gebhart/patrepeval huggingface dataset:
Detection of low-frequency FGFR3 mutations in the urine of patients with bladder cancer using next-generation deep sequencing. (2012)

59 Background: FGFR3 mutations have been identified in ~60-70% of low-stage, non-invasive tumors. Our group and others have developed assays to detect FGFR3 mutations in the urine of bladder cancer patients. However, urine-based assays have been limited by the technical ability to detect rare events in a dilute medium where there is a high background of normal DNA. In these assays, FGFR3 mutations are generally found in ~30% of the urine samples, which is &lt; 50% concordance with the expected detection in tissue. We have now developed an ultra-deep amplicon sequencing technique that increases FGFR3 mutation detection in urine to ~67%, close to the expected detection frequency if every mutation found in tissue could be detected in urine. Methods: Amplicons were designed against FGFR3 exons 7, 10, and 15 using PCR primers containing the adapter sequences for unidirectional sequencing. Primary amplification was performed from DNA isolated from 4 ml of urine. The resulting PCR products were used as template for emulsion PCR and these were then sequenced using the Roche 454 GS Junior. Samples were analyzed for total DNA reads per sample and number of mutant sequencing reads to determine percent mutation. Results: Urine samples from 43 patients with bladder cancer were analyzed by both our previously described qPCR method and the new ultra-deep sequencing approach. Using ultra-deep amplicon sequencing, 24 out of 43 (55.8%) were positive for FGFR3 mutations, while only 5 out of 43 (11.6%) were positive for mutations by qPCR. The urine samples from the 15 newly identified mutations using deep sequencing contained FGFR3 mutations as low as 0.05% mutant DNA. The sensitivity achieved using deep sequencing was 91% concordant with the FGFR3 mutations observed in tissue. Conclusions: We have developed a highly sensitive non-invasive urine based assay that can detect FGFR3 mutant DNA when present at &lt; 1% of the sample and is &gt; 90% concordance with the mutations found in tumor tissues. To our knowledge, this is the first practical application of next generation sequencing technology for diagnostic use.
Reduction Behavior and Structural Evolution of Iron Ores in Fluidized Bed Technologies. Part 1: Method for the Determination (2015)

Due to environmental and economic constraints, alternative iron‐making processes to the traditional blast furnace technology have been developed in recent decades. These are direct reduction and smelting reduction technologies, some using iron ore fines directly without prior agglomeration processes. This work deals with the development of a new method for the investigation of reduction behavior and structural evolution of iron ore fines under fluidized bed conditions – in order to optimize fluidized bed‐based technologies for iron‐ and steelmaking. Regarding iron ore fines reduction under fluidized bed conditions, several investigations have been performed in recent years. With previous methods, the reduction behavior during the process is evaluated by the extraction of samples and their chemical analysis. The advantage of the new method is the continuous measurement of the main relevant process parameters, especially the weight loss of the fluidized sample caused by reduction. Based on the gathered data, the process behavior and the reduction progress can be determined and compared with chemical analyses, morphology, and mass balances. A benefit of the applied method is that test conditions are closer to real industrial processes in comparison to prior research work.
Turbo code design for block fading channels (2004)

Shannon capacity approaching codes have been extensively studied during the last decade for ergodic channels. We propose and analyze new channel multiplexing/interleaving techniques for parallel turbo codes over non-ergodic block fading channels. We reveal word error probability performance at less than 1dB from outage capacity. The achieved word error probability is almost insensitive to the code length. The race to the outage capacity limit on block fading channels is declared open.
Abstract IA03: The evolutionary landscape of CLL: Therapeutic implications (2016)

Abstract Clonal evolution is a key feature of cancer progression and relapse. Recent studies across cancers have demonstrated the extensive degree of intratumoral heterogeneity present within individual cancers. We hypothesized that evolutionary dynamics contribute to the variations in disease tempo and response to therapy that are highly characteristic of chronic lymphocytic leukemia (CLL). We have recently investigated this phenomenon by developing a pipeline that estimates the fraction of cancer cells harboring each somatic mutation within a tumor through integration of whole-exome sequence (WES) and local copy number data (Landau et al., Cell 2013). By applying this analysis approach to 149 CLL cases, we discovered earlier and later cancer drivers, uncovered patterns of clonal evolution in CLL and linked the presence of subclones harboring driver mutations with adverse clinical outcome. Thus, our study, generated from a heterogeneous sample cohort, strongly supports the concept that CLL clonal evolution arises from mass extinction and therapeutic bottlenecks which lead to the emergence of highly fit (and treatment resistant) subclones. We further hypothesized that epigenetic heterogeneity also shapes CLL clonal evolution through interrelation with genetic heterogeneity. Indeed, in recent work, we have uncovered stochastic methylation disorder as the primary cause of methylation changes in CLL and cancer in general, and that this phenomena impacts gene transcription, genetic evolution and clinical outcome. Thus, integrated studies of genetic and epigenetic heterogeneity in CLL have revealed the complex and diverse evolutionary trajectories of these cancer cells. Immunotherapy is exquisitely suited for specifically and simultaneously targeting multiple lesions. We have developed an approach that leverages whole-exome sequencing to systematically identify personal tumor mutations with immunogenic potential, which can be incorporated as antigen targets in multi-epitope personalized therapeutic vaccines. We are pioneering this approach in an ongoing trial in melanoma and will now expand this concept to address diverse malignancies. Our expectation is that the choice of tumor neoantigens for a vaccine bypasses thymic tolerance and thus generates highly specific and potent high-affinity T cell responses to eliminate tumors in any cancer, including both trunk and branch lesions. Citation Format: Catherine J. Wu. The evolutionary landscape of CLL: Therapeutic implications. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Integrating Clinical Genomics and Cancer Therapy; Jun 13-16, 2015; Salt Lake City, UT. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(1_Suppl):Abstract nr IA03.
Bit Allocation Based on Motion Vector Analysis for H.264/AVC (2007)

In this paper we present a bit allocation approach based on motion vector analysis for improved rate-distortion performance. Bit allocation is done at the macroblock level such that the macroblock with high priority is coded finely and the one with low priority is coded coarsely. In order to calculate macroblock priorities, first reference counts for each pixel are determined through motion vector analysis. A reference count of a pixel is defined as total number of pixels in the remaining GOP which use that pixel as a reference. Then macroblock wise reference counts is obtained by summing the pixel wise reference counts, which are then scaled and prioritized. Based upon the priority value the given fixed quant of each frame is modulated at the macroblock level. The algorithm is applied to H.264/AVC encoding and PSNR gains of up to 1.4 dB are achieved
In Vitro and In Vivo Inhibition of Hydroxyapatite Formation and Dissolution by Bisacylphosphonates and Bishydroxyiminophosphonates (1993)

Abstract Certain irregularities in calcium metabolism such as Paget's disease, osteoporosis, as well as osteolysis in bone cancer, are characterized by excessive destruction of the bone by resorption. In contrast, a number of clinically important diseases, for example, atherosclerosis, kidney and renal calculu8, arthritis, and bioprosthetic heart valve calcification are characterized by the deposition of calcium phosphate. nis~hosphonates are a relct3vely new class of drugs, that have been used in these diseases to inhibit both mineralization and bone resorption, following the recognition, that they are stable analogs of endogenous pyrophosphate, which is a physiological inhibitor of calcification and bone resorption. A number of geminal bisphosphonates, namely, Pamidronate (ABP), Etidronate (HEBP), and Clodronate (ClMBP), have been approved for clinical use.
Estimating path delay distribution considering coupling noise (2007)

Accurately estimating critical path delays is extremely important for yield optimization and for path selection in delay testing. It is well known that dynamic effects such ascoupling noise can significantly affect critical path delays. In traditional static timing analysis, the coupling effect isincorporated by estimating the switching window overlaps between aggressor and victim and then assuming a constant (worst case) coupling factor if any overlap is present. However in path based statistical timing analysis, using a constant coupling factor can overestimate the mean delay while under estimating the delay variance. In this paper, we propose a technique to estimate the dynamic variation in pathdelay caused by coupling noise. We treat the effective coupling capacitance as a random variable that varies as a function of the relative signal arrival times between victim andaggressor nodes. A modeling technique to estimate the capacitance variation is shown and a framework that gives therelative signal arrival time distribution at the victim nodesis developed.
Color tunable light‐emitting diodes with modified pulse‐width modulation (2009)

Abstract In this study, a color tunable light source, operated by a modified pulse width modulation method, is investigated. By utilizing this method along with anti‐parallel connected discrete light‐emitting diodes (LEDs) and two electrical terminals, a wide range of the chromaticity coordinates is attained and varied by electrical control. Using the combination of a blue LED and a phosphor‐converted yellow LED (blue LED plus yellow phosphor), the chromaticity range is varied by electrical control from pure blue to pure yellow. In addition, using the modified pulse‐width modulation method and a combination of white and red LEDs, white light with correlated color temperatures ranging from 5000 K to 2000 K is demonstrated. (© 2009 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Practical Approximations and Tips (2013)

This chapter talks about practical approximations and tips for the conversion between bit error rate (BER) and equivalent Q-factor. The Q-factor is a more convenient parameter than the BER, as the latter varies by orders of magnitude. For testing purposes, a pseudorandom bit sequence (PRBS) instead of “real” data is often transmitted over a link. The chapter explains chromatic dispersion values and propagation constants that developed in a Taylor series.
Cooperative GNSS Positioning & Navigation (2011)

GNSS and WiFi enabled mobile devices are becoming more and more common place with the proliferation of smartphones and the penetration of GNSS and WiFi into other common electronics such as cameras, gaming devices, etc. This is creating a new paradigm around how such devices can cooperate with each other to improve their ability to compute position and navigate. In this work, we focus on cooperation at the position-engine level and on the case when the devices’ measurements are not synchronized in time. Both simulations and experiments from live data demonstrate two general conclusions from this work: 1) a device with strong measurement data can help a device with “weak” measurement data to compute its position; 2) two devices with “weak” measurement data can cooperate to improve their positioning accuracy and reliability. The implications of these conclusions are that devices can cooperate to compute their GNSS locations in some harsh environments where non-cooperative GNSS receivers fail.
Antibody-based immunotherapy: targeting CSPG4 on human basal breast cancer stem cells. (2009)

Abstract Abstract #5046 Introduction: Basal-like breast cancer is associated with high grade, poor prognosis, and younger patient age. Because tumors are estrogen receptor (ER) and HER2 negative, effective targeted treatment for basal breast cancer remains elusive. The lack of efficacy of currently used chemotherapies may reflect their inability to eradicate cancer stem cells (CSC) within a basal breast tumor.&amp;#x2028; Chondroitin sulfate proteoglycan 4 (CSPG4), a molecule initially identified in melanoma cells, is a cell surface antigen involved in migration and invasion of tumor cells. The rat homolog of the human CSPG4, named NG2, is expressed by progenitor cells in several types of tissues. Furthermore, NG2 expression is typically maximal when progenitor cells are mitotic and motile. As one important characteristic of cancer stem cells is their ability to migrate and metastasize, and both CSPG4 and NG2 play a role in tumor cell migration, we tested whether CSPG4 is expressed on cells with the CSC phenotype in ER negative/HER2 negative (basal-like) breast cancer, and can thus serve as a target for immunotherapy of breast CSC.&amp;#x2028; Methods and Results: The mRNA levels of CSPG4 in ER- and Her2- breast cancer were compared to ER-/Her2+, ER+/Her2-, and ER+/Her2+ breast cancer using a publicly available, clinically annotated breast cancer data set. The gene expression level of CSPG4 was elevated in the ER- and Her2- subgroup when compared to ER-/Her2+ (Mann Whitney, p=0.03), ER+/Her2- (Mann Whitney, p=0.01), and ER+/Her2+ (Mann Whitney, p=0.06). These results suggest that CSPG4 expression is best correlated with the basal phenotype of breast cancer. Flow cytometric analysis showed that CSPG4 is expressed on CD44+, CD24-/lo cells in the human basal breast cancer cell lines, i.e., MDA-MD-231, MDA-MB-435, HS578T and SUM149, but is not detectable on the luminal breast cancer cell lines, i.e., MCF-7, SK-BR-3 and T-47D. Furthermore CSPG4 is expressed on the cell surface of putative breast CSC identified as lineage-negative (CD2,3,10,16,18,31,45,64,140b), CD44+, CD24-/lo cells in pleural effusions of 12 patients with breast cancer. Further, inoculation of flow cytometric sorted CD44+CD24-/low CSPG4+ cells from the MDA-MB-231-luciferease expressing cell line, to the mammary fat pads of immunodeficient mice, led to the development of tumors detected by whole-body bioluminescent reporter imaging 3 weeks after the injection. In contrast, inoculation of CD44+CD24-/low CSPG4- cells, sorted from the same cell line, did not generate tumors. More importantly, CSPG4-specific mAb significantly inhibited post-surgery tumor recurrence and lung metastases in SCID mice transplanted with the human basal breast cancer cell line MDA-MB-435, which has the putative breast CSC phenotype (CD44+, CD24-/lo) in more than 99% of cells.&amp;#x2028; Conclusion: These results suggest that the CSPG4 is a potential new immunotherapeutic target for basal-like breast cancer and breast CSC. Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 5046.
P‐170: Molecular Design of Sensitizer for High Efficiency in Hyper‐fluorescent Organic Light‐Emitting Diodes (2018)

We synthesized two thermally activated delayed fluorescent (TADF) emitters sensitizers, 9,9′,9″‐(5‐(4,6‐diphenyl‐1,3,5‐triazin‐2‐yl)benzene‐1,2,3‐triyl)tris(3,6‐dimethyl‐9H‐carbazole) (TmCzTrz) and 9,9′,9″‐(5‐(4,6‐diphenyl‐1,3,5‐triazin‐2‐yl)benzene‐1,2,3‐triyl)tris(3,6‐di‐tert‐butyl‐9H‐carbazole) (TbCzTrz) to investigate as the sensitizers in hyper‐fluorescent organic light emitting diodes (OLEDs). The difference in two TADF sensitizers was the side group that was consisted of methyl and t‐butyl group. Although the efficiency of TbCzTrz based TADF device was lower than that of the TmCzTrz device, the efficiency of the hyper‐fluorescent device using the as sensitizers was almost the same.
Structure of the Interface in Sic-Based Ceramic Composites Formed by Tribo-Oxidation Under Dry Sliding Conditions (2012)

This chapter contains sections titled: Introduction Experimental Results and Discussion Summary and Conclusions Acknowledgement
The immunoregulatory and allergy‐associated cytokines in the aetiology of the otitis media with effusion (2004)

Inflammation in the middle ear mucosa, which can be provoked by different primary factors such as bacterial and viral infection, local allergic reactions and reflux, is the crucial event in the pathogenesis of otitis media with effusion (OME). Unresolved acute inflammatory responses or defective immunoregulation of middle inflammation can promote chronic inflammatory processes and stimulate the chronic condition of OME. Cytokines are the central molecular regulators of middle ear inflammation and can switch the acute phase of inflammation in the chronic stage and induce molecular-pathological processes leading to the histopathological changes accompanying OME. In this review we present cytokines identified in otitis media, immunoregulatory [interleukin (IL)-2, IL-10, transforming growth factor-beta]) and allergy associated (IL-4, IL-5, granulocyte-macrophage colony-stimulating factor), as crucial molecular regulators, responsible for chronic inflammation in the middle ear and the chronic condition of OME.
Bisphosphonates: Molecular Modelling, Structure-Activity Relationships and the Rational Design of New Analogs (1993)

Abstract A combination of 2D NMR spectroscopy, x-ray crystallography and molecular mechanics have been used in the structure determination of a conformationally rigid antiresorptive active bisphosphonate. This rigid structure has provided a template from which other conformationally restricted actives have been successfully designed.
Interleukin-32, α1 Anti-Trypsin (AAT-1) and Graft-Versus-Host-Disease (2010)

Abstract Abstract 522 Graft-versus-host disease (GVHD) is an important complication of allogeneic hematopoietic cell transplantation (HCT). The role of various cell populations, cytokines and chemokines, present pre and post-transplantation, in the development of GVHD has been studied extensively.We investigated the potential role of Interleukin (IL)-32 in alloreactivity and GVHD. IL-32 is the protein product of the NK4 transcript first reported in IL-2 activated T lymphocytes and natural killer cells. IL-32 has pro-inflammatory and pro-apoptotic properties and induces expression of TNF-α in several cell targets. We used one-way mixed lymphocyte cultures (MLC) as a simple in vitro model of GVHD to determine IL-32 expression upon alloactivation. The α and γ isforms of (IL)-32 protein were 2-fold upregulated in allogeneic MLC compared to autologous controls (n=4, p=0.037). Concurrently, the concentrations of TNF-α, IL-6 and IL-8 in the allogeneic MLC supernatants were, as expected, upregulated significantly. This finding led us to evaluate IL-32 expression as a potential marker for GVHD after allogeneic HCT in 45 patients with either active acute GVHD or chronic GVHD, and 16 patients who did not show clinical evidence of GVHD. IL-32 mRNA levels in peripheral blood unsorted white blood cells, correlated with acute GVHD (RT-PCR values expressed as mean +/− SEM of the ratio of expression of IL-32/GUS-B = 1.01, p=0.011, vs control values IL-32/GUS-B = 0.23) but not with chronic GVHD, (IL-32/GUS-B = 0.26, p=0.16) (Figure 1). As the serine protease neutrophil proteinase 3 (PR3) has been shown to serve as activator of IL-32, and to process several inflammatory cytokines, including IL-32, TNF-α and IL-8, we postulated that the addition of the serine protease inhibitor α-1 anti-trypsin (AAT), would interfere with the processing of IL-32 by PR3, and as a result would lead to decreased proliferation of cells in MLC, and reduced cytokine production. To test this hypothesis, MLCs were treated with AAT at concentrations of 1–20 ug/ml and expression of IL-32 and PR3 were determined. In MLCs treated with AAT at the optimal concentration of 5 ug/ml, added to cultures on alternate days for a period of 7 days T lymphocyte proliferation was suppressed when compared to vehicle-treated MLC, (mean CPM=33.000 versus CPM=67.000; p=0.012). Concurrently there was a 2.5 fold decrease in IL-32 and PR3 protein levels (n=4, p=0.023). CONCLUSION: IL-32 is upregulated in patients with acute GVHD. Determination of IL-32 in patients with suspected GVHD may support the diagnosis and the decision to treat.AAT interferred with T cell activation and the release of cytokines, including IL-32, suggesting that administration of AAT may have therapeutic potential in patients with acute GVHD. Disclosures: No relevant conflicts of interest to declare.
Nanoshell, nanosphere and nanowire geometries for hot spot formation in surface enhanced Raman scattering (2005)

Silver nanoshells, nanospheres and metal coated dielectric nanowires have been directly compared for their surface enhanced Raman (SERS) activity. SERS was measured from trace deposits of Rhodamine 6G (Rh6G). It was found that the SERS enhancement is largest for samples that are 3D in nature compared to 2D arrays. Furthermore Ag coated dielectric nanowires had the strongest SERS. These results demonstrate the importance of electric field hot spots and molecular orientation in the SERS process.
ChemInform Abstract: A Convenient and Versatile Route for the Stereoselective Synthesis of Monosaccharides via Key Chiral Synthons Prepared from Achiral Sources. (1992)

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.
Robust Parametrization of a Model Predictive Controller for a CNC\n Machining Center Using Bayesian Optimization (2020)

Control algorithms such as model predictive control (MPC) and state\nestimators rely on a number of different parameters. The performance of the\nclosed loop usually depends on the correct setting of these parameters. Tuning\nis often done manually by experts based on a simulation model of the system.\nTwo problems arise with this procedure. Firstly, experts need to be skilled and\nstill may not be able to find the optimal parametrization. Secondly, the\nperformance of the simulation model might not be able to be carried over to the\nreal world application due to model inaccuracies within the simulation. With\nthis contribution, we demonstrate on an industrial milling process how Bayesian\noptimization can automate the tuning process and help to solve the mentioned\nproblems. Robust parametrization is ensured by perturbing the simulation with\narbitrarily distributed model plant mismatches. The objective is to minimize\nthe expected integral reference tracking error, guaranteeing acceptable worst\ncase behavior while maintaining real-time capability. These verbal requirements\nare translated into a constrained stochastic mixed-integer black-box\noptimization problem. A two stage min-max-type Bayesian optimization procedure\nis developed and compared to benchmark algorithms in a simulation study of a\nCNC machining center. It is showcased how the empirical performance model\nobtained through Bayesian optimization can be used to analyze and visualize the\nresults. Results indicate superior performance over the case where only the\nnominal model is used for controller synthesis. The optimized parametrization\nimproves the initial hand-tuned parametrization notably.\n