals for each morphology. Better overall correlations were found if the minimal dV/dt on the downslope of the positive T waves was chosen to estimate the time of local repolarization (alternative method). Using this method, the mean A-R intervals were the same over the right and left ventricles. Cardiopulmonary bypass significantly prolonged the action potential duration equally at all parts of the epicardium. We conclude that in patients with right ventricular hypertrophy, the time of local repolarization can be estimated by our alternative method; the right ventricle completes activation and repolarization later than the left ventricle, and the distribution of T wave morphologies is nonuniform, with predominantly positive T waves observed over the left ventricle and negative or biphasic T waves observed over the right ventricle. These findings are compatible with the SI model of the generation of T waves.
Barrier-free substitutional doping of graphene sheets with boron atoms:Ab initiocalculations (2009)

Using ab initio methods, we propose a simple and effective way to substitutionally dope graphene sheets with boron. The method consists of selectively exposing each side of the graphene sheet to different elements. We first expose one side of the membrane to boron while the other side is exposed to nitrogen. Proceeding this way, the B atoms will be spontaneously incorporated into the graphene membrane without any activation barrier. In a second step, the system should be exposed to a H-rich environment, which will remove the CN radical from the layer and form HCN, leading to a perfect substitutional doping.
Modulation (2002)

Die Einführung zu diesem Kapitel wurde bereits mit dem Abschnitt 1.1.9 vorweggenommen.
Novel RZ signal format with alternate-chirp for suppression of nonlinear degradation in 40 Gb/s based WDM (2002)

A novel alternate-chirped RZ signal format is proposed. 2 dB improvement in nonlinear tolerance has been confirmed experimentally, compared to CS-RZ format in 40 Gb/s based WDM-480 km transmission experiment with 100-GHz channel spacing.
Miniaturized probe using 2 axis MEMS scanner for endoscopic multiphoton excitation microscopy (2008)

The practical limitation of in vivo multiphoton excitation microscopy (MPM) is the lack of a compact and flexible probe. Most MPM depends on the bench-top microscope, which prohibits expansion of in vivo application. In this study, we introduced a miniaturized MPM probe using a microelectromechanical system (MEMS) scanning mirror and a doubleclad photonic crystal fiber (DCPCF). Benefits from both a MEMS mirror and a DCPCF overcome current obstacles for probe development, such as size reduction, rapid scanning, efficient delivery of short pulses, and high collection rate of fluorescent signals. In this study, the completed probe was 1 cm in outer diameter and 14 cm in length. The probe was then integrated to the MPM system and used to image fluorescent beads, paper and biological specimens.