gebhart/patrepeval huggingface dataset:
Programmed death-ligand 1 (PD-L1) expression and HPV-associated p16 in oropharyngeal squamous cell carcinoma (OSCC) treated with primary curative radiotherapy (RT) (2018)

Background: PD-L1 expression in malignancies contributes to an immunosuppressive microenvironment and disruption of anti-tumoral immune responses. Data are limited on the association between PD-L1 expression and survival in OSCC, overall and by HPV p16 status. We explored the prognostic effect of PD-L1 and p16 in localized or locally advanced OSCC treated with primary RT. Methods: Patients (pts) diagnosed with OSCC from 2000-12 were identified from the Danish Head and Neck Cancer database (DAHANCA). PD-L1 expression was measured in tumor tissue using Agilent’s investigational PD-L1 imunohistochemistry (IHC) PharmDx Assay (clone 22C3). PDL1+ expression was defined as a score >1 using Tumor Proportion Score (TPS) as % of neoplastic cells expressing PDL1 at any intensity, Mononuclear Inflammatory Density Score (MIDS) as the estimate of PDL1 expressing mononuclear inflammatory cells associated with neoplastic cells, and Combined Positive Score (CPS) calculated using both TPS and MIDS. HPV oncogene expression was assessed using a > 70% cut-point for p16 IHC (clone E6H4). Data were analyzed using Cox proportional hazard model. Results: 303 OSCC pts with full clinical data, and PD-L1 and p16 staining were evaluated. Median follow up was 55 months (2-184). Median age (range) was 59 years (34-85), 72% were male, 91% had WHO 0-1 performance status, 55% were current smokers. All had primary RT, 66-68Gy, 2Gy/fx, 6 fx/wk, and 3% had concomitant cisplatin. 81% were UICC 7 stage 3-4 tumors. 55% were p16+. 76% were PD-L1+ by CPS, 35% by TPS, and 31% by MIDS. TPS was significantly associated with MIDS (Chi square p = 0.003). p16 was a strong prognostic factor for loco-regional control [crude hazard ratio (HR) of 0.31 (95% CI: 0.21-0.49)], disease-specific survival [0.39 (0.26-0.57)] and overall survival [0.34 (0.25-0.46)]. PD-L1 expressed as CPS, TPS or MIDS, was not prognostic of the clinical endpoints, overall or by p16 status. Adjustment for other covariates did not change the results. Conclusions: PD-L1 expression is not prognostic in localized or locally advanced OSCC, including p16 positive disease. p16 is affirmed the strongest biological prognostic factor in OSCC. Legal entity responsible for the study: The Danish Head and Neck Cancer Group (DAHANCA). Funding: Merck & Co, Inc. Disclosure: T. Steiniche: Research funding: Merck & Co, Inc. P-T. Vo, D.R. Chirovsky: Employement, stock ownership, research funding, travel and accommodations expenses: Merck & Co, Inc. J. Cheng: Employment, stock ownership: Merck & Co. D. Aurora-Garg, R. Swaby: Employment Merck & Co. All other authors have declared no conflicts of interest.
Impaired mitochondrial energy supply coupled to increased H2O2 emission under energy/redox stress leads to myocardial dysfunction during Type I diabetes (2015)

In Type I diabetic (T1DM) patients, both peaks of hyperglycaemia and increased sympathetic tone probably contribute to impair systolic and diastolic function. However, how these stressors eventually alter cardiac function during T1DM is not fully understood. In the present study, we hypothesized that impaired mitochondrial energy supply and excess reactive oxygen species (ROS) emission is centrally involved in T1DM cardiac dysfunction due to metabolic/redox stress and aimed to determine the mitochondrial sites implicated in these alterations. To this end, we used isolated myocytes and mitochondria from Sham and streptozotocin (STZ)-induced T1DM guinea pigs (GPs), untreated or treated with insulin. Relative to controls, T1DM myocytes exhibited higher oxidative stress when challenged with high glucose (HG) combined with β-adrenergic stimulation [via isoprenaline (isoproterenol) (ISO)], leading to contraction/relaxation deficits. T1DM mitochondria had decreased respiration with complex II and IV substrates and markedly lower ADP phosphorylation rates and higher H2O2 emission when challenged with oxidants to mimic the more oxidized redox milieu present in HG + ISO-treated cardiomyocytes. Since in T1DM hearts insulin-sensitivity is preserved and a glucose-to-fatty acid (FA) shift occurs, we next tested whether insulin therapy or acute palmitate (Palm) infusion prevents HG + ISO-induced cardiac dysfunction. We found that insulin rescued proper cardiac redox balance, but not mitochondrial respiration or contractile performance. Conversely, Palm restored redox balance and preserved myocyte function. Thus, stressors such as peaks of HG and adrenergic hyperactivity impair mitochondrial respiration, hampering energy supply while exacerbating ROS emission. Our study suggests that an ideal therapeutic measure to treat metabolically/redox-challenged T1DM hearts should concomitantly correct energetic and redox abnormalities to fully maintain cardiac function.
Recent Advances in the Gold-Catalysed Low-Temperature Water–Gas Shift Reaction (2018)

The low-temperature water–gas shift reaction (LTS: CO + H2O ⇌ CO2 + H2) is a key step in the purification of H2 reformate streams that feed H2 fuel cells. Supported gold catalysts were originally identified as being active for this reaction twenty years ago, and since then, considerable advances have been made in the synthesis and characterisation of these catalysts. In this review, we identify and evaluate the progress towards solving the most important challenge in this research area: the development of robust, highly active catalysts that do not deactivate on-stream under realistic reaction conditions.
Broadband light source using modulated quantum dot structures with sandwiched sub‐nano separator (SSNS) technique (2010)

Abstract A broadband light source for a wavelength range of around 1.2‐1.3 μm can be fabricated using a multi‐stacked and modulated InAs/InGaAs quantum dot (QD) structure with the sandwich sub‐nano separator (SSNS) technique. These techniques, such as use of the modulated QD structure and SSNS structure, are considered useful in obtaining a high‐quality and ultra‐broadband QD optical gain material for the laser and/or optical amplifier. A broadband (&gt;75 nm bandwidth) and bright (few tenths of a mW) light emission in its waveband is successfully demonstrated from a QD laser diode using a modulated QD optical gain with the SSNS technique. (© 2011 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
High-Throughput and High-Port-Count Optical Cross- Connents Using Flexible Waveband Routing (2020)

Currently deployed optical cross-connects (OXCs) cannot support the large traffic expected in the near future because of the limited port count of wavelength-selective switches (WSSs). To resolve this problem, we proposed an OXC architecture that combines joint-switch WSSs and space switches. This OXC architecture realizes high port counts with low hardware cost in return for the additional insertion loss. However, the attainable maximum port count is still limited since the insertion loss increases with the port count. In this paper, we newly propose an OXC architecture whose insertion loss is constant irrespective of the port count. Consequently, the port count is virtually unlimited. Computer simulations show its low hardware cost and good routing performance. A proof-of-concept experiment evaluates the transmission performance, where the net throughput of 2.15 Pbps with port count of 84 is demonstrated.
Chondrogenic Activity of the Heparan Sulfate Proteoglycan Perlecan Maps to the N-terminal Domain I (2002)

C3H10T1/2 cells differentiate along a chondrogenic pathway when plated onto the extracellular matrix (ECM) protein perlecan (Pln). To identify the region(s) within the large Pln molecule that provides a differentiation signal, recombinant Pln-sequence-based polypeptides representing distinct structural domains were assayed for their ability to promote chondrogenesis in C3H10T1/2 cells. Five distinct domains, along with structural variations, were tested. The N-terminal domain I was tested in two forms (IA and IB) that contain only heparan sulfate (HS) chains or both HS and chondroitin sulfate (CS) chains, respectively. A mutant form of domain I lacking attachment sites for both HS and CS (Pln I(mut)) was tested also. Other constructs consecutively designated Pln domains II, III(A-C), IV(A,B), and V(A,B) were used to complete the structure-function analysis. Cells plated onto Pln IA or Pln IB but no other domain rapidly assembled into cellular aggregates of 40-120 microm on average. Aggregate formation was dependent on the presence of glycosaminoglycan (GAG) chains, because Pln I-based polypeptides lacking GAG chains either by enzymatic removal or mutation of HS/CS attachment sites were inactive. Aggregates formed on GAG-bearing Pln IA stained with Alcian Blue and were recognized by antibodies to collagen type II and aggrecan but were not recognized by an antibody to collagen type X, a marker of chondrocyte hypertrophy. Collectively, these studies indicate that the GAG-bearing domain I of Pln provides a sufficient signal to trigger C3H10T1/2 cells to enter a chondrogenic differentiation pathway. Thus, this matrix proteoglycan (PG) found at sites of cartilage formation in vivo is likely to enhance early stage differentiation induced by soluble chondrogenic factors.
ColorMapGAN: Unsupervised Domain Adaptation for Semantic Segmentation Using Color Mapping Generative Adversarial Networks (2019)

Due to the various reasons such as atmospheric effects and differences in acquisition, it is often the case that there exists a large difference between spectral bands of satellite images collected from different geographic locations. The large shift between spectral distributions of training and test data causes the current state of the art supervised learning approaches to output unsatisfactory maps. We present a novel semantic segmentation framework that is robust to such shift. The key component of the proposed framework is Color Mapping Generative Adversarial Networks (ColorMapGAN), which can generate fake training images that are semantically exactly the same as training images, but whose spectral distribution is similar to the distribution of the test images. We then use the fake images and the ground-truth for the training images to fine-tune the already trained classifier. Contrary to the existing Generative Adversarial Networks (GANs), the generator in ColorMapGAN does not have any convolutional or pooling layers. It learns to transform the colors of the training data to the colors of the test data by performing only one element-wise matrix multiplication and one matrix addition operations. Thanks to the architecturally simple but powerful design of ColorMapGAN, the proposed framework outperforms the existing approaches with a large margin in terms of both accuracy and computational complexity.
ChemInform Abstract: Antisense Oligonucleotides (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Urolithiasis, Endourology and Laparoscopy (2002)

No AccessJournal of UrologyUROLOGICAL SURVEY: ABSTRACTS1 Aug 2002Urolithiasis, Endourology and Laparoscopy Ralph V. ClaymanM.D. Ralph V. ClaymanRalph V. Clayman More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(05)64792-1AboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "Urolithiasis, Endourology and Laparoscopy." The Journal of Urology, 168(2), p. 872 © 2002 by American Urological Association, Inc.FiguresReferencesRelatedDetails Volume 168Issue 2August 2002Page: 872 Advertisement Copyright & Permissions© 2002 by American Urological Association, Inc.MetricsAuthor Information Ralph V. Clayman More articles by this author Expand All Advertisement PDF DownloadLoading ...
Methylation of the Tumor Suppressor Gene PTPRO (Receptor-Type Protein Tyrosine Phosphatase) Is Associated with Expression of Important Apoptosis-Related Proteins in Chronic Lymphocytic Leukemia (CLL). (2004)

Abstract We previously demonstrated that apoptosis-inhibiting proteins (e.g., Bcl-2, Mcl-1, and XIAP) are important in predicting response to chemotherapy and antibody therapy for CLL. Additionally, genetic abnormalities and epigenetic control of gene expression have become increasingly important in understanding the prognosis and potential therapeutic opportunities in this disease. Greater than 80% of patients with CLL have genetic abnormalities detectable by FISH. Important subsets include those with a less favorable prognosis (deletions of 17p, 11q), an intermediate prognosis (trisomy 12), or a favorable outcome (deletion of 13q). PTPRO, encoding a receptor-type tyrosine phosphatase, is a specific tumor suppressor gene located in chromosomal region 12p12.3. PTPRO has been highly characterized as inhibiting anchorage-independent tumor growth in human lung carcinomas. This gene has been found to be silenced by promoter methylation, and can be re-expressed by hypomethylating agents in human lung tumor models. Thus, we examined the methylation profile of the promoter region of PTPRO in primary leukemic cells from patients with CLL, and in B cells obtained from normal volunteers. Analysis of the PTPRO CpG island by methylation-specific PCR and combined bisulfite restriction analysis (COBRA) demonstrated that this region was methylated in 91% of samples from 46 patients, whereas it was unmethylated in control B cells from normal volunteers. Specific quantitative determinations of important proteins related to apoptosis in the leukemic cells from 20 of these patients showed that, in the group with methylation of the PTPRO promoter, there was a significant elevation of Bcl-2 (p=0.079), Mcl-1 (p=0.004), XIAP (p=0.048), Bcl-2/BAX ratio (p=0.0024), and Mcl-1/BAX ratio (p=0.0017). There was no apparent relationship with FISH category or immunoglobulin VH mutational status. Thus, PTPRO promoter methylation analysis may identify a subset of CLL patients less likely to respond to therapy, and provide a potential reversible target for new therapeutic approaches to this disease. Finally, analysis of methylation of CLL samples by restriction landmark genome scanning also revealed methylation of genes for three additional protein tyrosine phosphatases: PTPRN2, PTPRZ2, and PTPN11. Increases in methylation of two of these (PTPRN2 and PTPRZ2) in CLL samples relative to control B cells was confirmed by COBRA. These results provide additional potential molecular targets for CLL therapy.
RF-MEMS technology platform for agile mobile and satellite communications (2006)

In the past years, the RF-MEMS activities have focused on the development of generic technology platforms integrating switches as well as tunable and fixed passives components. This is in strict opposition to a former device-centered development of the RF-MEMS technologies. Fruitful efforts were put at IMEC in the reliability analysis and modeling of the devices, the exploration of various packaging scenario and finally the process optimization to allow the handling of the devices throughout the full packaging chain. In this paper, we present several results of these developments. Various architectures of functional narrowband and wideband RF-MEMS capacitive switches are demonstrated all processed on a single wafer, in the same process flow. The demonstrated working frequencies are 40GHz, 35GHz, 18GHz and 6GHz with measured lifetimes in excess of 10 cycles at 100Hz switching frequency in N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> atmosphere. Representative insertion loss and isolation are respectively better than 0.4dB and 20dB. Finally, we report the realization of a hybrid MEMS/MCM-D filter for GPS-GALILEO band-switching
Understanding Synthetic Gradients and Decoupled Neural Interfaces (2017)

When training neural networks, the use of Synthetic Gradients (SG) allows layers or modules to be trained without update locking - without waiting for a true error gradient to be backpropagated - resulting in Decoupled Neural Interfaces (DNIs). This unlocked ability of being able to update parts of a neural network asynchronously and with only local information was demonstrated to work empirically in Jaderberg et al (2016). However, there has been very little demonstration of what changes DNIs and SGs impose from a functional, representational, and learning dynamics point of view. In this paper, we study DNIs through the use of synthetic gradients on feed-forward networks to better understand their behaviour and elucidate their effect on optimisation. We show that the incorporation of SGs does not affect the representational strength of the learning system for a neural network, and prove the convergence of the learning system for linear and deep linear models. On practical problems we investigate the mechanism by which synthetic gradient estimators approximate the true loss, and, surprisingly, how that leads to drastically different layer-wise representations. Finally, we also expose the relationship of using synthetic gradients to other error approximation techniques and find a unifying language for discussion and comparison.
On the treeness of internet latency and bandwidth (2009)

Existing empirical studies of Internet structure and path properties indicate that the Internet is tree-like. This work quantifies the degree to which at least two important Internet measures--latency and bandwidth--approximate tree metrics. We evaluate our ability to model end-to-end measures using tree embeddings by actually building tree representations. In addition to being simple and intuitive models, these trees provide a range of commonly-required functionality beyond serving as an analytical tool.
Faculty Opinions recommendation of Murine cytomegalovirus m157 mutation and variation leads to immune evasion of natural killer cells. (2003)

Effective natural killer (NK) cell recognition of murine cytomegalovirus (MCMV)-infected cells depends on binding of the Ly49H NK cell activation receptor to the m157 viral glycoprotein. Here we addressed the immunological consequences of variation in m157 sequence and function. We found that most strains of MCMV possess forms of m157 that evade Ly49H-dependent NK cell activation. Importantly, repeated passage of MCMV through resistant Ly49H+ mice resulted in the rapid emergence of m157 mutants that elude Ly49H-dependent NK cell responses. These data provide the first molecular evidence that NK cells can exert sufficient immunological pressure on a DNA virus, such that it undergoes rapid and specific mutation in an NK cell ligand enabling it to evade efficient NK cell surveillance. PMID: 14597723
Time-dependent polarization behavior as a function of soil type. Final report (1997)

Cathodic protection requirements for buried structures have traditionally been predicted by use of anode resistance equations which take into account the influence of anode geometry on the current distribution at the anode and the influence of soil resistivity on the driving force required to pass current to the structure to be protected. The conventional anode resistance formulas used for CP design were developed for bare pipes protected by remote anodes. Under these conditions, the current density at the anode is so much larger than that on the pipe that the current and potential distribution around the pipe can be ignored in resistance calculations. The current and potential distribution on the pipeline must, however, be considered for coated pipes with coating holidays or when anodes are placed in close proximity to the pipe. 45 refs., 237 figs., 13 tabs.
Coding Hand Movement Behavior and Gesture with NEUROGES Supported by Automatic Video Analysis (2014)

In many different research disciplines in humanities, very large multimodal corpora are being processed and analysed in order to solve quite a large variety of different research questions. Not only in the gesture community, but also in psycholinguistics and psychology, the way how human act with their hands and body is of relevance. To solve the different research questions, a detailed annotation of multimodal data (video and speech) is performed. This annotation is basically performed manually by human raters and it is usually a very time consuming process. In empirical analysis of hand movement behaviour and gesture, the coding system NEUROGES and the annotation tool ELAN are very useful tools in this research domain [1][2]. Although, the manual annotation process is supported very well, it is still a very time consuming process to get at least the basic assignment such as start and end of hand movements to perform the seemingly most simple step, i.e., to segment the ongoing flow of behaviour into natural units. We present an automatic video analysis tool that supports the researchers in this exhaustive exercise inspecting and analysing videos that substantially facilitates the segmentation and annotation processes. Many significant events in human body motion can be detected quite robust by modern video analysis tools and therefore speed up the annotation process by a serious amount. The NEUROGES coding system provides a seven steps algorithm to analyse hand movement behaviour including gestures. It consists of three modules progressing from segmenting and annotating behaviour according to Activation, Structure, and Focus (Module I) to analyzing the relation of the right and left hands concerning Contact and Formal Relation (Module II) to finally assessing the Function and Type of the movements (Module III). The developed video analysis tool is able to support the annotation in a fully automatic way and therefore can speed up the overall annotation process significantly.
Analysis of Myocilin Mutations in 1703 Glaucoma Patients From Five Different Populations (1999)

A glaucoma locus, GLC1A, was identified previously on chromosome 1q. A gene within this locus (encoding the protein myocilin) subsequently was shown to harbor mutations in 2-4% of primary open angle glaucoma patients. A total of 1703 patients was screened from five different populations representing three racial groups. There were 1284 patients from primarily Caucasian populations in Iowa (727), Australia (390) and Canada (167). A group of 312 African American patients was from New York City and 107 Asian patients from Japan. Overall, 61 different myocilin sequence variations were identified. Of the 61 variations, 21 were judged to be probable disease-causing mutations. The number of probands found to harbor such mutations in each population was: Iowa 31/727 (4.3%), African Americans from New York City 8/312 (2.6%), Japan 3/107 (2.8%), Canada 5/167 (3.0%), Australia 11/390 (2.8%) and overall 58/1703 (3. 4%). Overall, 16 (76%) of 21 mutations were found in only one population. The most common mutation observed, Gln368Stop, was found in 27/1703 (1.6%) glaucoma probands and was found at least once in all groups except the Japanese. Studies of genetic markers flanking the myocilin gene suggest that most cases of the Gln368Stop mutations are descended from a common founder. Although the specific mutations found in each of the five populations were different, the overall frequency of myocilin mutations was similar ( approximately 2-4%) in all populations, suggesting that the increased rate of glaucoma in African Americans is not due to a higher prevalence of myocilin mutations.