gebhart/patrepeval huggingface dataset:
Loss of heterozygosity and tumor suppressor gene mutations in chondrosarcomas. (1996)

Loss of heterozygosity (LOH) of chromosomes 13q and 17p and mutations of the retinoblastoma (Rb) and p53 gene were studied in 28 tumors from 22 patients with chondrosarcomas. Allele loss at polymorphic loci on 13q was found in 36% of tumors and the frequency was much higher in grade II (56%) or high grade (40%) tumors than in grade I tumors (18%). LOH of 17p, which was detected in 25% of all tumors, was of low frequency in low grade tumors (8% in grade I and 20% in grade II), whereas 80% of tumors with high grade tumors were positive for LOH. These observations may imply that LOH on 13q and 17p contributes to the tumor development at different stages. In low grade cases (grade I and II), tumor recurrence was observed more frequently in primary tumors with LOH on 13q (86%) than those without (8%), suggesting the significance of LOH analysis in the assessment of biological behavior of tumors. Structural alteration of the Rb gene was found in one dedifferentiated tumor, and point mutations of the p53 gene were found in all of five high grade tumors, indicating that high grade chondrosarcomas were genetically equivalent to other high grade sarcomas such as osteosarcomas.
Oxonia‐Cope Prins Cyclizations: A Facile Method for the Synthesis of Tetrahydropyranones Bearing Quaternary Centers. (2005)

A new cationic cascade reaction has been developed that produces 4-tetrahydropyranones in good yield. The reaction is based on the facile 2-oxonia Cope rearrangement of allyl-substituted oxocarbenium ions. In the presence of a more nucleophilic silyl enol ether, such systems rearrange and cyclize to produce tetrahydropyranones. The substrates were prepared by silyl ketene acetal addition to ketenes. The rearrangement is compatible with tetrasubstituted silyl enol ethers, which result in the diastereoselective introduction of quaternary centers at the C3 position of the tetrahydropyran ring. The oxonia-Cope Prins rearrangement is a versatile new route to tetrahydropyrans.
Figure S6 from Screening of Conditionally Reprogrammed Patient-Derived Carcinoma Cells Identifies ERCC3–MYC Interactions as a Target in Pancreatic Cancer (2023)

&lt;p&gt;Supplemental data for Figure 4.&lt;/p&gt;
A Dynamic Grouping Strategy for Beyond Diagonal Reconfigurable Intelligent Surfaces with Hybrid Transmitting and Reflecting Mode (2022)

Beyond diagonal reconfigurable intelligent surface (BD-RIS) is a novel branch of RIS which breaks through the limitation of traditional RIS with diagonal scattering matrices. However, the existing research focuses on BD-RIS with fixed architectures regardless of channel state information (CSI), which limit the achievable performance of BD-RIS. To solve this issue, in this paper, we propose a novel dynamically group-connected BD-RIS based on a dynamic grouping strategy. Specifically, RIS antennas are dynamically divided into several subsets adapting to the CSI, yielding a permuted block-diagonal scattering matrix. To verify the effectiveness of the proposed dynamically group-connected BD-RIS, we propose an efficient algorithm to optimize the BD-RIS with dynamic grouping for a BD-RIS-assisted multi-user multiple-input single-output system. Simulation results show that the proposed dynamically group-connected architecture outperforms fixed group-connected architectures.
Quantum serial turbo-codes (2007)

We present a theory of quantum serial turbo-codes, describe their iterative decoding algorithm, and study their performances numerically on a depolarization channel. Our construction offers several advantages over quantum LDPC codes. First, the Tanner graph used for decoding is free of 4-cycles that deteriorate the performances of iterative decoding. Secondly, the iterative decoder makes explicit use of the code's degeneracy. Finally, there is complete freedom in the code design in terms of length, rate, memory size, and interleaver choice. We define a quantum analogue of a state diagram that provides an efficient way to verify the properties of a quantum convolutional code, and in particular its recursiveness and the presence of catastrophic error propagation. We prove that all recursive quantum convolutional encoder have catastrophic error propagation. In our constructions, the convolutional codes have thus been chosen to be non-catastrophic and non-recursive. While the resulting families of turbo-codes have bounded minimum distance, from a pragmatic point of view the effective minimum distances of the codes that we have simulated are large enough not to degrade the iterative decoding performance up to reasonable word error rates and block sizes. With well chosen constituent convolutional codes, we observe an important reduction of the word error rate as the code length increases.
Astrophysically triggered searches for gravitational waves: status and prospects (2008)

In gravitational-wave detection, special emphasis is put onto searches that focus on cosmic events detected by other types of astrophysical observatories. The astrophysical triggers, e.g. from γ-ray and x-ray satellites, optical telescopes and neutrino observatories, provide a trigger time for analyzing gravitational-wave data coincident with the event. In certain cases the expected frequency range, source energetics, directional and progenitor information are also available. Beyond allowing the recognition of gravitational waveforms with amplitudes closer to the noise floor of the detector, these triggered searches should also lead to rich science results even before the onset of Advanced LIGO. In this paper we provide a broad review of LIGO's astrophysically triggered searches and the sources they target. © 2008 IOP Publishing Ltd.
CrossMDA: Arcabouço para integração de interesses transversais no desenvolvimento orientado a modelos (2007)

CrossMDA é um arcabouço que incorpora um processo de transformação para integração de interesses transversais em sistemas orientados a modelo. Essa integração é feita combinando as capacidades de separação de interesses existentes nas abordagens MDA e Programação Orientada a Aspectos (POA). CrossMDA usa o conceito de separação horizontal de interesses da POA pra criar modelos de negócio e aspectos independentes, integrando-os através de transformações MDA (separação vertical de interesses). CrossMDA provê um processo de desenvolvimento e um conjunto de serviços e ferramental de apoio para dar suporte ao processo.
Structural Flexibility and Functional Valence of CD4-IgG2 (PRO 542): Potential for Cross-Linking Human Immunodeficiency Virus Type 1 Envelope Spikes (2001)

CD4-immunoglobulin G2 (CD4-IgG2) incorporates four copies of the D1D2 domains of CD4 into an antibody-like molecule that potently neutralizes primary human immunodeficiency virus type 1. Here electron microscopy was used to explore the structure and functional valence of CD4-IgG2 in complex with gp120. CD4-gamma2, a divalent CD4-immunoglobulin fusion protein, was evaluated in parallel. Whereas CD4-gamma2-gp120 complexes adopted a simple Y-shaped structure, CD4-IgG2-gp120 complexes consisted of four gp120s arrayed about a central CD4-IgG2 molecule, a structure more reminiscent of complement C1q. Molecular modeling corroborated the electron microscopy data and further indicated that CD4-IgG2 but not CD4-gamma2 has significant potential to cross-link gp120-gp41 trimers on the virion surface, suggesting a mechanism for the heightened antiviral activity of CD4-IgG2.
Chemotherapy response and recurrence-free survival in neoadjuvant breast cancer depends on biomarker profiles: results from the I-SPY 1 TRIAL (CALGB 150007/150012; ACRIN 6657) (2020)

Neoadjuvant chemotherapy for breast cancer allows individual tumor response to be assessed depending on molecular subtype, and to judge the impact of response to therapy on recurrence-free survival (RFS). The multicenter I-SPY 1 TRIAL evaluated patients with ≥3cm tumors by using early imaging and molecular signatures, with outcomes of pathologic complete response (pCR) and RFS. The current analysis was performed using data from patients who had molecular profiles and did not receive trastuzumab. The various molecular classifiers tested were highly correlated. Categorization of breast cancer by molecular signatures enhanced the ability of pCR to predict improvement in RFS compared to the population as a whole. In multivariate analysis, the molecular signatures that added to the ability of HR and HER2 receptors, clinical stage, and pCR in predicting RFS included 70-gene signature, wound healing signature, p53 mutation signature, and PAM50 risk of recurrence. The low risk signatures were associated with significantly better prognosis, and also identified additional patients with a good prognosis within the no pCR group, primarily in the hormone receptor positive, HER-2 negative subgroup. The I-SPY 1 population is enriched for tumors with a poor prognosis but is still heterogeneous in terms of rates of pCR and RFS. The ability of pCR to predict RFS is better by subset than it is for the whole group. Molecular markers improve prediction of RFS by identifying additional patients with excellent prognosis within the no pCR group.Electronic supplementary materialThe online version of this article (doi:10.1007/s10549-011-1895-2) contains supplementary material, which is available to authorized users.
FLT3-ITD transduces autonomous growth signals during its biosynthetic trafficking in acute myelogenous leukemia cells (2021)

Abstract FMS-like tyrosine kinase 3 (FLT3) in hematopoietic cells binds to its ligand at the plasma membrane (PM), then transduces growth signals. FLT3 gene alterations that lead the kinase to assume its permanently active form, such as internal tandem duplication (ITD) and D835Y substitution, are found in 30~40% of acute myelogenous leukemia (AML) patients. Thus, the drugs for molecular targeting of FLT3 mutants have been developed for the treatment of AML. Several groups have reported that compared with wild-type FLT3 (FLT3-wt), FLT3 mutants are retained in organelles, resulting in low levels of PM localization of the receptor. However, the precise subcellular localization of mutant FLT3 remains unclear, and the relationship between oncogenic signaling and the mislocalization is not completely understood. In this study, we show that in cell lines established from AML patients, endogenous FLT3-ITD but not FLT3-wt clearly accumulates in the perinuclear region. Our co-immunofluorescence assays demonstrate that Golgi markers are co-localized with the perinuclear region, indicating that FLT3-ITD mainly localizes to the Golgi region in AML cells. FLT3-ITD biosynthetically traffics to the Golgi apparatus and remains there in a manner dependent on its tyrosine kinase activity. A tyrosine kinase inhibitor midostaurin (PKC412) markedly decreases in FLT3-ITD retention and increases in the PM levels of the mutant. FLT3-ITD activates downstream in the endoplasmic reticulum (ER) and the Golgi apparatus during its biosynthetic trafficking. Results of our trafficking inhibitor treatment assays show that FLT3-ITD in the ER activates STAT5, whereas that in the Golgi can cause the activation of AKT and ERK. We provide evidence that FLT3-ITD signals from the early secretory compartments before reaching the PM in AML cells.
High-Rate Analysis of Source Coding for Symmetric Error Channels (2006)

In this paper, new results are derived for the high-rate performance of source coding for symmetric error channels (i.e., a channel where all index errors are equally likely) for a large class of distortion measures. Expressions are derived for the expected distortion including the effect of channel errors as the number of quantization levels N gets large. It is shown that the distortion can asymptotically be approximated as the sum of the source quantization distortion and the channel error induced distortion. In addition, the expressions obtained can be used to glean key insights on the relative amounts of source and channel coding necessary to attain a balanced system, i.e., one where neither the distortion caused by the source quantization nor the distortion caused by channel errors dominate the performance. Optimization of the codebook for minimizing the expected distortion is also considered, and theoretical expressions are derived for the optimal point density.
The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2 (2022)

Understanding the circumstances that lead to pandemics is important for their prevention. We analyzed the genomic diversity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) early in the coronavirus disease 2019 (COVID-19) pandemic. We show that SARS-CoV-2 genomic diversity before February 2020 likely comprised only two distinct viral lineages, denoted "A" and "B." Phylodynamic rooting methods, coupled with epidemic simulations, reveal that these lineages were the result of at least two separate cross-species transmission events into humans. The first zoonotic transmission likely involved lineage B viruses around 18 November 2019 (23 October to 8 December), and the separate introduction of lineage A likely occurred within weeks of this event. These findings indicate that it is unlikely that SARS-CoV-2 circulated widely in humans before November 2019 and define the narrow window between when SARS-CoV-2 first jumped into humans and when the first cases of COVID-19 were reported. As with other coronaviruses, SARS-CoV-2 emergence likely resulted from multiple zoonotic events.
C5a elevation in convalescents from severe COVID-19 is not associated with early complement activation markers C3bBbP or C4d (2022)

Numerous publications have underlined the link between complement C5a and the clinical course of COVID-19. We previously reported that levels of C5a remain high in the group of severely ill patients up to 90 days after hospital discharge. We have now evaluated which complement pathway fuels the elevated levels of C5a during hospitalization and follow-up. The alternative pathway (AP) activation marker C3bBbP and the soluble fraction of C4d, a footprint of the classical/lectin (CP/LP) pathway, were assessed by immunoenzymatic assay in a total of 188 serial samples from 49 patients infected with SARS-CoV-2. Unlike C5a, neither C3bBbP nor C4d readouts rose proportionally to the severity of the disease. Detailed correlation analyses in hospitalization and follow-up samples collected from patients of different disease severity showed significant positive correlations of AP and CP/LP markers with C5a in certain groups, except for the follow-up samples of the patients who suffered from highly severe COVID-19 and presented the highest C5a readouts. In conclusion, there is not a clear link between persistently high levels of C5a after hospital discharge and markers of upstream complement activation, suggesting the existence of a non-canonical source of C5a in patients with a severe course of COVID-19.
Antiandrogenic Activity of Resveratrol Analogs in Prostate Cancer LNCaP Cells (2012)

The suppression of androgen signaling is a therapeutic target for the treatment of prostate cancer. Resveratrol (3,4',5-trihydroxystilbene) is known to inhibit the function of the androgen receptor (AR). In the present study, we investigated the antiandrogenic activities of resveratrol analogs in order to identify a potent antiandrogen compound. Resveratrol analogs were isolated from plants or were semisynthesized from resveratrol. AR transcriptional activity was measured in prostate cancer LNCaP cells using a luciferase assay with the MMTV-luc reporter plasmid. Among the resveratrol analogs tested, 4'-O-methylresveratrol (3,5-dihydroxy-4'-methoxystilbene) was the most effective inhibitor of AR transcriptional activity. Introduction of a methoxy group to the C-4' of resveratrol and its analogs increased their antiandrogenic activity compared with the unmodified counterparts. Conversely, modification of the 3- and/or 5-hydroxyl groups reduced the antiandrogenic activity. 4'-O-methylresveratrol was more effective than resveratrol in inhibiting Akt phosphorylation, which is related to AR signaling, in LNCaP cells. The hydroxyl groups in resveratrol play a key role in their antiandrogenic effect by modulating AR transcriptional activity.
Semantic Segmentation in Art Paintings (2022)

Abstract Semantic segmentation is a difficult task even when trained in a supervised manner on photographs. In this paper, we tackle the problem of semantic segmentation of artistic paintings, an even more challenging task because of a much larger diversity in colors, textures, and shapes and because there are no ground truth annotations available for segmentation. We propose an unsupervised method for semantic segmentation of paintings using domain adaptation. Our approach creates a training set of pseudo‐paintings in specific artistic styles by using style‐transfer on the PASCAL VOC 2012 dataset, and then applies domain confusion between PASCAL VOC 2012 and real paintings. These two steps build on a new dataset we gathered called DRAM (Diverse Realism in Art Movements) composed of figurative art paintings from four movements, which are highly diverse in pattern, color, and geometry. To segment new paintings, we present a composite multi‐domain adaptation method that trains on each sub‐domain separately and composes their solutions during inference time. Our method provides better segmentation results not only on the specific artistic movements of DRAM, but also on other, unseen ones. We compare our approach to alternative methods and show applications of semantic segmentation in art paintings. The code and models for our approach are publicly available at: https://github.com/Nadavc220/SemanticSegmentationInArtPaintings .
A Pyridinium–Barbiturate–Betaine Dye with Pronounced Negative Solvatochromism: A New Approach for Molecular Recognition (2009)

World record: The betaine dye 1 exhibits the highest negative solvatochromic range yet seen. Because of its pronounced push–pull system, 1 is suitable for the detection of polarity changes, acid–base reactions, and the formation of complexes with complementary hydrogen-bond sequences, which can even be followed by the naked eye.
High Temperature Direct Double Side Cooled Inverter Module for Hybrid Electric Vehicle Application (2007)

In this paper a novel approach to the design and fabrication of a high temperature inverter module for hybrid electrical vehicles is presented. Firstly, SiC power electronic devices are considered in place of the conventional Si devices. Use of SiC raises the maximum practical operating junction temperature to well over 200°C, giving much greater thermal headroom between the chips and the coolant. In the first fabrication, a SiC Schottky barrier diode (SBD) replaces the Si pin diode and is paired with a Si-IGBT. Secondly, doublesided cooling is employed, in which the semiconductor chips are sandwiched between two substrate tiles. The tiles provide electrical connections to the top and the bottom of the chips, thus replacing the conventional wire bonded interconnect. Each tile assembly supports two IGBTs and two SBDs in a half-bridge configuration. Both sides of the assembly are cooled directly using a high-performance liquid impingement system. Specific features of the design ensure that thermo-mechanical stresses are controlled so as to achieve long thermal cycling life. A prototype 10 kW inverter module is described incorporating three half-bridge sandwich assemblies, gate drives, dc-link capacitance and two heat-exchangers. This achieves a volumetric power density of 30W/cm3.
Improvements to "A Software-Defined GPS and Galileo Receiver: Single-Frequency Approach" (2007)

This paper presents a brief overview of an open-source, MATLAB software Global Positioning System (GPS) receiver. All functions from signal acquisition to position solution are described. The focus is then turned to developments at the University of Colorado, Boulder related to the software receiver. A Universal Serial Bus (USB) intermediate frequency (IF) data sampler module is described that researchers can use to collect data to support their research. Student projects that were the outcome of a graduate level global navigation satellite system (GNSS) receiver architecture course are also described. These projects included signal acquisition and tracking in a field-programmable gate array (FPGA), multi-correlator signal tracking, L2C acquisition, and Galileo signal tracking. The validity of the existing software receiver as a base for future research was confirmed by the success of these projects. The results from Wide Area Augmentation System (WAAS) ranging, WAAS correction decoding, and navigation solution filtering are described all with the intent of improving positioning accuracy.
Injectable cartilage tissue engineering (2004)

Cartilage is the tissue that lines the surface of bones in articulating joints, allowing painless joint movement. Cartilage loss is an increasingly significant problem, particularly with the ageing of active baby boomers, with few efficacious treatments available at present. Tissue engineering is a field that has evolved over recent years to combat tissue loss by providing a living tissue equivalent or substitute that can mimic the properties of the lost tissue. The general strategy of tissue engineering is to place cells on a biomaterial scaffold that is designed to promote cell function and form new tissue. This review describes the status of materials that are available as injectable scaffolds for tissue engineering and the numerous cell types that can be applied to cartilage repair, including cells derived from cartilage and stem cells. The current state of injectable cartilage tissue engineering and the hurdles that remain for widespread clinical application are discussed.
Isolation and Characterization of Membrane-boundl-Sorbose Dehydrogenase fromGluconobacter melanogenusUV10 (1991)

Membrane-bound l-sorbose dehydrogenase was purified from the membrane fraction of Gluconobacter melanogenus UV10. The reaction with 2,6-dichlorophenolindophenol or phenazine methosulfate as acceptor was formulated as; l-sorbose + acceptor →l-sorbosone + reduced acceptor. The enzyme was purified by DEAE-Cellulose, DEAE-Sepharose, and Sephadex G-200 column chromatographies after differential solubilization with Triton X-100 and Tween 80, and appeared as a single band in a SDS-PAGE gel at the molecular weight of about 58,000. It was most active at pH 7.0 and 48°C, and rather stable at around 7.0 in a buffer containing 200 mm l-sorbose, below 30°C. It showed high substrate specificity for l-sorbose, and its activity was stimulated by Fe3 + and Co2 +, and inhibited by Cu2 +, quinine, mono-iodoacetate, and sodium fluoroacetate.
Back-end 3D integration of HfO<inf>2</inf>-based RRAMs for low-voltage advanced IC digital design (2013)

This paper gives an overview of our research work on Oxide Resistive switching memory (OxRAM) at technology and design level. The OxRAM technology has been developed in order to be co-integrated with low-voltage advanced CMOS technologies. The device electrical characteristics show: (i) a switching time of 100ns at 1V, (ii) an excellent data retention at 150°C and (iii) a high endurance up to 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">8</sup> cycles. The second part of this paper focuses on circuit design. The benefits of 3D integration of non-volatile devices on CMOS are highlighted. Performance and area gains are discussed as well as new application features.