gebhart/patrepeval huggingface dataset:
Integrative genomics analysis reveals the multilevel dysregulation and oncogenic characteristics of TEAD4 in gastric cancer (2013)

Tumorigenesis is a consequence of failures of multistep defense mechanisms against deleterious perturbations that occur at the genomic, epigenomic, transcriptomic and proteomic levels. To uncover previously unrecognized genes that undergo multilevel perturbations in gastric cancer (GC), we integrated epigenomic and transcriptomic approaches using two recently developed tools: MENT and GENT. This integrative analysis revealed that nine Hippo pathway-related genes, including components [FAT, JUB, LATS2, TEA domain family member 4 (TEAD4) and Yes-associated protein 1 (YAP1)] and targets (CRIM1, CYR61, CTGF and ITGB2), are concurrently hypomethylated at promoter CpG sites and overexpressed in GC tissues. In particular, TEAD4, a link between Hippo pathway components and targets, was significantly hypomethylated at CpG site cg21637033 (P = 3.8 × 10(-) (20)) and overexpressed (P = 5.2 × 10(-) (10)) in 108 Korean GC tissues compared with the normal counterparts. A reduced level of methylation at the TEAD4 promoter was significantly associated with poor outcomes, including large tumor size, high-grade tumors and low survival rates. Compared with normal tissues, the TEAD4 protein was more frequently found in the nuclei of tumor cells along with YAP1 in 53 GC patients, demonstrating the posttranslational activation of this protein. Moreover, the knockdown of TEAD4 resulted in the reduced growth of GC cells both in vitro and in vivo. Finally, chromatin immunoprecipitation-sequencing and microarray analysis revealed the oncogenic properties of TEAD4 and its novel targets (ADM, ANG, ARID5B, CALD1, EDN2, FSCN1 and OSR2), which are involved in cell proliferation and migration. In conclusion, the multilevel perturbations of TEAD4 at epigenetic, transcriptional and posttranslational levels may contribute to GC development.
Expression and clinical significance of complement C3, complement C4b1 and apolipoprotein E in pancreatic cancer (2013)

Pancreatic cancer (PC) remains a devastating disease with a five-year survival rate of <5%. The difficulty in making an early diagnosis and the frequent occurrence of metastasis are important reasons for this poor prognosis. In China, the incidence of PC has been increasing steadily. Therefore, the present study aimed to identify effective markers in the early and advanced stages of PC. The expression levels of complement C3, complement C4b1 and apolipoprotein E (ApoE) in the various stages of PC were assessed by immunohistochemistry, RT-PCR and western blotting. Additionally, the statistical significance of the results was analyzed. The expression levels of complement C3, complement C4b1 and apoE were higher in PC compared with normal pancreatic tissues. No correlations were observed between complement C3 and tumor TNM staging or lymph node metastasis. However, complement C4b1 and apoE were markedly correlated with tumor TNM staging and lymph node metastasis. Complement C3 may be used as a marker for the diagnosis of early-stage PC, while complement C4b1 and apoE are closely correlated with tumor development, reflecting the biological behavior of PC, and thus may be used as diagnostic markers of advanced PC.
Penetrating Micropores Increase Patency and Achieve Extensive Endothelialization in Small Diameter Polymer Skin Coated Vascular Grafts (1996)

This article points to the importance of penetrating micropores through the graft wall to minimize thrombosis and to enhance endothelialization in small diameter polymer skin coated vascular grafts. Four types of spongy polyurethane-polydimethylsiloxane vascular grafts (PUG) fabricated by a spray, phase-inversion technique, 1.5 mm inner diameter, 1.5-1.9 cm in length, were implanted end-to-end in the infrarenal aorta of 26 adult rats. Some had a continuous inner skin and a hydraulic permeability (HP) of 0 ml/min/cm2/ 120 mmHg (PUG-S-O). Some had an inner skin with varying amounts of isolated penetrating micropores and a mean hydraulic permeability of 11 (PUG-S-11), 37 (PUG-S-37), or 58 ml/min/cm2/120 mmHg (PUG-S-58). Twelve PUG-S-O, 6 PUG-S-11, 4 PUG-S-11, and 4 PUG-S-58 were evaluated between 2 hr and 3 months after implantation. All PUG-S-O occluded soon after implantation. The PUG that had a HP of more than 11 ml/min/cm2 showed acceptable patency. However, endothelialization was limited to anastomoses in patent PUG-S-11. In contrast, the patent PUG-S-37 and PUG-S-58 were largely endothelialized. In all patent grafts at 3 months, numerous host cells had migrated, and newly formed capillaries were seen in the voids of the graft wall, which appeared moderately to highly cellular. In conclusion, it appears that penetrating micropores through the graft wall increase patency and that a highly porous structure is needed to achieve extensive endothelialization in small diameter polymer skin coated vascular grafts.
Regulatory Role of IL-1R8 in Immunity and Disease (2016)

Interleukin-1 receptor family members (ILRs) and toll-like receptors (TLRs) are characterized by the presence of a conserved intracellular domain and the toll-IL-1resistance (TIR) domain and are key players in immunity and inflammation. ILR and TLR signaling is tightly regulated at different levels. All cell types of the innate immune system express ILRs and TLRs. In addition, IL-1 family members are emerging as key players in the differentiation and function of innate and adaptive lymphoid cells. IL-1R8, also known as TIR8 or SIGIRR, is a fringe member of the ILR family and acts as a negative regulator of ILR and TLR signaling, which dampens ILR- and TLR-mediated cell activation. IL-1R8 is a component of the receptor recognizing human IL-37. Here, we summarize our current understanding of the structure and function of IL-1R8, focusing on its role in different pathological conditions, ranging from infectious and sterile inflammation to autoimmunity and cancer-related inflammation.
Role of ERCC1 gene in non-small cell lung cancer (2009)

Chemotherapy is one of the principal means of combined therapy in non-small cell lung cancer,but drug resistance is the major factor that impairs the therapeutic effect.Excision repair cross-complementation group 1(ERCC1) is the key gene for nucleotide excision repair.Its expression and polymorphisms are related to platinum resistance,which may affect the chemotherapy sensititivity and efficacy for non-small cell lung cancer.
Extraction and partial purification of a hepatic stimulatory substance in rats, mice, and dogs. (1987)

A factor has been isolated from weanling rat liver which stimulates in vivo hepatic DNA synthesis in a dose dependent manner when injected into 40% hepatectomized rats. The factor has been partially purified by successive steps, involving ethanol precipitation, ultrafiltration through an Amicon PM 30 membrane, and finally fast protein liquid chromatography, resulting in a 38,000-fold increase in specific activity over that in the original cytosol. The factor contains a few bands in the molecular weight range of 14,000-50,000 on sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Active fractions from fast protein liquid chromatography (F150), when injected into 40% hepatectomized rats, increased hepatic DNA synthesis 3-fold over the background stimulation due to the hepatectomy. The response was dose dependent over a range from 1.76 micrograms to 6.8 micrograms per 200-g (body weight) rat. Mitotic and labeling indexes confirmed that F150 stimulates both replicative DNA synthesis and cell proliferation. The factor is heat and neuraminidase resistant, trypsin sensitive, organ specific, but not species specific.
Water-Retention Effect of Composite Membranes with Different Types of Nanometer Silicon Dioxide (2008)

Four kinds of composite membranes were prepared by the solution-cast method with Nafion resin, poly(tetrafluoroethylene), and different types of SiO(2). They are SiO(2) sulfonated by 1,3-propane sultone (denoted as SiO(2)-1,3PS), SiO(2) sulfonated by H(2)SO(4) (denoted as SiO(2)-SO(3)H), and pure SiO(2). The SiO(2) content was controlled at 5% in the composite membranes. Combined with the results of the electrochemical impedance spectroscopy, water uptake, and fuel cell performance of different membranes, it suggested the organically modified SiO(2) has a weak water uptake ability due to the organic molecule chain. (C) 2008 The Electrochemical Society.
Bacterial lipoteichoic acid sensitizes host cells for destruction by autologous complement. (1986)

Lipoteichoic acids (LTA) released by gram-positive bacteria can spontaneously bind to mammalian cell surfaces. In the present study, erythrocytes (E) sensitized with pneumococcal LTA (LTA-E) were used as a model system to determine if LTA could render host cells susceptible to damage by autologous complement. Complement (C)-mediated lysis of LTA-E from normal rats and normal humans occurred when these cells were incubated in their respective autologous sera in vitro. In addition, when LTA-E from a C2-deficient human and from C4-deficient guinea pigs were incubated in their autologous sera, there was significant lysis in vitro, demonstrating a role for the alternative pathway. The in vivo survival of 51Cr-labeled autologous LTA-E was also studied. Only 2.9% of autologous LTA-E remained in the circulation of normal rats after 90 min. In contrast, 31.2% of autologous LTA-E remained in the circulation of rats depleted of C3. Intravascular hemolysis accounted for the clearance of LTA-E in the normal rats, whereas liver sequestration was responsible for clearance in the C3-depleted rats. These results demonstrate that LTA can render the host's cells susceptible to damage by its own complement system, establishing this as a possible mechanism of tissue damage in natural bacterial infections.
Production of L(+)‐lactic acid from glucose and starch by immobilized cells of Rhizopus oryzae in a rotating fibrous bed bioreactor (2002)

A rotating fibrous-bed bioreactor (RFB) was developed for fermentation to produce L(+)-lactic acid from glucose and cornstarch by Rhizopus oryzae. Fungal mycelia were immobilized on cotton cloth in the RFB for a prolonged period to study the fermentation kinetics and process stability. The pH and dissolved oxygen concentration (DO) were found to have significant effects on lactic acid productivity and yield, with pH 6 and 90% DO being the optimal conditions. A high lactic acid yield of 90% (w/w) and productivity of 2.5 g/L.h (467 g/h.m(2)) was obtained from glucose in fed-batch fermentation. When cornstarch was used as the substrate, the lactic acid yield was close to 100% (w/w) and the productivity was 1.65 g/L.h (300 g/h.m(2)). The highest concentration of lactic acid achieved in these fed-batch fermentations was 127 g/L. The immobilized-cells fermentation in the RFB gave a virtually cell-free fermentation broth and provided many advantages over conventional fermentation processes, especially those with freely suspended fungal cells. Without immobilization with the cotton cloth, mycelia grew everywhere in the fermentor and caused serious problems in reactor control and operation and consequently the fermentation was poor in lactic acid production. Oxygen transfer in the RFB was also studied and the volumetric oxygen transfer coefficients under various aeration and agitation conditions were determined and then used to estimate the oxygen transfer rate and uptake rate during the fermentation. The results showed that the oxygen uptake rate increased with increasing DO, indicating that oxygen transfer was limited by the diffusion inside the mycelial layer.
On the performance of regression and step-initialized IIR clutter filters for color Doppler systems in diagnostic medical ultrasound (1995)

One of the major issues in color Doppler ultrasound is the suppression of clutter that arises from stationary or slowly moving tissue. If not adequately suppressed, clutter can severely affect the ability of color Doppler systems to accurately estimate the Doppler mean frequency and power of blood, resulting in a potentially misleading depiction of flow. In this study, the performances of two classes of clutter suppression techniques-step-initialized infinite impulse response (IIR) and regression filters-were evaluated and compared by means of extensive simulations. The performance indicators used were the accuracy and precision of the mean frequency and the power estimates after clutter filtering. In summary, the ability of both filter classes to suppress clutter was found to vary considerably depending on factors such as the clutter-to-flow-signal ratio and the ensemble length. In particular, the performance of step-initialized IIR filters was shown to be noticeably inferior to that predicted by their steady-state response. Regression filters were found to offer significantly better performance than step-initialized IIR filters under heavy clutter conditions and, given their steeper roll-off, appear to be more effective clutter suppressors for power Doppler imaging. However, it should be noted that, as demonstrated by the simulations, the performance of IIR filters is severely degraded by their transient response which, in turn, is determined by the initialization scheme used. Therefore, more elaborate schemes-with superior transient characteristics than step-initialization-could significantly improve the effectiveness of IIR filtering under heavy clutter conditions.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A genetic linkage map of cucumber (Cucumis sativus L) combining SRAP and ISSR markers (2007)

Sequence-related amplified polymorphism (SRAP) and Inter-simple sequence repeat (ISSR) markers are both simple and efficient maker systems adapted to many crops and for multiple purposes. In this study a genetic map based on SRAP and ISSR markers was constructed for cucumber (Cucumis sativus&nbsp;L.) based on the segregations of SRAP and ISSR markers in 112 plants of F2&nbsp;population derived from a cross between two cucumber inbred lines PW0832 and PW0801. In the investigation of polymorphisms with 50 ISSR primers and 132 SRAP primer combinations, 13 (26%) ISSR primers and 26 (20%) SRAP primer pairs were polymorphic generating a total of 109 polymorphic markers of which 48 were ISSR and 61 were SRAP. The average polymorphic bands were four for ISSR and two for SRAP. All the 109 polymorphic markers were scored for segregation of which 86 satisfied the Mandelian segregation ratio of 3:1. These data were used to construct an integrated linkage map for cucumber consisting of 62 loci, distributed in seven linkage groups (LGs) spanning a total of 992.2 cM, with an average distance of 16.0 cM between two adjacent loci. These markers would be very useful tool for marker assisted selection in cucumber breeding as well as for studies in quantitative traits. &nbsp; Key words:&nbsp;SRAP, ISSR, linkage mapping, cucumber.
Evaluation of the HER2/neu-derived peptide GP2 for use in a peptide-based breast cancer vaccine trial (2005)

Mittendorf, Elizabeth A. MD; Storrer, Catherine BS; Shriver, Craig MD; Ponniah, Sathibalan PhD; Peoples, George MD Author Information
Effects of RNA Interference-mediated Silencing of γ-Secretase Complex Components on Cell Sensitivity to Caspase-3 Activation (2004)

Familial Alzheimer's disease mutations in the presenilin 1 gene (PSEN1) have been previously shown to potentiate caspase activation and apoptosis in transfected cells and transgenic mice. However, the mechanism underlying this effect is not known. We set out to determine whether cellular sensitivity to caspase activation could be affected by modulating presenilin 1 (PS1) processing. PS1 processing was altered using RNA interference (RNAi) aimed at silencing the expression of the genes encoding the four components of the gamma-secretase complex, PSEN1, APH-1, PEN-2, and nicastrin. RNAi for these genes was carried out in naive H4 human neuroglioma cells, as well as H4 cell lines overexpressing either wild-type PSEN1 or the Familial Alzheimer's disease mutant PSEN1-Delta9 (PS1-mutant), that were induced to undergo apoptosis. In wild-type PSEN1 cells, RNAi for PEN-2, as expected, increased levels of full-length PS1 (PS1-FL) and decreased PS1 endoproteolysis. This was accompanied by potentiated caspase-3 activation in response to an apoptotic stimulus. In contrast, nicastrin RNAi, which only decreased levels of PS1-amino-terminal fragment and did not affect PS1-FL levels, had no effect on caspase-3 activation during apoptosis. Surprisingly, in the PS1-mutant cells, RNAi for PEN-2 (and APH-1) did not increase but instead reduced the levels of PS1-FL deleted for exon 9. In turn, this was accompanied by attenuated caspase-3 activation in response to an apoptotic stimulus. Finally, in naive H4 cells, PSEN1 RNAi also attenuated caspase-3 activation in response to an apoptotic stimulus. Collectively, these findings indicate that cellular sensitivity to caspase activation correlates with overall PS1 protein levels, particularly with levels of FL-PS1.
Comparison of dexmedetomidine versus midazolam for intranasal premedication in children posted for elective surgery: a double-blind, randomised study (2015)

Objective: The aim of this study was to compare the effect of dexmedetomidine with midazolam for intranasal premedication in children posted for elective surgery.
System Software Framework for System of Systems Avionics (2006)

Project Constellation implements NASA's vision for space exploration to expand human presence in our solar system. The engineering focus of this project is developing a system of systems architecture. This architecture allows for the incremental development of the overall program. Systems can be built and connected in a "Lego style" manner to generate configurations supporting various mission objectives. The development of the avionics or control systems of such a massive project will result in concurrent engineering. Also, each system will have software and the need to communicate with other (possibly heterogeneous) systems. Fortunately, this design problem has already been solved during the creation and evolution of systems such as the Internet and the Department of Defense's successful effort to standardize distributed simulation (now IEEE 1516). The solution relies on the use of a standard layered software framework and a communication protocol. A standard framework and communication protocol is suggested for the development and maintenance of Project Constellation systems. The ARINC 653 standard is a great start for such a common software framework. This paper proposes a common system software framework that uses the Real Time Publish/Subscribe protocol for framework-to-framework communication to extend ARINC 653. It is highly recommended that such a framework be established before development. This is important for the success of concurrent engineering. The framework provides an infrastructure for general system services and is designed for flexibility to support a spiral development effort.
Binary‐offset‐carrier modulation techniques with applications in satellite navigation systems (2006)

Abstract An important aspect in designing the modulation scheme for various satellite systems, such as the modernized GPS and Galileo, is to obtain good spectral properties and suitable spectral shaping. For example, in the future satellite navigation systems, some of the main goals are: low interference with the existing GPS signals, good root‐mean‐square (RMS) bandwidth, good time resolution (in order to allow the separation between channel paths and to decrease the synchronization errors) etc. Starting from the recently proposed cosine‐ and sine‐BOC modulation families for GPS and Galileo systems, we introduce a new, generalized family, denoted here by double‐BOC (DBOC) modulation. We derive and analyze the properties of the power spectral densities (PSD) and autocorrelation functions (ACF) of the DBOC modulation with various orders, we show its relationship with BPSK, sine‐ and cosine‐BOC modulations, and we illustrate via several examples how to choose optimally the parameters of this new modulation family, according to different optimization criteria. The examples are targeting at applications such as the design of suitable modulations for Galileo open service (OS) and public regulated service (PRS) signals, but the authors believe that the DBOC concept might be useful to other satellite‐based applications, when the available bandwidth is large enough. Copyright © 2006 John Wiley &amp; Sons, Ltd.
New in 2005 (2005)

Starting with this issue of Clinics in Colon and Rectal Surgery, readers and subscribers will notice several changes and what we hope will be improvements. The Editorial Board has been expanded with the addition of an international member. I am pleased to welcome Dr. Martin E. Kreis from Germany.
Computational image sensor for on sensor compression (1997)

We propose a novel integration of image compression and sensing in order to enhance the performance of an image sensor. By integrating a compression function onto the sensor focal plane, the image signal to be read out from the sensor is significantly reduced and the pixel rate of the sensor ran consequently be increased. The potential applications of the proposed sensor are in high pixel-rate imaging, such as high frame-rate image sensing and high-resolution image sensing. The compression scheme we employ is a conditional replenishment, which detects and encodes moving areas. In this paper, we introduce two architectures for on-sensor compression; one is the pixel parallel approach and the other is the column parallel approach. We prototyped a VLSI chip of the proposed sensor based on the pixel parallel architecture. We show the design and describe the results of the experiments obtained by the prototype chip.
Making sense of polymer-based biosensors (1999)

In this issue of PNAS, Chen et al. (1) show feasibility for producing a highly sensitive biosensor, capable of detecting nanomolar quantities of biologically interesting molecules in “real time.” If the phenomenon can be generalized to other systems, it could have significant implications for a wide variety of fields, including toxicology and medical diagnostics.
Formation of Joint DNA Molecules by Two Eukaryotic Strand Exchange Proteins Does Not Require Melting of a DNA Duplex (1989)

We have examined whether DNA strand exchange activities from nuclear extracts of HeLa cells or Drosophila melanogaster embryos have detectable helicase or melting activities. The partially purified recombinases have been shown to recognize homologous single strand and double strand DNA molecules and form joint molecules in a DNA strand exchange reaction. The joint molecule product consists of a linear duplex joined at one end by a region of DNA heteroduplex to a homologous single strand circular DNA. Using two different partially duplex helicase substrates, we are unable to detect any melting of duplex regions under conditions that promote joint molecule formation. One substrate consists of a 32P-labeled oligonucleotide 20 or 30 bases long annealed to M13mp18 circular single strand DNA. The second substrate consists of a linear single strand region flanked at each end by short duplex regions. We observe that even in the presence of excess recombinase protein or after prolonged incubation no helicase activity is apparent. Control experiments rule out the possibility that a helicase is masked by reannealing of displaced single strand fragments. Based on these findings and other data, we conclude that the human and D. melanogaster recombinases recognize and pair homologous sequences without significant melting of duplex DNA prior to strand exchange.