gebhart/patrepeval huggingface dataset:
Transcriptional response to hypoxic stress in melanoma and prognostic potential of GBE1 and BNIP3 (2017)

Gradients of hypoxia occur in most solid tumors and cells found in hypoxic regions are associated with the most aggressive and therapy-resistant fractions of the tumor. Despite the ubiquity and importance of hypoxia responses, little is known about the variation in the global transcriptional response to hypoxia in melanoma. Using microarray technology, whole genome gene expression profiling was first performed on established melanoma cell lines. From gene set enrichment analyses, we derived a robust 35 probes signature (hypomel for HYPOxia MELanoma) associated with hypoxia-response pathways, including 26 genes up regulated, and 9 genes down regulated. The microarray data were validated by RT-qPCR for the 35 transcripts. We then validated the signature in hypoxic zones from 8 patient specimens using laser microdissection or macrodissection of Formalin fixed-paraffin-embedded (FFPE) material, followed with RT-qPCR. Moreover, a similar hypoxia-associated gene expression profile was observed using NanoString technology to analyze RNAs from FFPE melanoma tissues of a cohort of 19 patients treated with anti-PD1. Analysis of NanoString data from validation sets using Non-Negative Matrix Factorization (NMF) analysis (26 genes up regulated in hypoxia) and dual clustering (samples and genes) further revealed that the increased level of BNIP3 (Bcl-2 adenovirus E1B 19 kDa-interacting protein 3)/GBE1 (glycogen branching enzyme1) differential pair correlates with the lack of response of melanoma patients to anti-PD1 (pembrolizumab) immunotherapy. These studies suggest that through elevated glycogenic flux and induction of autophagy, hypoxia is a critical molecular program that could be considered as a prognostic factor for melanoma.
Fabrication of GaN‐based light emitting diodes using direct heteroepitaxial lateral overgrowth on patterned sapphire substrates with thick SiO2 masks (2008)

Abstract We have successfully obtained high‐quality GaN films directly on thick SiO 2 patterned sapphire substrates by utilizing modified facet‐controlled epitaxial lateral overgrowth (FACELO). GaN films were grown by metalorganic vapour phase epitaxy on the stripe patterned substrates with the SiO 2 thickness of 1.2 μm. The threading dislocation density reached a value as low as 5 × 10 7 cm –2 . We have also fabricated Light emitting diodes (LEDs). The output power and external quantum efficiency of the LED operated at 20 mA were 20.74 mW and 37.1%, respectively. This is due to not only the reduced dislocation density but also the improved light extraction efficiency because of the light scattering at the patterned GaN/thick‐SiO 2 ‐masks interface. (© 2008 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Abstract 2105: An EWS-FLI1/MRTF gene regulatory network in Ewing sarcoma (2015)

Abstract The pediatric bone cancer Ewing sarcoma (ES) is characterized by the expression of the chimeric transcription factor EWS-FLI1, derived from a chromosomal translocation t(11;22)(q24;q12). The early onset of metastasis in ES leads to poor overall survival and limited treatment options. Remodeling of the actin cytoskeleton is a prerequisite of a tumor cell in order to become metastatic. Previous studies suggest that EWS-FLI1 alters cell morphology and deregulates various cytoskeletal genes. The major point of convergence of extracellular signals influencing cytoskeletal regulation is the Rho pathway. Activation of Rho GTPases promotes polymerization of monomeric G-actin into stress fibers (F-actin) thereby releasing the myocardin-related transcription factor family (MRTF-A, MRTF-B) of transcriptional coactivators. MRTFs translocate to the nucleus and interact with the transcription factor serum response factor (SRF) bound on CArG promoter elements of genes. However, the ternary complex factor (TCF) family, a class of transcriptional coactivators activated downstream of Ras signaling, competes with MRTFs for SRF binding in presence of ets binding sites adjacent to the CArG consensus sequence. The ets-transcription factor EWS-FLI1 has been shown to substitute for TCFs and interact with SRF. We hypothesized that EWS-FLI1 competes with MRTFs for SRF binding and uncouples target gene expression from Rho signaling. In combinatorial knockdown experiments of MRTFA/B and EWS-FLI1 we demonstrate that global changes in gene expression elicited by EWS-FLI1 silencing largely depend on the presence of MRTFs, suggesting that the fusion oncogene prohibits MRTF activity. Using gene expression analysis we identified six different patterns of MRTF/EWS-FLI1 interaction, with predominance of EWS-FLI1 inversely regulating MRTF target genes. Furthermore, we found MRTF transcriptional effects are already present in the absence of serum in A673 ES cells. MRTFB, however, is cytoplasmic under serum starved conditions and translocates to the nucleus only upon serum stimulation unless latrunculin B (LatB), an actin polymerization inhibitor, is added. In contrast, MRTFA is constitutively nuclear even under serum starved conditions or upon LatB treatment indicating that MRTFA might be uncoupled from actin regulation. These findings reveal a previously unknown role of MRTFs and the “CArGome” in EWS-FLI1 driven transcriptional dysregulation. Supported by the Liddy Shriver Sarcoma Initiative. Citation Format: Anna M. Katschnig, Maximilian Kauer, Raphaela Schwentner, Dave N.T Aryee, Elizabeth Lawlor, Heinrich Kovar. An EWS-FLI1/MRTF gene regulatory network in Ewing sarcoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2105. doi:10.1158/1538-7445.AM2015-2105
HIV-specific Cytotoxic T Cells from Long-Term Survivors Select a Unique T Cell Receptor (2004)

HIV-specific cytotoxic T lymphocytes (CTL) are important in controlling HIV replication, but the magnitude of the CTL response does not predict clinical outcome. In four donors with delayed disease progression we identified Vbeta13.2 T cell receptors (TCRs) with very similar and unusually long beta-chain complementarity determining region 3 (CDR3) regions in CTL specific for the immunodominant human histocompatibility leukocyte antigens (HLA)-B8-restricted human immunodeficiency virus-1 (HIV-1) nef epitope, FLKEKGGL (FL8). CTL expressing Vbeta13.2 TCRs tolerate naturally arising viral variants in the FL8 epitope that escape recognition by other CTL. In addition, they expand efficiently in vitro and are resistant to apoptosis, in contrast to FL8-specific CTL using other TCRs. Selection of Vbeta13.2 TCRs by some patients early in the FL8-specific CTL response may be linked with better clinical outcome.
Comparison of the relative roles of the F and HN surface glycoproteins of the paramyxovirus simian virus 5 in inducing protective immunity (1987)

To compare the relative roles of the paramyxovirus simian virus 5 (SV5) major surface glycoproteins, fusion (F) and hemagglutinin-neuraminidase (HN), in inducing protective immunity, two recombinant vaccinia viruses were constructed. The F and HN polypeptides expressed by the recombinant viruses were indistinguishable from their authentic SV5 counterparts in electrophoretic mobility, glycosylation, and, for the F protein, cleavage of the precursor, F0, to the disulfide-linked subunits F1 and F2. Injection of rabbits and hamsters with live recombinant virus elicited an antibody response to either F or HN and provided a source of monospecific polyclonal antisera to the SV5 proteins. The vaccinia virus-SV5 F (vaccinia-F) recombinant induced higher levels of neutralizing antibody than did the vaccinia-HN recombinant, but animals inoculated with vaccinia-HN were better protected from challenge with SV5. Animals infected with both the vaccinia-HN and vaccinia-F viruses were nearly as well protected from challenge as were animals infected with SV5.
Thermally enhanced blue light-emitting diode (2015)

We investigate thermoelectric pumping in wide-bandgap GaN based light-emitting diodes (LEDs) to take advantage of high junction temperature rather than avoiding the problem of temperature-induced efficiency droop through external cooling. We experimentally demonstrate a thermally enhanced 450 nm GaN LED, in which nearly fourfold light output power is achieved at 615 K (compared to 295 K room temperature operation), with nearly no reduction in the wall-plug efficiency (i.e., electrical-optical energy conversion efficiency) at bias V< ℏ ω/q. The LED is shown to work in a mode similar to a thermodynamic heat engine operating with charged carriers pumped into the active region by a combination of electrical work and Peltier heat (phonons) drawn from the lattice. In this optimal operating regime at 615 K, the LED injection current (3.26 A/cm[superscript 2]) is of similar magnitude to the operating point of common high power GaN based LEDs (5–35 A/cm[superscript 2]). This result suggests the possibility of removing bulky heat sinks in current high power LED products thus realizing a significant cost reduction for solid-state lighting.
Evolution of AlN buffer layers on silicon and effects on the properties of epitaxial GaN films (2003)

The morphological evolution of AlN buffer layers grown on (111) silicon at high-temperature has been studied using atomic force microscopy (AFM) and transmission electron microscopy (TEM). The structure and morphology of subsequently grown GaN films were characterized using scanning electron microscopy (SEM), X-ray diffraction (XRD), and photoluminescence (PL) measurements. It was found that even though thicker AlN buffer layers are the poor single crystal with some defects like mis-oriented domains, stacking faults, they provide better templates for subsequent growth of GaN films with better crystalline and optical properties, compared to the GaN grown on a thin AlN buffer layer. To prevent the formation of SiNx layers at the interface, TMA was flowed for several seconds prior to the introduction of ammonia into the chamber. The AFM result showed that quasi 2-dimensional growth was quickly achieved for the AlN buffer layer with TMA pre-treatment. (© 2003 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)
A CMOS-compatible Low Back Reflection Grating Coupler for On-chip Laser Sources Integration (2016)

We demonstrate a low back reflection grating coupler on a SOI CMOS-compatible process designed for vertical integration of on-chip laser sources. It showed &lt;-26dB back reflection and 1.9dB coupling loss to a 4-μm-diameter laser mode.
Effect of carbon doping on threshold voltage and mobility of In-Si-O thin-film transistors (2018)

In this study, a co-sputtering method with In2O3 and SiC targets was used to fabricate carbon-doped In-Si-O (In1-xSixO1-yCy) as the channel material for oxide thin-film transistors (TFTs). Three types of In1-xSixO1-yCy channels, namely, In0.88Si0.12O0.99C0.01 (Si0.12C0.01), In0.76Si0.24O0.99C0.01 (Si0.24C0.01), and In0.60Si0.40O0.98C0.02 (Si0.40C0.02), were prepared. After annealing at 300 °C, the Si0.24C0.01 and Si0.40C0.02 films retained an amorphous structure, while the Si0.12C0.01 films exhibited a body-centered-cubic structure. However, all the In1-xSixO1-yCy films maintained a smooth surface with a root-mean-square roughness of approximately 0.28 nm, despite structural differences. Results showed that the conductivities of all the In1-xSixO1-yCy films were not sensitive to the O2 partial pressure during sputtering, indicating that In1-xSixO1-yCy films exhibit more stable electrical conductivity than other InOx-based oxides. The field-effect mobility (μFE) with respect to the Si concentration of In1-xSixO1-yCy and In1-xSixO TFTs showed very similar behavior. In contrast, the threshold voltage (Vth) behavior of the two types varied dramatically, with the In1-xSixO TFTs Vth value increasing drastically from −57.7 to 9.7 V with increasing Si concentration, and the Vth of In1-xSixO1-yCy TFTs increasing only gradually from −9.2 to 2.4 V. This indicates that incorporated carbon has a significant effect on Vth at a low Si concentration due to strong C—O bond formation. The highest bond dissociative energy occurs between O and C atoms in the In1-xSixO1-yCy channel. The amount of oxygen vacancy in Si0.12C0.01, Si0.24C0.01, and Si0.40C0.02 was 18.9%, 13.3%, and 12.9%, respectively. As a result, the Si0.12C0.01 TFT exhibited superior transistor properties of Vth = −9.2 V while maintaining a μFE of 32.4 cm2/Vs. Therefore, an In1-xSixO1-yCy film is significantly advantageous as a channel material for oxide TFTs given that it can result in mobility exceeding 30 cm2/Vs.
Fleets: Scalable Services in a Factored Operating System (2011)

Current monolithic operating systems are designed for uniprocessor systems, and their architecture reflects this. The rise of multicore and cloud computing is drastically changing the tradeoffs in operating system design. The culture of scarce computational resources is being replaced with one of abundant cores, where spatial layout of processes supplants time multiplexing as the primary scheduling concern. Efforts to parallelize monolithic kernels have been difficult and only marginally successful, and new approaches are needed. This paper presents fleets, a novel way of constructing scalable OS services. With fleets, traditional OS services are factored out of the kernel and moved into user space, where they are further parallelized into a distributed set of concurrent, message-passing servers. We evaluate fleets within fos, a new factored operating system designed from the ground up with scalability as the first-order design constraint. This paper details the main design principles of fleets, and how the system architecture of fos enables their construction. We describe the design and implementation of three critical fleets (network stack, page allocation, and file system) and compare with Linux. These comparisons show that fos achieves superior performance and has better scalability than Linux for large multicores; at 32 cores, fos's page allocator performs 4.5 times better than Linux, and fos's network stack performs 2.5 times better. Additionally, we demonstrate how fleets can adapt to changing resource demand, and the importance of spatial scheduling for good performance in multicores.
1281 – Association Between Tobacco Smoking And Bipolar Affective Disorder: Clinical, Epidemiological, Cross-sectional, Retrospective Study In Outpatients (2013)

Purpose Although high rates of smoking have been reported among psychiatric patients, only a few studies examined the prevalence of smoking in bipolar disorder, and findings are inconsistent. We investigated smoking among bipolar patients. Methods We examined the prevalence of smoking in of 102 patients that met Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition criteria for bipolar I disorder in Israel and evaluated the relationship between smoking and demographic and clinical data. Results Fifty-five of the bipolar patients (53.9%) smoked, with a rate that is 2.36 times higher than among the general population in Israel (22.8%). Significant relationships were revealed between smoking and lifetime history of alcohol dependence/abuse (P = .02), between smoking and history of drug use (P ≤ .01), and between smoking and age of illness onset (P = .04). Limitations The cross-sectional nature of the study and the relatively small sample size preclude generalization of the findings. Nicotine levels were not measured; thus, the information regarding smoking was subjective. Conclusions Bipolar patients smoke more than the general population. Bipolar patients that are moderate or heavy smokers are more likely than nonsmokers to consume alcohol and abuse psychoactive substances. Contrary to findings of previous studies, no association was found between clinical variables of bipolar patients and smoking.
Endomucin Plays a Role in Retinal Vascular Development and in VEGF‐Induced Endothelial Cell Migration, Growth, and Morphogenesis (2015)

Angiogenesis is central to both normal and pathologic processes. Endothelial cells (ECs) express high levels of O‐glycoproteins that are believed to play important roles in vascular development and stability. Endomucin‐1 (EMCN) is a type I O‐glycosylated, sialic‐rich glycoprotein, specifically expressed by venous and capillary endothelium. Although ECs express high levels of EMCN, its possible role in vascular development has not been examined. A role for EMCN in angiogenesis was studied by modulating gene expression in vitro and in vivo. Postnatal day (P) four C57BL/6 mice were injected intravitreally with siEMCN or scramble siRNA (siCtrl). Knockdown of EMCN mRNA was significant at 48 hrs after injection compared to siCtrl mice. We observed a delay in radial expansion of the developing mouse vasculature in siEMCN‐injected P6 mice (51±2.2 vs. 69±1.8%, P&lt;0.0001), accompanied by reduced vessel density (49±1.9 vs. 66±4.8%, P&lt;0.01), branch point number (43±1.1 vs. 64±4.0 mm 2 , P&lt;0.0001), and tip cell number (18±0.6 vs. 28± 2.1 mm, P&lt;0.05) when compared to siCtrl mice. Knockdown of EMCN in human retinal ECs led to a reduction in VEGF‐induced migration (22±1.3 vs. 59±2.7%, P&lt;0.0001), proliferation (1.51 x 10 4 ±125.0 vs. 2.25 x 10 4 ±1500 cell/cm 2 , P&lt;0.05), and morphogenesis (7201±86 vs. 9157±273.0 mm, P&lt;0.005) compared to siCtrl cells, without compromising cell survival. VEGF stimulation of siEMCN transfected ECs showed reduction in phospho‐VEGFR2, phospho‐ERK1/2 and phospho‐Akt levels. Taken together, our study indicates a novel role for EMCN as an important regulator of angiogenesis.
Supplementary Figure S5 from Genomic Instability and Protumoral Inflammation Are Associated with Primary Resistance to Anti–PD-1 + Antiangiogenesis in Malignant Pleural Mesothelioma (2023)

&lt;p&gt;Gating strategy for flow cytometry analyses of T cells infiltration on tumor biopsies.&lt;/p&gt;
Fimbriae/pili from oral bacteria. (2014)

<title>Abstract</title> This chapter focuses on fimbriae and pili and the recent advances made in understanding their role in bacterial adhesion and invasion in the oral cavity. The two primary groups of gram-positive bacteria present in the oral cavity are <italic>Streptococcus</italic> and <italic>Actinomyces</italic>. Gram-negative species often comprise the later colonizers of the oral cavity and the noticeable ones are often regarded as periodontal disease-associated pathogens, including <italic>Aggregatibacter actinomycetemcomitans</italic>, <italic>Porphyromonas gingivalis</italic> and <italic>Fusobacterium nucleatum</italic>. In this chapter, these bacteria are used as models to discuss bacterial surface structures pili and fimbriae, and their contributions to bacterial adhesion and invasion.
Control of synthesis and distribution of acyl moieties in etiolated Euglena gracilis (1973)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTControl of synthesis and distribution of acyl moieties in etiolated Euglena gracilisAbdul A. Khan and P. E. KolattukudyCite this: Biochemistry 1973, 12, 10, 1939–1948Publication Date (Print):May 1, 1973Publication History Published online1 May 2002Published inissue 1 May 1973https://pubs.acs.org/doi/10.1021/bi00734a017https://doi.org/10.1021/bi00734a017research-articleACS PublicationsRequest reuse permissionsArticle Views52Altmetric-Citations36LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Household hygiene practices in relation to dampness at home and current wheezing and rhino‐conjunctivitis among school age children (2005)

Good household hygiene practices may improve indoor air quality in the domestic environment. Conversely, a 'hygiene hypothesis' is challenging the importance of hygiene and sanitation at home. This study aims to investigate the relationship between household hygiene practices and dampness at home and current wheezing, asthma and other allergic conditions among Australian children. Nine hundred and ninety-six children from four primary schools in Perth, Western Australia, were recruited for a domestic environmental and health survey during March and April of 2002. The results showed that high cleanliness scores were negatively associated with moulds at home before and after adjustment for age of dwelling (p < 0.001). High ventilation scores were inversely related with damp patches, condensation and moulds at home (p < 0.05). However, households with high cleanliness scores appeared to have significantly higher prevalence of current wheezing (p < 0.05) and current rhino-conjunctivitis (p < 0.05) in children. The association remained even after controlling for confounders such as age and gender of children, asthma history of parents, passive smoking and dampness at home.
The impact of la-doping on the reliability of low Vth high-k/metal gate nMOSFETs under various gate stress conditions (2008)

La-doped HfSiO samples show lower threshold voltage (V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sub> ) and gate current (I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">gate</sub> ), which is attributed to dipole formation at the high-k/SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> interface. At low and intermediate field stress, La-doped devices exhibit better immunity to positive bias temperature instability (PBTI) due to their lower charge trapping efficiency than the control HfSiO, which mainly results from a dipole-induced greater barrier offset. However, the primary cause for defect generation at high field stress is attributed to the La atoms in the interfacial SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> layer. By optimizing the technique to incorporate nitrogen into the bottom interface, this high field reliability issue can be minimized while maintaining good device characteristics.
Landscape of somatic single nucleotide variants and indels in colorectal cancer and impact on survival (2020)

Colorectal cancer (CRC) is a biologically heterogeneous disease. To characterize its mutational profile, we conduct targeted sequencing of 205 genes for 2,105 CRC cases with survival data. Our data shows several findings in addition to enhancing the existing knowledge of CRC. We identify PRKCI, SPZ1, MUTYH, MAP2K4, FETUB, and TGFBR2 as additional genes significantly mutated in CRC. We find that among hypermutated tumors, an increased mutation burden is associated with improved CRC-specific survival (HR = 0.42, 95% CI: 0.21-0.82). Mutations in TP53 are associated with poorer CRC-specific survival, which is most pronounced in cases carrying TP53 mutations with predicted 0% transcriptional activity (HR = 1.53, 95% CI: 1.21-1.94). Furthermore, we observe differences in mutational frequency of several genes and pathways by tumor location, stage, and sex. Overall, this large study provides deep insights into somatic mutations in CRC, and their potential relationships with survival and tumor features.