gebhart/patrepeval huggingface dataset:
microRNA expression profiling identifies a four microRNA signature as a novel diagnostic and prognostic biomarker in triple negative breast cancers (2014)

Triple Negative Breast Cancers (TNBC) is a heterogeneous disease at the molecular and clinical level with poor outcome. Molecular subclassification of TNBCs is essential for optimal use of current therapies and for development of new drugs. microRNAs (miRNA) are widely recognized as key players in cancer progression and drug resistance; investigation of their involvement in a TNBC cohort may reveal biomarkers for diagnosis and prognosis of TNBC. Here we stratified a large TNBC cohort into Core Basal (CB, EGFR and/or CK5, 6 positive) and five negative (5NP) if all markers are negative. We determined the complete miRNA expression profile and found a subset of miRNAs specifically deregulated in the two subclasses.We identified a 4-miRNA signature given by miR-155, miR-493, miR-30e and miR-27a expression levels, that allowed subdivision of TNBCs not only into CB and 5NP subgroups (sensitivity 0.75 and specificity 0.56; AUC=0.74) but also into high risk and low risk groups. We tested the diagnostic and prognostic performances of both the 5 IHC marker panel and the 4-miRNA expression signatures, which clearly identify worse outcome patients in the treated and untreated subcohorts. Both signatures have diagnostic and prognostic value, predicting outcomes of patient treatment with the two most commonly used chemotherapy regimens in TNBC: anthracycline or anthracycline plus taxanes. Further investigations of the patients’ overall survival treated with these regimens show that regardless of IHC group subdivision, taxanes addition did not benefit patients, possibly due to miRNA driven taxanes resistance. TNBC subclassification based on the 5 IHC markers and on the miR-155, miR-493, miR-30e, miR-27a expression levels are powerful diagnostic tools. Treatment choice and new drug development should consider this new subtyping and miRNA expression signature in planning low toxicity, maximum efficacy therapies.
[Introduction of an enzyme method for determining pyrophosphate in urine--a comparative study between patients with calculi and normal probands]. (1989)

Interest aroused towards pyrophosphate as a possible inhibitor in calcium oxalate and phosphate lithiasis. A procedure for the quantitative determination of pyrophosphate in urine suitable for use in clinical laboratories is described. The reproducibility of the method was assessed by within-run and between-run reproducibility studies and the accuracy of the method was obtained by determining the amount of pyrophosphate recovered in urine samples. The present study compares the pyrophosphate excretion and concentration between a control group and a calcium oxalate stone former group.
CsF-Catalyzed Fluoroacylation of Tetrafluoroethylene Using Acyl Fluorides for the Synthesis of Pentafluoroethyl Ketones (2020)

Abstract A catalytic method for the synthesis of pentafluoroethyl ketones­ has been developed. The cesium fluoride catalyst can be used to convert acyl fluorides into the pentafluoroethyl ketones under tetrafluoroethylene pressure without generating stoichiometric quantities of chemical waste. Mechanistic studies suggest that high reaction temperature is crucial for the ketone to be the major product.
Ti3C2Tx nanosheet wrapped core–shell MnO2 nanorods @ hollow porous carbon as a multifunctional polysulfide mediator for improved Li–S batteries (2020)

Lithium-sulfur (Li-S) batteries are regarded as potential next-generation energy storage systems due to their high theoretical energy densities. However, the dissolution of lithium polysulfides (LiPSs) upon cycling can result in severe capacity degradation. Achieving high rate capabilities with good cycling stability remains a huge obstacle for the practical implementation of Li-S batteries. Here we developed a novel, multifunctional, hierarchical structure by self-assembling core-shell MnO<sub>2</sub> nanorods @ hollow porous carbon with 2D Ti<sub>3</sub>C<sub>2</sub>T<sub>x</sub> nanosheets, labelled as MCT, as an efficient polysulfide mediator for Li-S cathodes. The integration of the polar MnO<sub>2</sub> core and hollow porous carbon shell captures LiPSs two ways: physical confinement and chemisorption. The conductive Ti<sub>3</sub>C<sub>2</sub>T<sub>x</sub> nanosheets construct a continuous and conductive network, which not only promotes charge transfer and ion diffusion but also boosts LiPS adsorption and conversion. Based on these merits, the MCT/S cathode delivers good rate capability (688 mA h g<sup>-1</sup> at 2.0C) and outstanding long-term cyclability (0.044% capacity decay per cycle over 600 cycles at 2.0C).
An Analysis of Delay-Constrained Opportunistic Scheduling for Cellular Wireless Systems (2004)

Base station schedulers in 3G and evolving 4G cellular systems use knowledge of the time-varying channel conditions of mobile users to exploit the multiuser diversity inherent in wireless networks. Although such opportunistic schedulers significantly improve the system throughput by scheduling users when their channel conditions are most favorable, they could degrade the user experience as a result of unfair resource allocation and increased variability in the scheduled rate and delay. The growing need to provide service differentiation between delay-sensitive multimedia traffic and non real-time data traffic over packet switched air-interfaces underscores the need for these schedulers to incorporate delay constraints. In this work, we focus primarily on the trade-off between the realization of multiuser diversity gain and the provision of delay guarantees. Our main contribution is an analytical characterization of the distributions of the delay and rate offered by an opportunistic scheduler. The scheduling metric used in the algorithm combines the rate requested by the user and scheduling delay in a general form. Our analysis of a wireless system with a finite number of users in discrete time is strongly supported by system simulations of a time-slotted cellular downlink shared by multiple mobile users with independent, fading channels. We also compute closed form expressions for the scheduler statistics using a continuous approximation. The results in this paper can be used to evaluate system performance and provision resources to support Quality of Service (QoS) guarantees in broadband wireless networks.
Focusing in transmit-receive mode through inhomogeneous media: The matched filter approach (2003)

It has previously been shown that in contrast to time delay focusing techniques that can only correct distortions produced by a thin aberrator located close to the transducer array, transmit-receive mode (TRM) focusing is able to compensate for distortion independently of the aberrator position. However, TRM focusing has only been described in the transmit mode. The extension of this matched filter focusing technique in the receive mode is presented. It is shown that it can be achieved using adaptive convolution techniques instead of delay line techniques. Theoretical and experimental results are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Low-Voltage Organic Thin-Film Transistors with Improved Stability and Large Transconductance (2007)

Pentacene is among the most popular organic semiconductors for organic thin-film transistors (TFTs), due to its relatively large carrier mobility. However, the stability of pentacene TFTs under continuous dynamic operation may be insufficient for future applications. Here we compare the static and dynamic performance and the operational stability of low-voltage organic TFTs based on pentacene and a recently synthesized organic semiconductor, di(phenylvinyl)anthracene (DPVAnt).
Measurement of self-phase modulation of amplified spontaneous emission: the role of second-order degree of coherence in determining the Kerr effect (2001)

We have experimentally characterized the self-phase-modulation-induced spectral broadening of continuous-wave amplified spontaneous emission (ASE) propagating in dispersion-shifted fiber samples. Experimental results for polarized and unpolarized beams show a dependence of the Kerr effect on the second-order degree of coherence of light g/sub 11//sup (2)/(0). In particular, the difference in second-order statistics for laser and ASE light must be properly accounted for when estimating the Kerr effect for a reliable modeling of transmission in long-haul amplified optical links. Whenever the g/sub 11//sup (2)/(0)=2 value for ASE light cannot be properly reproduced in simulated transmission, an enhanced value for the Kerr coefficient n/sub 2/ with respect to the coherent light case, must be used in computing the effects of self-phase modulation for the ASE portion of light.
Supplementary Figure 6 from miR-31 Is a Broad Regulator of β1-Integrin Expression and Function in Cancer Cells (2023)

&lt;p&gt;PDF file - 19K&lt;/p&gt;
Pigeon: A Specification Language for Mobile Agent Applications (2004)

Recently, research of formal models and specification languages of mobile agents is growing in order to cope with problems in using mobile agents such as security and control of complicated behaviors including migration. Such models and languages require the following features to be widely used in practical applications. The first is customizability to conform to a variety of agent platforms whose features may include various migration and communication modes and various agent architectures. The second is sufficient descriptive power to handle various requirements such as security and safety. However, existing models and languages are not satisfactory in these aspects. In this paper, we propose Pigeon, a specification language for mobile agent applications. We can customize not only the syntax of Pigeonbut also its semantics by representing the semantics in a logical framework called RL/R (reflective rewriting logic) and making the representation changeable. The high descriptive power of Pigeonis realized by the reflection feature of RL/R. We illustrate the practical advantage of Pigeonby applying it to an example of a B2B EC electronic catalog system and comparing other models and languages.
Transradial renal salvage after complex endovascular aneurysm repair complicated by left renal artery thrombosis (2019)

Transradial access has been used for percutaneous coronary interventions with success; however, there is limited literature on its use for visceral stenting in the setting of complex endovascular aneurysm repair. We present a case of transradial left renal salvage after renal artery thrombosis in the setting of complex endovascular aneurysm repair.
Biogenesis, structure and function of membrane transport proteins (2001)

1. On the travel of ribosomes toward and along the cytoplasmic membrane: An essential pathway for proper biosynthesis of integral membrane proteins. Cytoplasmic membrane proteins have indispensable functions in cellular physiology, metabolism, structure and communication. In all living cells the biogenesis of these proteins requires the Signal Recognition Particle (SRP) system (Fig. 1A), which mediates there translation on membranebound ribosomes. We are studying central mechanistic and structural aspects of the SRP system in E. coli, in the context of the biosynthetic pathway of membrane proteins. We have demonstrated that the bacterial homologue of the mammalian SRP receptor (FtsY) is essential for targeting ribosomes to the membrane and for expression of membrane proteins. In contrast, in the absence of the SRP itself, ribosome targeting and membrane protein synthesis continue, although their proper assembly is severely impaired. These observations, combined with additional considerations, led us to propose a testable model for ribosome targeting in E. coli (Fig. 1B). We propose that ribosomes are targeted to the membrane in an SRP-receptor-dependent, SRPindependent manner. After targeting, the transfer of ribosomes to the membrane insertion machinery is mediated by SRP. This scenario implies that the SRP might function downstream to the SRP receptor during the biosynthesis of membrane proteins. This model is currently being investigated using genetic screens, biochemical tools and structural analyses. These studies will clarify the order of events during the biosynthetic pathway of membrane proteins and the mechanism by which membranes are equipped with ribosomes.
Robust Graph-Theoretic Clustering Approaches Using Node-Based Resilience Measures (2016)

This paper examines a schema for graph-theoretic clustering using node-based resilience measures. Node-based resilience measures optimize an objective based on a critical set of nodes whose removal causes some severity of disconnection in the network. Beyond presenting a general framework for the usage of node based resilience measures for variations of clustering problems, we emphasize the unique potential of such methods to accomplish the following properties: (i) clustering a graph in one step without knowing the number of clusters a priori, and (ii) removing noise from noisy data. We first present results of clustering experiments using a β-parametrized generalization of vertex attack tolerance, showing high clustering accuracy for both real datasets and equal density synthetic data sets, as well as successful removal of noise nodes. It is shown that arbitrarily increasing β increases the number of noise nodes removed in some cases, and that internal validation measures can be used to determine the correct number of clusters in a class of datasets. Further results are presented using five different resilience measures with a general node-based resilience clustering technique. In a subset of cases a resilience measure, such as integrity, is able to cluster to high accuracy in one step, giving the correct clustering while also determining the correct number of clusters. Integrity is also shown to be promising with respect to noise removal, removing up to 80% of noise on some datasets.
Simian-Human Immunodeficiency Virus Escape from Cytotoxic T-Lymphocyte Recognition at a Structurally Constrained Epitope (2003)

Virus-specific cytotoxic T lymphocytes (CTL) exert intense selection pressure on replicating simian immunodeficiency virus (SIV) and human immunodeficiency virus type 1 (HIV-1) in infected individuals. The immunodominant Mamu-A(*)01-restricted Gag p11C, C-M epitope is highly conserved among all sequenced isolates of SIV and therefore likely is structurally constrained. The strategies used by virus isolates to mutate away from an immunodominant epitope-specific CTL response are not well defined. Here we demonstrate that the emergence of a position 2 p11C, C-M epitope substitution (T47I) in a simian-human immunodeficiency virus (SHIV) strain 89.6P-infected Mamu-A(*)01(+) monkey is temporally correlated with the emergence of a flanking isoleucine-to-valine substitution at position 71 (I71V) of the capsid protein. An analysis of the SIV and HIV-2 sequences from the Los Alamos HIV Sequence Database revealed a significant association between any position 2 p11C, C-M epitope mutation and the I71V mutation. The T47I mutation alone is associated with significant decreases in viral protein expression, infectivity, and replication, and these deficiencies are restored to wild-type levels with the introduction of the flanking I71V mutation. Together, these data suggest that a compensatory mutation is selected for in SHIV strain 89.6P to facilitate the escape of that virus from CTL recognition of the dominant p11C, C-M epitope.
Binaural Cues for a Single Sound Source (2007)

This chapter contains sections titled: Introduction HRTF parameterization Sound source position dependencies HRTF set dependencies Single ITD approximation Conclusions
Effect of Rebamipide on Cell Death Induced by Combined Treatment of Mild Heat Shock and Quercetin in RGM-1 Cells: A Role for HSP70 Induction (2001)

The mechanism by which rebamipide inhibits cell death induced by combined treatment of mild heat shock and quercetin in RGM-1 cells was examined. Cells were incubated at 42 degrees C for 1 h with or without quercetin. Expression of HSP70 was detected by immunoblot analysis and cell viability was determined by the MTT method. Upon treatment of cells with heat shock in the presence of quercetin, cell viability was significantly decreased 24 h after heat shock, with strong inhibition of HSP70 expression. Rebamipide suppressed both cell death and a reduction in HSP70 induced by the combined treatment of heat shock and quercetin. The combination of heat shock and quercetin resulted in DNA fragmentation, but rebamipide managed to inhibit such fragmentation. The protective effect of rebamipide was eliminated by cycloheximide or actinomycin D. Based upon these findings, it was concluded that rebamipide inhibited cell death resulting from combined treatment of mild heat shock and quercetin. The protective action of rebamipide appears to be at least partially due to maintenance of the HSP70 level.
Selecting Best Ink Color for Sparse Watermark (2017)

A method of watermarking print ready image data used in the commercial packaging industry is described. A significant proportion of packages are printed using spot colors, therefore various tools to support watermarking spot colors are required. Previously we have described a method which assumes that the package design contains process colors CMY as well as the spot colors to insert a chrominance watermark. Some package designs do not include the process colors CMY or are being printed with a print process which allows limited overprinting, and require a different approach. For simplicity of press control, a binary watermarking system was developed. The binary watermark is inserted in a single ink color with values of 0 and 100%. For the binary watermark to be used in a package design, a method is required which evaluates the ink colors used in a package design and ranks them for use with a modern barcode scanner at the Point of Sale (POS) station.
Subcellular distributions of adenosine A1 and A2A receptors in the rat dorsomedial nucleus of the solitary tract at the level of the area postrema (2006)

Adenosine A1 and A2A receptors mediate distinct cardiovascular components of defense reactions that are ascribed, in part, to opposing actions within the nucleus tractus solitarius. To assess the cellular sites of relevance to these actions, we examined the light and electron microscopic immunolabeling of adenosine A1 and A2A receptors in the rat dorsomedial nucleus of the solitary tract at the level of the area postrema (dmNTS-AP), a region crucial for cardiovascular regulation involving vagal baroreceptor afferents. Immunoreactivity for each receptor was independently localized to distinct segments of plasma membranes and endomembranes in somatodendritic, axonal, and glial profiles. The dendritic labeling for each receptor also was detected within and near asymmetric, excitatory-type synapses. Of all peroxidase labeled profiles exclusive of somata, approximately 58% were A1- and 39% were A2A-labeled dendrites. Dendrites and astrocytic glia were the profiles that most often expressed both subtypes of adenosine receptors. The axonal labeling for A2A receptors was seen mainly in unmyelinated axons, whereas the A1 receptors were prominently localized within axon terminals. These terminals often formed single or multisynaptic excitatory-type junctions or single symmetric synapses on dendrites, a few of which expressed A1 and A2A receptors. These results provide the first ultrastructural evidence that A1 and A2A receptors have distributions conductive to their dual involvement in modulating the output of single neurons and glial function in the dmNTS-AP, where the predominate presynaptic effects of adenosine are mediated through A1 receptors.
GnRH-Gemcitabine Conjugates for the Treatment of Androgen-Independent Prostate Cancer: Pharmacokinetic Enhancements Combined with Targeted Drug Delivery (2014)

Gemcitabine, a drug with established efficacy against a number of solid tumors, has therapeutic limitations due to its rapid metabolic inactivation. The aim of this study was the development of an innovative strategy to produce a metabolically stable analogue of gemcitabine that could also be selectively delivered to prostate cancer (CaP) cells based on cell surface expression of the Gonadotropin Releasing Hormone-Receptor (GnRH-R). The synthesis and evaluation of conjugated molecules, consisting of gemcitabine linked to a GnRH agonist, is presented along with results in androgen-independent prostate cancer models. NMR and ligand binding assays were employed to verify conservation of microenvironments responsible for binding of novel GnRH-gemcitabine conjugates to the GnRH-R. In vitro cytotoxicity, cellular uptake, and metabolite formation of the conjugates were examined in CaP cell lines. Selected conjugates were efficacious in the in vitro assays with one of them, namely, GSG, displaying high antiproliferative activity in CaP cell lines along with significant metabolic and pharmacokinetic advantages in comparison to gemcitabine. Finally, treatment of GnRH-R positive xenografted mice with GSG showed a significant advantage in tumor growth inhibition when compared to gemcitabine.
Supplementary Video 6 from Cell Surface Delivery of TRAIL Strongly Augments the Tumoricidal Activity of T Cells (2023)

&lt;p&gt;WMV file - 1159K&lt;/p&gt;
Experimental thermal characterization and thermal model validation of 3D packages using a programmable thermal test chip (2015)

In this paper, we present the experimental characterization of 3D packages using a dedicated stackable test chip. An advanced CMOS test chip with programmable power distribution has been designed, fabricated, stacked and packaged in molded and bare die 3D packages. The packages have been experimentally characterized in test sockets with and without cooling, and soldered to the PCB. Using uniform and localized hot spot power distribution, the thermal self-heating and thermal coupling resistance and the lateral spreading in the 3D packages have been studied. Furthermore, thermal finite element and compact models are experimentally validated using a dedicated power map with multiple heat sources. Finally, the 3D test package is used to emulate the thermal behavior of a packaged memory-on-logic stack and to assess the thermal interaction between the chips.
Surgical strategies for treatment of malignant pancreatic tumors: extended, standard or local surgery? (2008)

Tumor related pancreatic surgery has progressed significantly during recent years. Pancreatoduodenectomy (PD) with lymphadenectomy, including vascular resection, still presents the optimal surgical procedure for carcinomas in the head of pancreas. For patients with small or low-grade malignant neoplasms, as well as small pancreatic metastases located in the mid-portion of pancreas, central pancreatectomy (CP) is emerging as a safe and effective option with a low risk of developing de-novo exocrine and/or endocrine insufficiency. Total pancreatectomy (TP) is not as risky as it was years ago and can nowadays safely be performed, but its indication is limited to locally extended tumors that cannot be removed by PD or distal pancreatectomy (DP) with tumor free surgical margins. Consequently, TP has not been adopted as a routine procedure by most surgeons. On the other hand, an aggressive attitude is required in case of advanced distal pancreatic tumors, provided that safe and experienced surgery is available. Due to the development of modern instruments, laparoscopic operations became more and more successful, even in malignant pancreatic diseases. This review summarizes the recent literature on the above mentioned topics.