gebhart/patrepeval huggingface dataset:
Androgen receptor (AR) amplification in patients with metastatic castration-resistant prostate cancer (mCRPC) refractory to therapy with abiraterone acetate or enzalutamide: Preliminary results from the SU2C/PCF/AACR West Coast Prostate Cancer Dream Team (WCDT). (2014)

5020 Background: The mechanisms of resistance to androgen signaling inhibitors such as Abiraterone (Abi) or Enzalutamide (Enz) are poorly understood. AR amplification (AR+) has been observed in Abi/Enz naive mCRPC patients (pts), but its role in Abi/Enz resistant pts is not known. Progressive mCRPC has historically been challenging to biopsy and characterize on a molecular basis because of its bone tropism. As part of the WCDT project which aims to identify genetic pathways underlying primary and acquired resistance to Abi and Enz, AR+ was assessed in mCRPC biopsies. Methods: Following central radiologic review, eligible mCRPC pts underwent biopsy at one of 5 WCDT clinical sites, using a uniform biopsy protocol. Tissue was both frozen, and formalin fixed/paraffin embedded (FFPE). FFPE tissue underwent a CLIA-certified assessment of a mutational panel, IHC for PTEN, and fluorescence in situ hybridization (FISH) for AR+. Results: 60 of 300 planned mCRPC pts have undergone a metastasis biopsy. To date, 33 pts have had biopsies successfully evaluated by AR FISH, including 12 from bone, 11 from lymph nodes, 8 from liver and 2 from other soft tissues. Of 16 Abi and Enz naive pts, 13 (81%) were AR+. By contrast, only 1/11 Abi resistant pts (9%) was AR+. 4/6 Enz resistant pts (67%) were AR+. Of 6 AR+ patients that went on to receive Abi or Enz, 3 (50%) had a response (PCWG2 criteria), whereas of 5 pts without AR+ who went on to receive Abi/Enz, just 1 (20%) had a response. Conclusions: AR amplification can be evaluated by FISH in small biopsies of mCRPC, including bone, and it was observed in 18/33 samples (55%). AR+ was common in mCRPC patients prior to therapy with Abi or Enz (81%). However, once resistance developed, Abi resistant pts had a far lower likelihood of AR+ (9%) than Enz resistant pts (67%). These data support the hypothesis that treatment with Abiraterone selects for non-AR amplified cells, whereas Enzalutamide does not. In this relatively small cohort, mCRPC pts with AR+ are more likely to respond to subsequent AR targeted therapeutics than pts without AR+.
A new evaluation method of plasma process-induced Si substrate damage by the voltage shift under constant current injection at metal/Si interface (2002)

We propose a new evaluation method of plasma process induced Si substrate damage, which utilizes the voltage shift under constant-current injection (VSCCI) at metal-Si interface. This method is applied to the plasma damaged Si substrate and the obtained depth profile of the defects in the Si correlates well with the electrical metal/Si contact property.
Palladium Catalyzed α,β-Homodiarylation of Vinyl Esters in Aqueous Medium (2021)

Abstract A palladium catalyzed 1,2-diarylation of vinyl esters with sustainable arylbornic acids in water has been developed. This newly elaborated protocol features good functional group tolerance and provides a one-step access to 1,2-diaryletahol derivatives under mild reaction conditions. The presented reaction can be carried out in water smoothly without the addition of any ligands at ambient temperature what makes this procedure environmentally benign. The transformation occurs within a single catalytic cycle and is feasible due to the modification of transition metal catalytic activity through the influence of π-acceptor olefin (benzoquinone) as well as the polar protic reaction medium (water in particular). Moreover, the protocol allows to generate entire compounds libraries (highly profitable in medicinal chemistry) and utilizes sustainable arylboronic acid as coupling partners under mild conditions.
Scalable Imprinting of Flexible Multiplexed Sensor Arrays with Distributed Piezoelectricity‐Enhanced Micropillars for Dynamic Tactile Sensing (2020)

Abstract The ongoing revolution of human–robot interactions and electronic skins has created new requirements for tactile sensors, including good mechanical flexibility, high sensitivity, and the availability of distributed pixels for detecting force distribution. Here, a highly sensitive flexible sensor array based on piezoelectricity‐enhanced vertically aligned P(VDF‐TrFE) micropillars is developed for dynamic tactile sensing. The core piezoelectric sensing micropillars are fabricated using a straightforward and scalable nanoimprinting technology and then sandwiched between a pair of cross electrode arrays to construct multiplexed sensor arrays. Due to the proposed structural design and nanoimprinting methodology, the sensor pixels exhibit uniform output generation, robust output stability, and scalable fabrication ability. In addition, taking advantage of the high compressibility and enhanced strain of the piezoelectric micropillars compared to planar films, the microstructured sensors show an enhanced sensitivity of 228.2 mV N −1 and a highly linear response to loads. By integrating the flexible sensor with a portable signal processing circuit, a complete tactile sensing system is successfully developed to provide clear intuitive user interfaces. The good flexibility and robust stability of the sensor arrays enable them to be attached onto curved surface for real‐time tracking of dynamic force and imaging the force distribution.
Tolerance to the Neuron-Specific Paraneoplastic HuD Antigen (2009)

Experiments dating back to the 1940's have led to the hypothesis that the brain is an immunologically privileged site, shielding its antigens from immune recognition. The paraneoplastic Hu syndrome provides a powerful paradigm for addressing this hypothesis; it is believed to develop because small cell lung cancers (SCLC) express the neuron-specific Hu protein. This leads to an Hu-specific tumor immune response that can develop into an autoimmune attack against neurons, presumably when immune privilege in the brain is breached. Interestingly, all SCLC express the onconeural HuD antigen, and clinically useful tumor immune responses can be detected in up to 20% of patients, yet the paraneoplastic neurologic syndrome is extremely rare. We found that HuD-specific CD8+ T cells are normally present in the mouse T cell repertoire, but are not expanded upon immunization, although they can be detected after in vitro expansion. In contrast, HuD-specific T cells could be directly activated in HuD null mice, without the need for in vitro expansion. Taken together, these results demonstrate robust tolerance to the neuronal HuD antigen in vivo, and suggest a re-evaluation of the current concept of immune privilege in the brain.
Correction: Let-7b/c Enhance the Stability of a Tissue-Specific mRNA during Mammalian Organogenesis as Part of a Feedback Loop Involving KSRP (2012)

Gene silencing mediated by either microRNAs (miRNAs) or Adenylate/uridylate-rich elements Mediated mRNA Degradation (AMD) is a powerful way to post-transcriptionally modulate gene expression. We and others have reported that the RNAbinding protein KSRP favors the biogenesis of select miRNAs (including let-7 family) and activates AMD promoting the decay of inherently labile mRNAs. Different layers of interplay between miRNA-and AMD-mediated gene silencing have been proposed in cultured cells, but the relationship between the two pathways in living organisms is still elusive. We conditionally deleted Dicer in mouse pituitary from embryonic day (E) 9.5 through Cre-mediated recombination. In situ hybridization, immunohistochemistry, and quantitative reverse transcriptase-PCR revealed that Dicer is essential for pituitary morphogenesis and correct expression of hormones. Strikingly, aGSU (alpha glycoprotein subunit, common to three pituitary hormones) was absent in Dicer-deleted pituitaries. aGSU mRNA is unstable and its half-life increases during pituitary development. A transcriptome-wide analysis of microdissected E12.5 pituitaries revealed a significant increment of KSRP expression in conditional Dicer-deleted mice. We found that KSRP directly binds to aGSU mRNA, promoting its rapid decay; and, during pituitary development, aGSU expression displays an inverse temporal relationship to KSRP. Further, let-7b/c downregulated KSRP expression, promoting the degradation of its mRNA by directly binding to the 39UTR. Therefore, we propose a model in which let-7b/c and KSRP operate within a negative feedback loop. Starting from E12.5, KSRP induces the maturation of let-7b/c that, in turn, post-transcriptionally downregulates the expression of KSRP itself. This event leads to stabilization of aGSU mRNA, which ultimately enhances the steady-state expression levels. We have identified a posttranscriptional regulatory network active during mouse pituitary development in which the expression of the hormone aGSU is increased by let7b/c through downregulation of KSRP. Our study unveils a functional crosstalk between miRNAand AMD-dependent gene regulation during mammalian organogenesis events.
ChemInform Abstract: Transformation Chemistry with Nucleic Acid Purines (2009)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 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.
Homogeneous Superpixels from Markov Random Walks (2012)

This paper presents a novel algorithm to generate homogeneous superpixels from Markov random walks. We exploit Markov clustering (MCL) as the methodology, a generic graph clustering method based on stochastic flow circulation. In particular, we introduce a graph pruning strategy called compact pruning in order to capture intrinsic local image structure. The resulting superpixels are homogeneous, i.e. uniform in size and compact in shape. The original MCL algorithm does not scale well to a graph of an image due to the square computation of the Markov matrix which is necessary for circulating the flow. The proposed pruning scheme has the advantages of faster computation, smaller memory footprint, and straightforward parallel implementation. Through comparisons with other recent techniques, we show that the proposed algorithm achieves state-of-the-art performance.
Enantioselective Folding of Enynes by Gold(I) Catalysts with a Remote <i>C</i><sub>2</sub>-Chiral Element (2019)

Chiral gold(I) catalysts have been designed based on a modified JohnPhos ligand with a distal <i>C</i><sub>2</sub>-2,5-diarylpyrrolidine that creates a tight binding cavity. The <i>C</i><sub>2</sub>-chiral element is close to where the C-C bond formation takes place in cyclizations of 1,6-enynes. These chiral mononuclear catalysts have been applied for the enantioselective 5-<i>exo</i>-dig and 6-<i>endo</i>-dig cyclization of different 1,6-enynes as well as in the first enantioselective total synthesis of three members of the carexane family of natural products. Opposite enantioselectivities have been achieved in seemingly analogous reactions of 1,6-enynes, which result from different chiral folding of the substrates based on attractive aryl-aryl interactions.
Design of Tunable Nanophotonic Devices (2020)

This tutorial addresses design of tunable nanophotonic arrays, enabling dynamic, active control of the properties of light - amplitude, phase, wavevector, wavelength and polarization - opening new applications such as optical beam steering, focusing and wavefront engineering.
Deadlock- and livelock-free routing protocols for wave switching (2002)

Wave switching is a hybrid switching technique for high performance routers. It combines wormhole switching and circuit switching in the same router architecture. Wave switching achieves very high performance by exploiting communication locality. When two nodes are going to communicate frequently, a physical circuit is established between them. By combining circuit switching, pre-established physical circuits and wave pipelining across channels and switches, it is possible to increase network bandwidth considerably, also reducing latency for communications that use pre-established physical circuits. In this paper we propose two protocols for routers implementing wave switching. The first protocol handles the network as a cache of circuits, automatically establishing a circuit when two nodes are going to communicate. Subsequent communications use the previously established circuit. When a new circuit requests channels belonging to another circuit, a replacement algorithm selects the circuit to be torn down. The second protocol relies on the programmer and/or the compiler to decide when a circuit should be established or torn down for a set of messages. Also, we show that the proposed protocols are always able to deliver messages, and are deadlock- and livelock-free.
Mechanisms that decrease human Neprilysin gene expression in cigarette smoke‐induced pulmonary vascular disease (2012)

We previously demonstrated that lung neprilysin (NEP) may be protective against cigarette smoke (CS)‐induced pulmonary vascular remodeling, a major contributor to pulmonary hypertension (PHTN) in lung disorders/diseases, such as chronic obstructive pulmonary disease (COPD). We found decreased NEP levels in COPD lung, at least some of which are due to changes in NEP transcription that may involve epigenetic mechanisms, but not ROS‐induced NEP gene damage or NEP gene promoter methylation. The goal of the present study is to identify CS‐induced mechanisms that decrease NEP gene transcription. We now present evidence that histone proteins may be modified (methylated, deacetylated) and decrease NEP transcription in response to CS. This is shown with human PA SMCs in ChIP experiments with antibodies to modified histone proteins (H3ac, H3K9me2), and with the compounds 5‐Aza‐2′deoxycytidine, Trichostatin A, or Valproic Acid. CS‐specific changes in regulatory or transcription factor (HIF‐1 and 2, NFkB) binding to the NEP gene that could decrease NEP transcription are also investigated in ChIP experiments with PA SMCs. Our results may suggest new ways to increase endogenous pulmonary NEP levels to treat or prevent smoke or hypoxia‐induced pulmonary vascular remodeling. Support: NHLBI RO3‐HL‐095430, NHLBI PPG P05 HL014985 and VA Merit.
Efficacy of influenza vaccination in adult liver transplant recipients (2000)

To assess the efficacy of influenza vaccination in immunocompromised adult liver transplant (LTx) recipients, the serum antibody responses of 61 of these patients and 35 liver cirrhosis patients with those of 45 of their healthy spouses were compared, after one and two vaccinations with a commercial trivalent subunit influenza vaccine. In addition, virus-specific proliferative T-cell responses were measured in LTx recipients and their healthy spouses. In all three study groups, significant rises in geometric mean antibody titers were observed for all three antigens after one vaccination. These titers did not continue to increase significantly after the second vaccination in patients with cirrhosis and control subjects but did rise for LTx recipients. The overall antibody response to all three influenza virus strains proved to be significantly lower in the LTx recipients than in the group of healthy subjects after both one and two vaccinations. More than 68% of the LTx recipients developed hemagglutination-inhibiting serum antibody titers ≥40 against all three vaccine strains after the first vaccination and more than 80% after the second vaccination. These findings correlated with the T-cell responses determined for the group of LTx recipients and healthy control individuals. Testing of the respective serum samples against influenza virus A/Sydney/5/97, which circulated in the 1997–1998 influenza season and showed a considerable mismatch with the vaccine strain A/Nanchang/933/95, indicated that such a mismatch may have significant consequences for vaccine efficacy, especially for LTx recipients. Collectively the data show that LTx recipients can be vaccinated effectively against influenza despite immunosuppressive therapy. A two-dose vaccination regimen improved vaccination efficacy in LTx recipients. Whether transplant patients generally benefit from a two-dose vaccination regimen should be evaluated further. J. Med. Virol. 61:85–93, 2000. © 2000 Wiley-Liss, Inc.
Synthesis and characterization of mononuclear pyrazolyl complexes of palladium(II) and platinum(II). Crystal structures of [NBu4][M(C6F5)2(pyrazole)(pyrazolato)] (M = Pd, Pt) (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and characterization of mononuclear pyrazolyl complexes of palladium(II) and platinum(II). Crystal structures of [NBu4][M(C6F5)2(pyrazole)(pyrazolato)] (M = Pd, Pt)Gregorio Lopez, Jose Ruiz, Consuelo Vicente, Jose M. Marti, Gabriel Garcia, Penny A. Chaloner, Peter B. Hitchcock, and Robin M. HarrisonCite this: Organometallics 1992, 11, 12, 4090–4096Publication Date (Print):December 1, 1992Publication History Published online1 May 2002Published inissue 1 December 1992https://doi.org/10.1021/om00060a027RIGHTS & PERMISSIONSArticle Views99Altmetric-Citations32LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (868 KB) Get e-AlertsSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Direct Coupling of Semi-micro Liquid Chromatography and Sonic Spray Ionization Mass Spectrometry for Pesticide Analysis (1996)

Direct coupling of semi-micro liquid chromatography and sonic spray ionization mass spectrometry is demonstrated and shown to be a very powerful technique for pesticide analysis. Direct coupling is achieved by using a high flow rate of nitrogen gas in sonic spray ionization and a high operating temperature in the sampling orifice of the atmospheric ionization mass spectrometer. The detection limit for simazine is about 300 fmol based on quantitative analysis in the range between 1 pmol and 1 nmol. A mixture of three pesticides was successfully analyzed using semi-micro liquid chromatography/mass spectrometry.
Depression and helplessness impact interstitial cystitis/bladder pain syndrome pain over time (2018)

Reducing feelings of helplessness and increasing patient feelings of control are important ways to limit the effect of low mood on patient pain experience. De-catastrophizing interventions should be part of the referral strategy for IC/BPS symptom management.
Autonomic Secure HPC Architecture Against Power Attacks (2018)

High Performance Computing (HPC) systems are enabling broad computing capabilities across scientific simulations, data analytics, and machine learning. Such HPC systems are composed of high-end compute elements (CPUs, accelerators, co-processors...) to handle high throughput and high parallelism, which results in significant power consumption. However, the power infrastructures built for such systems are proportionately older and may not be built to sustain system's peak power for extensive periods of time. Therefore, innovative power management schemes are used to allocate power across all system's components within a given power limit. HPC power management systems regulate resources' power within budget constraints and the overall system's power limit. Failing not to limit system's power consumption can result in operational failures that can bring down the whole system. Additionally, system reliability would be compromised under extensive computational system power and temperature. In addition to power consumption, possible attack scenarios can cause reliability issues where the attackers can manipulate the reported data of the measured power that is used for power management, which in turn can misguide the schedulers or can assign tasks that will result in exceeding the power limits, leading to system failures. Hence, intrusion detection systems (IDS) for power attacks are extremely important. This paper presents a framework for power attack IDS and describe each steps to be taken.
Revisiting Symptom-Based Fault Tolerant Techniques against Soft Errors (2021)

Aggressive technology scaling and near-threshold computing have made soft error reliability one of the leading design considerations in modern embedded microprocessors. Although traditional hardware/software redundancy-based schemes can provide a high level of protection, they incur significant overheads in terms of performance and hardware resources. The considerable overheads from such full redundancy-based techniques has motivated researchers to propose low-cost soft error protection schemes, such as symptom-based error protection schemes. The main idea behind a symptom-based error protection scheme is that soft errors in the system will quickly generate some symptoms, such as exceptions, branch mispredictions, cache or TLB misses, or unpredictable variable values. Therefore, monitoring such infrequent symptoms makes it possible to cover the manifestation of failures caused by soft errors. Symptom-based protection schemes have been suggested as shortcuts to achieve acceptable reliability with comparable overheads. Since the symptom-based protection schemes seem attractive due to their generality and simplicity, even state-of-the-art protection schemes exploit them as the baseline protections. However, our detailed analysis of the fault coverage and performance overheads of such schemes reveals that the user-visible failure coverage, particularly of ReStore, is limited (29% on average). By contrast, the runtime overheads are significant (40% on average) because the majority of the fault injection experiments, which were considered as detected/recovered failures by low-level symptoms, are actually benign faults by program-level masking effects.