gebhart/patrepeval huggingface dataset:
Abstract 4298: Defects in DNA repair genes and sensitivity to cisplatin based neoadjuvant chemotherapy (NAC) for bladder cancer (2015)

Abstract Background: Cisplatin based NAC prior to cystectomy is standard of care for MIBC, with 40-50% expected to respond with ≤pT1N0M0. Biomarkers predictive of response are lacking. Methods: MIBC pts who received 3 cycles of cisplatin based NAC on 1 of 2 prospective multicenter clinical trials were included. Pts treated with accelerated methotrexate, vinblastine, doxorubicin + cisplatin (AMVAC) provided the discovery set [n = 34, 15/34 (44%) ≤pT1N0M0]. Pts treated with dose dense gemcitabine + cisplatin (DDGC) provided the validation set [n = 24, 11/24 (46%) ≤pT1N0M0]. DNA from pre-treatment tumor tissue underwent sequencing for all coding exons of 287 cancer related genes and was analyzed for presence of base substitutions, indels, copy number alterations, and selected re-arrangements. The mean number of variants and variant status for each gene were correlated with response using two-sample t-test and Fisher's exact tests. Variant data were used to create a classification tree to discriminate responders vs. non-responders in the AMVAC discovery cohort. The resulting decision rule was then tested in the independent DDGC validation set. Overall survival analysis was performed using Kaplan-Meier. Results: Pts with pT0 had significantly more alterations than those with residual tumor in both the AMVAC discovery (p = .024) and DDGC validation (p = 0.018) set. In the AMVAC discovery set, alteration in ≥1 of the three DNA repair genes ATM, RB1 or FANCC predicted for ≤pT1N0M0 (p&amp;lt;0.001, 87% sensitivity, 100% specificity) and improved overall survival (OS) (p = 0.007). This test remained predictive for ≤pT1N0M0 in the DDGC validation set (p = 0.033), with a trend towards improved OS (p = 0.07) at short median follow up of 14.3 mo. Conclusions: Alterations in ≥1 of ATM, RB1 and FANCC predict response to cisplatin based chemotherapy defined as ≤pT1N0M0 in both our AMVAC discovery and DDGC validation sets. We hypothesize that defects in these genes, which are important for maintenance of chromatin structure and DNA repair, confer sensitivity to DNA damaging chemotherapy and explain the accumulation of alterations seen among pts with pT0. External validation in collaboration with the cooperative groups is planned. Citation Format: Elizabeth R. Plimack, Roland L. Dunbrack, Timothy A. Brennan, Mark D. Andrake, Yan Zhou, Ilya Serebriiskii, Essel Dulaimi Al-Saleem, Jean Hoffman-Censits, Marijo Bilusic, Yu-Ning Wong, Alexander Kutikov, Rosalia Viterbo, Richard Greenberg, David Chen, Costas D. Lallas, Edouard J. Trabulsi, Roman Yelensky, Vincent A. Miller, Erica Golemis, Eric Ross. Defects in DNA repair genes and sensitivity to cisplatin based neoadjuvant chemotherapy (NAC) for bladder cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4298. doi:10.1158/1538-7445.AM2015-4298
How Tolerance Shapes the Development of the HIV-1 Broadly Neutralizing Antibody 2F5 (2016)

Abstract An effective HIV-1 vaccine is likely to require induction of broadly neutralizing antibodies (bnAbs), which neutralize multiple HIV-1 strains. Generating HIV-1 bnAbs has been challenging due partly to a number of viral immune evasion mechanisms, including viral molecular mimicry of host in order to exploit immunological tolerance. Indeed, generation of neutralizing antibodies to the 2F5 epitope of HIV-1 gp41 is proscribed by immune tolerance. However, the specific mechanisms by which tolerance relieves the autoreactivity of B cells expressing the VH and VL regions (dKI) or the VH region (sKI) of the 2F5 bnAb are not well understood. To compare the reactivity and repertoire of 2F5 dKI and sKI B cells before and after immune tolerance checkpoints, we used a newly developed in vitro single B cell culture system that induces B cell expansion and differentiation into Ab-secreting plasmacytes. The reactivities of expanded B cell clones were determined by ELISA, while repertoire was determined by recovering the V(D)J rearrangements using RT-PCR and Sanger sequencing. In 2F5 dKI mice, the great majority of cells in the small-pre-B compartment express the knock in heavy- and light-chains, and maintain HIV-1 gp41-reactivity. However, 2F5 dKI B cells that survive tolerance checkpoints to become mature B cells have undergone extensive light-chain editing and are purged of gp41- and KYNU-reactivity. Importantly, the peripheral 2F5 dKI IgM−IgD+ (anergic) B cell subset retains a substantial fraction of HIV-1- and KYNU-reactive cells. In conclusion, our study provides mechanistic insights into how immunological tolerance impairs humoral responses to HIV-1, and suggests activation of anergic B cells as a potential target for HIV-1 vaccination.
Figure S1 from Integrative Kinome Profiling Identifies mTORC1/2 Inhibition as Treatment Strategy in Ovarian Clear Cell Carcinoma (2023)

&lt;p&gt;Supplementary Figure 1 | Kinome sequencing variant filtering. Pipeline for filtering of kinome sequencing variants.&lt;/p&gt;
Charge Transfer Energies of Metal Complexes. Nature of the Lowest Charge Transfer Excited State of Hexacyanocobaltate(1ll) (1985)

Abstract The principles underlying correlations of charge transfer energies for related metal complexes are examined in light of data that have become available in recent years. As a consequence, the charge transfer absorption band of Co(CN)3- 6 at 50,600 cm−1 is assigned to a σ(CN) → do∗Co) transition.
Design of a Quadratic, Antagonistic, Cable-Driven, Variable Stiffness Actuator (2021)

Abstract Antagonistically actuated variable stiffness actuators (VSAs) take inspiration from biological muscle structures to control both the stiffness and positioning of a joint. This paper presents the design of an elastic mechanism that utilizes a cable running through a set of three pulleys to displace a linear spring, yielding quadratic spring behavior in each actuator. A joint antagonistically actuated by two such mechanisms yields a linear relationship between force and deflection from a selectable equilibrium position. A quasi-static model is used to optimize the mechanism. Testing of the fabricated prototype yielded a good match to the desired elastic behavior.
The Pto Kinase of Tomato, Which Regulates Plant Immunity, Is Repressed by Its Myristoylated N Terminus (2006)

Specific recognition of the Pseudomonas syringae effector proteins AvrPto and AvrPtoB in tomato is mediated by Pto kinase resulting in induction of defense responses, including hypersensitive cell death via a signaling pathway requiring the nucleotide-binding leucine-rich repeats protein Prf. Pto is a myristoylated protein, and N-myristoylation is required for signaling. Here we demonstrated a role for N-myristoylation in controlling Pto kinase activity. A myristoylated peptide corresponding to Pto residues 2-10 significantly impaired the kinase activity of N-truncated Pto. We show that kinase inhibition was specific to the myristoylated form of the peptide and that free myristate supplied in trans was a potent suppressor of Pto kinase activity. Thus, myristate, but not Pto residues 2-10, contributes to suppression of kinase activity in vitro. Accordingly, elimination of the in vivo myristoylation potential of Pto de-repressed kinase activity. The increased potency of free myristate relative to the myristoylated N-peptide inhibitor suggested that the peptide moiety is antagonistic to repression by myristate. Suppression of related protein kinases by myristate declined with similarity to Pto, and the inhibitory activity could be attributed to hydrophobicity. We present evidence that inhibition of Pto by the myristoylated N-peptide is mediated through a previously identified surface regulatory patch. The data show a role for negative regulation of Pto by N-myristoylation, in addition to the previously demonstrated positive role, and are consistent with a model in which the acylated N terminus is sequestered in the catalytic cleft prior to release by Pto activation.
Nonparametric Modeling and Prognosis of Condition Monitoring Signals Using Multivariate Gaussian Convolution Processes (2017)

Condition monitoring (CM) signals play a critical role in assessing the remaining useful life of in-service components. In this article, an alternative view on modeling CM signals is proposed. This view draws its roots from multitask learning and is based on treating each CM signal as an individual task. Each task is then expressed as a convolution of a latent function drawn from a Gaussian process (GP), and the transfer of knowledge is achieved through sharing these latent functions between historical and in-service CM signals. Aside from being nonparametric, the flexible and individualistic approach in our model can account for heterogeneity in the data and automatically infer the commonalities between the new testing observations and CM signals in the historical dataset. The robustness and advantageous features of the proposed method are demonstrated through numerical studies and a case study with real-world data in the application to find the remaining useful life prediction of automotive lead-acid batteries. Technical details and additional numerical results are available in the supplementary materials.
Low-complexity interference variance estimation methods for coded multicarrier systems: application to SFN (2013)

For single-frequency network (SFN) transmission, the echoes coming from different transmitters are superimposed at the reception, giving rise to a frequency selective channel. Although multicarrier modulations lower the dispersion, the demodulated signal is sensitive to be degraded by inter-symbol interference (ISI) and inter-carrier interference (ICI). In view of this, we use channel coding in conjunction either with filter bank multicarrier (FBMC) modulation or with orthogonal frequency division multiplexing (OFDM). To deal with the loss of orthogonality, we have devised an interference-aware receiver that carries out a soft detection under the assumption that the residual interference plus noise (IN) term is Gaussian-distributed. To keep the complexity low, we propose to estimate the variance of the IN term by resorting to data-aided algorithms. Experimental results show that regardless of the method, FBMC provides a slightly better performance in terms of coded bit error rate than OFDM, while the spectral efficiency is increased when FBMC is considered.
Fabrication-Tolerant Efficient Dual-Etch Grating Couplers with Low Back Reflections (2018)

Using inverse electromagnetic design, we optimize dual-etch grating couplers with a 100 nm minimum feature size compatible with DUV lithography that achieve a record peak coupling efficiency of -0.7 dB and unprecedented low back reflection of <; -40 dB.
New Frontiers in Energy-Efficient Computing [Guest editors' introduction] (2016)

Energy-efficient computing remains a critical challenge across the wide range of future data-processing engines — from ultra-low-power embedded systems to servers, mainframes, and supercomputers. In addition, the advent of cloud and mobile computing as well as the explosion of IoT technologies have created new research challenges in the already complex, multidimensional space of modern and future computer systems. These new research challenges led to the establishment of the IEEE Rebooting Computing Initiative, which specifically addresses novel low-power solutions and technologies as one of the main areas of concern.With this in mind, we thought it timely to survey the state of the art of energy-efficient computing.
Modeling infrared behavior of multilayer diffractive optical elements using Fourier optics (2021)

In this paper, we propose to explore the infrared (IR) behavior of multilayer diffractive optical elements (MLDOEs). IR MLDOEs are designed for the development of space instruments dedicated to Earth observation. The phase effect of the MLDOE on a paraxial plane wave is studied using exact kinoform shapes for each layer. The modeling of the optical path difference uses thin element approximation. Until now, MLDOEs have been designed and simulated on ray-tracing software with binary diffractive layers. In this study, after passing through the MLDOE, the field is propagated using a method that utilizes the angular spectrum of plane waves. The Strehl ratio is used to determine the "best focus" plane, where it is shown that the focalization efficiency is above 95% for the working order in the mid- and long-wave IR bands. This result, along with the very low energy content of the other orders, proves the strong imaging potential of MLDOEs for dual-band applications. It is also demonstrated that the MLDOE has the same chromatic behavior as standard DOEs, making it a very useful component for IR achromatization.
Going Deeper With Neural Networks Without Skip Connections (2020)

We propose the training of very deep neural networks (DNNs) without shortcut connections known as PlainNets. Training such networks is a notoriously hard problem due to: (1) the relatively popular challenge of vanishing and exploding activations, and (2) the less studied ‘near singularity’ problem. We argue that if the aforementioned problems are tackled together, the training of deeper PlainNets becomes easier. Subsequently, we propose the training of very deep PlainNets by leveraging Leaky Rectified Linear Units (LReLUs), parameter constraint and strategic parameter initialization. Our approach is simple and allows to successfully train very deep PlainNets having up to 100 layers without employing shortcut connections. To validate this approach, we validate on five challenging datasets; namely, MNIST, CIFAR-10, CIFAR100, SVHN and ImageNet datasets. We report the best results known on the ImageNet dataset using a PlainNet with top-1 and top-5 error rates of 24.1% and 7.3%, respectively.
A Fully Collusion Resistant Broadcast, Trace, and Revoke System. (2006)

We introduce a simple primitive called Augmented Broadcast Encryption (ABE) that is sufficient for constructing broadcast encryption, traitor-tracing, and trace-and-revoke systems. These ABE-based constructions are resistant to an arbitrary number of colluders and are secure against adaptive adversaries. Furthermore, traitor tracing requires no secrets and can be done by anyone. These broadcast systems are designed for broadcasting to arbitrary sets of users. We then construct a secure ABE system for which the resulting concrete trace-and-revoke system has ciphertexts and private keys of size √ N where N is the total number of users in the system. In particular, this is the first example of a fully collusion resistant broadcast system with sublinear size ciphertexts and private keys that is secure against adaptive adversaries. The system is publicly traceable. 1
Effect of particle-particle interactions on the acoustic radiation force in an ultrasonic standing wave (2015)

Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter Facebook Reddit LinkedIn Tools Icon Tools Reprints and Permissions Cite Icon Cite Search Site Citation Bart Lipkens, Yurii A. Ilinskii, Evgenia A. Zabolotskaya; Effect of particle-particle interactions on the acoustic radiation force in an ultrasonic standing wave. AIP Conference Proceedings 28 October 2015; 1685 (1): 040007. https://doi.org/10.1063/1.4934402 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAIP Publishing PortfolioAIP Conference Proceedings Search Advanced Search |Citation Search
Novel T‐Shaped 14‐Electron Platinum(II) Complexes Stabilized by One Agostic Interaction (2003)

Die stereoelektronischen Eigenschaften von Liganden des Typs PR2(2,6-Me2C6H3) (R=Ph, Cy) lassen sich nutzen, um eine neue Klasse von Platin(II)-14-Elektronen-Komplexen zu stabilisieren. Beim Cyclohexylderivat wurde eine agostische Wechselwirkung zwischen dem Pt-Zentrum und einer ortho-Methylgruppe nachgewiesen (siehe Bild). Durch Reaktion mit H2 bilden sich schnell (und reversibel) unter Spaltung einer Pt-C-Bindung Platin-Hydrido-Komplexe. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2001/2003/z50047_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
ADJUSTMENT OF DRY WEIGHT IN HEMODIALYSIS PATIENTS USING CONTINUOUS INTRADIALYTIC MEASUREMENT OF CALF MUL-TIFREQUENCY BIOIMPEDANCE (2004)

Background. Current concepts of dry weight (DW) prescription are largely based on clinical symptoms because of the difficulty in assessing extracellular fluid volume (ECV) during dialysis. We hypothesized that relative changes in extracellular resistance (Re)of the calf, expressed as [Re-o/Re-t], will become very low when ECV is contracted and individual DW is reached. Method. Continuous calf BIS was recorded repeatedly in 15 HD patients (n = 120). The first measurement was performed at clinical dry weight (CDW) as prescribed by the physician. Next measurements were made after post-HD body weight was gradually decreased by 0.2-0.3 kg per treatment. This procedure was iterated over several subsequent treatments until a treatment was observed where changes in Re-o/Re-t were <1 %. Weight at the end of this treatment was defined as “achieved dry weight (ADW)”. Results. Mean ADW (80.5 ± 34.1 kg) were significantly lower than CDW (81.4±32.0 kg, p <0.001). When ADW was achieved, pre-dialysis systolic blood pressure (SBP) was lower than at CDW (139.3±32.5 mmHg, vs. 129.4±33 mmHg, p<0.05), post-HD SBP did not differ. The incidence of clinical symptoms of underhydration was 15 % at CDW, but 46% at ADW. Conclusion. Continuous calf BIS during dialysis allows the assessment of changes in extracellular resistance as an indicator of changes in extracellular fluid volume. This method appears to be a promising new tool for the prediction of dry weight in hemodialysis patients.
Towards a one-way American Sign Language translator (2004)

Inspired by the Defense Advanced Research Projects Agency's (DARPA) previous successes in speech recognition, we introduce a new task for sign language recognition research: a mobile one-way American sign language translator. We argue that such a device should be feasible in the next few years, may provide immediate practical benefits for the deaf community, and leads to a sustainable program of research comparable to early speech recognition efforts. We ground our efforts in a particular scenario, that of a deaf individual seeking an apartment and discuss the system requirements and our interface for this scenario. Finally, we describe initial recognition results of 94% accuracy on a 141 sign vocabulary signed in phrases of fours signs using a one-handed glove-based system and hidden Markov models (HMMs).
Analyzing Prospects for Quantum Advantage in Topological Data Analysis (2022)

Lloyd et al. were first to demonstrate the promise of quantum algorithms for computing Betti numbers, a way to characterize topological features of data sets. Here, we propose, analyze, and optimize an improved quantum algorithm for topological data analysis (TDA) with reduced scaling, including a method for preparing Dicke states based on inequality testing, a more efficient amplitude estimation algorithm using Kaiser windows, and an optimal implementation of eigenvalue projectors based on Chebyshev polynomials. We compile our approach to a fault-tolerant gate set and estimate constant factors in the Toffoli complexity. Our analysis reveals that super-quadratic quantum speedups are only possible for this problem when targeting a multiplicative error approximation and the Betti number grows asymptotically. Further, we propose a dequantization of the quantum TDA algorithm that shows that having exponentially large dimension and Betti number are necessary, but insufficient conditions, for super-polynomial advantage. We then introduce and analyze specific problem examples which have parameters in the regime where super-polynomial advantages may be achieved, and argue that quantum circuits with tens of billions of Toffoli gates can solve seemingly classically intractable instances.
PLASMONIC NANOPARTICLE DEPOSITION ON A MICROPILLAR ARRAY AS A 3D NANOSENSOR (2013)

A sensitive and compact 3D plasmonic nanosensor was developed by deposition of gold nanoparticles (AuNPs) on a silicon micropillar array for label-free biosensing. This silicon micropillar array also worked as an autonomous capillary pump, capable of transporting a specific amount of bio-samples into the sensing area without external pumping requirement. The developed device greatly decreased system complexity and sample consumption. Both the extinction spectra peak position and the maximum extinction exhibited good linear relationships with the surrounding refractive index of the environment.
Changes in the tension in dsDNA alter the conformation of RecA bound to dsDNA–RecA filaments (2011)

The RecA protein is an ATPase that mediates recombination via strand exchange. In strand exchange a single-stranded DNA (ssDNA) bound to RecA binding site I in a RecA/ssDNA filament pairs with one strand of a double-stranded DNA (dsDNA) and forms heteroduplex dsDNA in site I if homology is encountered. Long sequences are exchanged in a dynamic process in which initially unbound dsDNA binds to the leading end of a RecA/ssDNA filament, while heteroduplex dsDNA unbinds from the lagging end via ATP hydrolysis. ATP hydrolysis is required to convert the active RecA conformation, which cannot unbind, to the inactive conformation, which can unbind. If dsDNA extension due to RecA binding increases the dsDNA tension, then RecA unbinding must decrease tension. We show that in the presence of ATP hydrolysis decreases in tension induce decreases in length whereas in the absence of hydrolysis, changes in tension have no systematic effect. These results suggest that decreases in force enhance dissociation by promoting transitions from the active to the inactive RecA conformation. In contrast, increases in tension reduce dissociation. Thus, the changes in tension inherent to strand exchange may couple with ATP hydrolysis to increase the directionality and stringency of strand exchange.
ChemInform Abstract: Chemistry of L‐Ascorbic and D‐Isoascorbic Acids. Part 4. An Efficient Synthesis of 2‐Deoxypentofuranoses. (1991)

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.