gebhart/patrepeval huggingface dataset:
Effect of PD-0332991, a potent and selective inhibitor of cyclin-dependent kinase 4/6, on proliferation in renal cell carcinoma at nanomolar concentrations and prediction of sensitivity by molecular markers. (2013)

413 Background: Cell cycle dysregulation is prevalent in renal cell carcinoma (RCC). PD-0332991 is an orally active, potent, and selective inhibitor of cyclin-dependent kinases (CDK) 4 and 6, blocking retinoblastoma (Rb) phosphorylation at nanomolar concentrations. Methods: 28 RCC and immortalized kidney cell lines were used to examine the effects of PD-0332991 on proliferation to determine the half maximal inhibitory concentration (IC 50 ). Effects of PD-0332991 on cell-cycle, apoptosis, and Rb phosphorylation were assessed with flow cytometry and western blot analysis for five of the cell lines: RCC-HB and SW 156 (sensitive/malignant), R444 and Hs 891.T (resistant/malignant), and CCD 1103 (resistant/immortalized non-malignant). Molecular markers for response prediction were studied using array CGH and gene expression profiling. Results: Concentration-dependent inhibition of proliferation was identified in response to PD-0332991, with IC 50 values ranging from 25.0nM up to 700nM; five cell lines were identified as completely resistant at 1000nM. PD-0332991 induced G0/G1 cell cycle arrest, as well as induction of late apoptosis in SW 156, and Rb phosphorylation was blocked in a time-dependent fashion in both sensitive cell lines, while resistant lines were unaffected. Genotype and expression data of CDKN2A and CDKN2B were combined and a consensus was made regarding p16 and p15 status; significant association between loss and sensitivity to PD-0332991 was identified for p16 (p = 0.027). For CCND1, CCNE1, E2F1, Rb, CDK4, and CDK6 no amplifications or homozygous deletions were identified by array CGH; cell lines were then classified as having high or low expression for each of these markers. E2F1 had low expression levels significantly associated with response to PD-0332991 (p = 0.041). Conclusions: PD-0332991 shows anti-proliferative activity in RCC through blockade of the cell cycle. The decreased expression of molecular markers p16 and E2F1 predict for sensitivity to PD-0332991 in RCC.
Quickr (2016)

We present a system that approximates the answer to complex ad-hoc queries in big-data clusters by injecting samplers on-the-fly and without requiring pre-existing samples. Improvements can be substantial when big-data queries take multiple passes over data and when samplers execute early in the query plan. We present a new, universe, sampler which is able to sample multiple join inputs. By incorporating samplers natively into a cost-based query optimizer, we automatically generate plans with appropriate samplers at appropriate locations. We devise an accuracy analysis method using which we ensure that query plans with samplers will not miss groups and that aggregate values are within a small ratio of their true value. An implementation on a cluster with tens of thousands of machines shows that queries in the TPC-DS benchmark use a median of 2X fewer resources. In contrast, approaches that construct input samples even when given 10X the size of the input to store samples improve only 22% of the queries, i.e., a median speed up of 0X.
Plasmid-Based System for High-Level Gene Expression and Antisense Gene Knockdown in Bartonella henselae (2009)

Six broad-host-range plasmid vectors were developed to study gene expression in Bartonella henselae. The vectors were used to express a beta-galactosidase reporter gene in B. henselae and to generate antisense RNA for gene knockdown. When applied to ompR, a putative transcription response regulator of B. henselae, this antisense RNA gene knockdown strategy reduced bacterial invasion of human endothelial cells by over 60%.
Dynamical Measurement of the Effective Radiation Area SD (2010)

The effective radiation area SD is one of the most important loudspeaker parameters because it determines the acoustical output (SPL, sound power) and efficiency of the transducer. This parameter is usually derived from the geometrical size of the radiator considering the diameter of half the surround area. This conventional technique fails for microspeakers and headphone transducers where the surround geometry is more complicated and the excursion does not vary linearly versus radius. The paper discusses new methods for measuring the SD more precisely. The first method uses a laser sensor and microphone to measure the voice coil displacement and the sound pressure generated by the transducer while mounted in a sealed enclosure. The second method uses only the mechanical vibration and geometry of the radiator measured by using a laser triangulation scanner. The paper checks the reliability and reproducibility of conventional and the new methods and discusses the propagation of the measurement error on the T/S parameters using test box perturbation technique and other derived parameters (sensitivity).
Natural Variation inSER1andENA6Underlie Condition-Specific Growth Defects inSaccharomyces cerevisiae (2017)

Despite their ubiquitous use in laboratory strains, naturally occurring loss-of-function mutations in genes encoding core metabolic enzymes are relatively rare in wild isolates of <i>Saccharomyces cerevisiae</i> Here, we identify a naturally occurring serine auxotrophy in a sake brewing strain from Japan. Through a cross with a honey wine (white tecc) brewing strain from Ethiopia, we map the minimal medium growth defect to <i>SER1</i>, which encodes 3-phosphoserine aminotransferase and is orthologous to the human disease gene, <i>PSAT1</i> To investigate the impact of this polymorphism under conditions of abundant external nutrients, we examine growth in rich medium alone or with additional stresses, including the drugs caffeine and rapamycin and relatively high concentrations of copper, salt, and ethanol. Consistent with studies that found widespread effects of different auxotrophies on RNA expression patterns in rich media, we find that the <i>SER1</i> loss-of-function allele dominates the quantitative trait locus (QTL) landscape under many of these conditions, with a notable exacerbation of the effect in the presence of rapamycin and caffeine. We also identify a major-effect QTL associated with growth on salt that maps to the gene encoding the sodium exporter, <i>ENA6</i> We demonstrate that the salt phenotype is largely driven by variation in the <i>ENA6</i> promoter, which harbors a deletion that removes binding sites for the Mig1 and Nrg1 transcriptional repressors. Thus, our results identify natural variation associated with both coding and regulatory regions of the genome that underlie strong growth phenotypes.
Modeling and exploiting spatial locality trade-offs in wavelet-based applications under varying resource requirements (2010)

Future dynamic applications will require new mapping strategies to deliver power-efficient performance. Fully static design-time mappings will not be able to optimally address the unpredictably varying application characteristics and system resource requirements. Instead, the platforms will not only need to be programmable in terms of instruction set processors, but also at least partial reconfigurability will be required, while the applications themselves will need to exploit this increased freedom at runtime to adapt to the dynamism. In this context, it is important for applications to optimally exploit the memory hierarchy under varying memory availability. This article presents an analysis of spatial locality trade-offs in wavelet-based applications, to be used in dynamic execution environments: Depending on the encountered runtime conditions, the execution switches to different memory optimized instantiations or localizations, optimally exploiting temporal and spatial locality under these conditions. This is enabled by systematic mapping guidelines, indicating how the miss-rate behavior of a localization is influenced by a specific execution condition, under which conditions a certain localization is optimal and which miss-rate gains may be obtained by switching to that localization.
Shedding Light on Structure–Property Relationships for Conjugated Microporous Polymers: The Importance of Rings and Strain (2013)

The photophysical properties of insoluble porous pyrene networks, which are central to their function, differ strongly from those of analogous soluble linear and branched polymers and dendrimers. This can be rationalized by the presence of strained closed rings in the networks. A combined experimental and computational approach was used to obtain atomic scale insight into the structure of amorphous conjugated microporous polymers. The optical absorption and fluorescence spectra of a series of pyrene-based materials were compared with theoretical time-dependent density functional theory predictions for model clusters. Comparison of computation and experiment sheds light on the probable structural chromophores in the various materials.
Correction: Cartilage-inspired superelastic ultradurable graphene aerogels prepared by the selective gluing of intersheet joints (2016)

Correction for ‘Cartilage-inspired superelastic ultradurable graphene aerogels prepared by the selective gluing of intersheet joints’ by Jin-Yong Hong, et al., Nanoscale, 2016, DOI: 10.1039/c6nr01986b.
Reduction of Thermal‐Gradient‐Induced Stresses in Composites Using Mixed Fibers (2004)

The possibility of using fibers of varying thermal expansivities to reduce stresses generated from thermal gradients in service was explored. Laminates of aluminosilicate‐ and alumina‐matrix composites were fabricated using a combination of Nextel 610™ and Nextel 720™ fibers. The composites were tested for mechanical behavior and thermomechanical behavior in comparison to control composite specimens which contained a single type of fiber. Mixed‐fiber composites show strength and fracture behavior similar to those of single‐fiber‐type composites. Their thermomechanical behavior is consistent with 2D laminate models, making it possible to design composites using such models. Interlaminar shear stress is a key, but sole limitation and the use of gradation in fiber mixture is suggested.
Photoinduced second-harmonic generation in Tm-doped fibers (1993)

We have investigated the influence of Nd:YAG laser light at 1064 nm on the grating growth and erasure processes for 790/395-nm light in Tm-doped fibers. The addition of 1064-nm light to the writing pair of 790/395 nm was observed to cause at most a slight increase in writing speed in a low-Tm fiber; in a high-Tm fiber, however, it caused a rapid drop in second- harmonic generation (SHG). This drop is determined to result from Nd:YAG-induced photodarkening, which can be partially reversed by prolonged exposure to 790-nm light. These results imply either that intense Nd:YAG irradiation does not produce mobile electrons or that the mechanism of second-harmonic generation in these fibers does not involve static macroscopic electric fields.
Data from Fluorescent Image–Guided Surgery with an Anti-Prostate Stem Cell Antigen (PSCA) Diabody Enables Targeted Resection of Mouse Prostate Cancer Xenografts in Real Time (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; The inability to visualize cancer during prostatectomy contributes to positive margins, cancer recurrence, and surgical side effects. A molecularly targeted fluorescent probe offers the potential for real-time intraoperative imaging. The goal of this study was to develop a probe for image-guided prostate cancer surgery.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; An antibody fragment (cys-diabody, cDb) against prostate stem cell antigen (PSCA) was conjugated to a far-red fluorophore, Cy5. The integrity and binding of the probe to PSCA was confirmed by gel electrophoresis, size exclusion, and flow cytometry, respectively. Subcutaneous models of PSCA-expressing xenografts were used to assess the biodistribution and &lt;i&gt;in vivo&lt;/i&gt; kinetics, whereas an invasive intramuscular model was utilized to explore the performance of Cy5-cDb–mediated fluorescence guidance in representative surgical scenarios. Finally, a prospective, randomized study comparing surgical resection with and without fluorescent guidance was performed to determine whether this probe could reduce the incidence of positive margins.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Cy5-cDb demonstrated excellent purity, stability, and specific binding to PSCA. &lt;i&gt;In vivo&lt;/i&gt; imaging showed maximal signal-to-background ratios at 6 hours. In mice carrying PSCA&lt;sup&gt;+&lt;/sup&gt; and negative (−) dual xenografts, the mean fluorescence ratio of PSCA&lt;sup&gt;+/−&lt;/sup&gt; tumors was 4.4:1. In surgical resection experiments, residual tumors &lt;1 mm that were missed on white light surgery were identified and resected using fluorescence guidance, which reduced the incidence of positive surgical margins (0/8) compared with white light surgery alone (7/7).&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; Fluorescently labeled cDb enables real-time &lt;i&gt;in vivo&lt;/i&gt; imaging of prostate cancer xenografts in mice, and facilitates more complete tumor removal than conventional white light surgery alone. &lt;i&gt;Clin Cancer Res; 22(6); 1403–12. ©2015 AACR&lt;/i&gt;.&lt;/p&gt;&lt;p&gt;&lt;i&gt;See related commentary by van Leeuwen and van der Poel, p. 1304&lt;/i&gt;&lt;/p&gt;&lt;/div&gt;
Pair correlation function characteristics of nearly jammed disordered and ordered hard-sphere packings (2005)

We study the approach to jamming in hard-sphere packings and, in particular, the pair correlation function g(2) (r) around contact, both theoretically and computationally. Our computational data unambiguously separate the narrowing delta -function contribution to g(2) due to emerging interparticle contacts from the background contribution due to near contacts. The data also show with unprecedented accuracy that disordered hard-sphere packings are strictly isostatic: i.e., the number of exact contacts in the jamming limit is exactly equal to the number of degrees of freedom, once rattlers are removed. For such isostatic packings, we derive a theoretical connection between the probability distribution of interparticle forces P(f) (f) , which we measure computationally, and the contact contribution to g(2) . We verify this relation for computationally generated isostatic packings that are representative of the maximally random jammed state. We clearly observe a maximum in P(f) and a nonzero probability of zero force, shedding light on long-standing questions in the granular-media literature. We computationally observe an unusual power-law divergence in the near-contact contribution to g(2) , persistent even in the jamming limit, with exponent -0.4 clearly distinguishable from previously proposed inverse-square-root divergence. Additionally, we present high-quality numerical data on the two discontinuities in the split-second peak of g(2) and use a shared-neighbor analysis of the graph representing the contact network to study the local particle clusters responsible for the peculiar features. Finally, we present the computational data on the contact contribution to g(2) for vacancy-diluted fcc crystal packings and also investigate partially crystallized packings along the transition from maximally disordered to fully ordered packings. We find that the contact network remains isostatic even when ordering is present. Unlike previous studies, we find that ordering has a significant impact on the shape of P(f) for small forces.
Air Conformal Ice Detection System (A.C.I.D.S) for the Power Optimised, Ice Protected Aircraft / Rotorcraft (2003)

&lt;div class="htmlview paragraph"&gt;Ice accretion on flying surfaces affects the aerodynamic performance and handling qualities of the aircraft, and may require different pilot corrective action, dependent upon the surface that ice is accreting onto. The current methodology for ice detection usually relies on an indirect method, normally based on ambient air temperature, and liquid water content. When a pre-set threshold level is reached, the ice protection system is activated, whether or not ice is accreting on critical surfaces. This method is not cost effective or efficient for an ice protection system.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;Air Conformal Ice Detection obviates these problems by using a ‘direct’ method of detection, local to the critical area being monitored.&lt;/div&gt;
5G Field Experimental Trials on URLLC Using New Frame Structure (2017)

The fifth generation mobile communications (5G) system will need to support ultra-reliable and low-latency communications (URLLC) to enable future mission-critical applications, e.g., self-driving cars and remote control. With the aim to verify the feasibility of URLLC related 5G requirements under real environments, field experimental trials of URLLC using new frame structure were conducted in Yokohama, Japan. In this paper, we present the trial results and investigate the impact of 5G new frame structure and retransmission method on URLLC performance. To reduce the user-plane latency and improve the packet success probability, a 60-kHz subcarrier spacing, self-contained frame structure and acknowledgement/negative acknowledgement-less (ACK/NACK-less) retransmission are adopted. We test these techniques in real field using our prototype test-bed. The field trial results show that the URLLC related requirements defined by 3GPP are achieved even for a low signal-to-noise ratio or non-line-of-sight locations.
Opioid peptides Synthesis and binding properties of dermorphin related heptapeptides (1989)

C-Terminal amino acid residues of dermorphin (H-Tyr-D-Ala-Phe-Gly-Tyr-Pro-Ser-NH2) were replaced by N alpha-methyl- or D-amino acids in order to examine the effect on opioid activity. In binding studies based on displacement of mu, delta, and kappa opioid receptor selective radiolabels from guinea pig brain membranes, the 13 new analogues showed, like dermorphin, a negligible affinity for the kappa binding site. The introduction of N alpha-methyl- or D-amino acid residues at position 5, 6, or 7 of dermorphin, when matched with C-terminal amide function modifications, generally produced analogues with reversed mu/delta specificity.
Development of low-loss band-pass filters using SAW resonators for portable telephones (2003)

A bandpass filter using surface acoustic wave (SAW) resonators in a ladder circuit structure for portable telephone systems is reported. For filter design, a simulation tool is used to consider the effects of electrodes (their apertures, the number of paired elements, thickness, and bulk wave radiation). Filter input and output impedance conditions are designed by the resonator capacitance to match the line impedance. The insertion loss and stopband rejection values are traded off against each other and are controlled by the ratio of capacitances between the parallel arm and series arm resonators, 800-MHz and 1.9-GHz band filters mounted in 3.8 mm*3.8-mm*1.5-mm ceramic packages were fabricated. They are suitable for surface mount technology (SMT). Typical frequency response characteristics are 2.5-dB maximum insertion loss in the 25-MHz passband and a stopband rejection of 25 dB.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Learning statistical models of phenotypes using noisy labeled training data (2016)

Abstract Objective Traditionally, patient groups with a phenotype are selected through rule-based definitions whose creation and validation are time-consuming. Machine learning approaches to electronic phenotyping are limited by the paucity of labeled training datasets. We demonstrate the feasibility of utilizing semi-automatically labeled training sets to create phenotype models via machine learning, using a comprehensive representation of the patient medical record. Methods We use a list of keywords specific to the phenotype of interest to generate noisy labeled training data. We train L1 penalized logistic regression models for a chronic and an acute disease and evaluate the performance of the models against a gold standard. Results Our models for Type 2 diabetes mellitus and myocardial infarction achieve precision and accuracy of 0.90, 0.89, and 0.86, 0.89, respectively. Local implementations of the previously validated rule-based definitions for Type 2 diabetes mellitus and myocardial infarction achieve precision and accuracy of 0.96, 0.92 and 0.84, 0.87, respectively. We have demonstrated feasibility of learning phenotype models using imperfectly labeled data for a chronic and acute phenotype. Further research in feature engineering and in specification of the keyword list can improve the performance of the models and the scalability of the approach. Conclusions Our method provides an alternative to manual labeling for creating training sets for statistical models of phenotypes. Such an approach can accelerate research with large observational healthcare datasets and may also be used to create local phenotype models.
A global atlas of genetic associations of 220 deep phenotypes (2020)

Abstract Current genome-wide association studies (GWASs) do not yet capture sufficient diversity in populations and scope of phenotypes. To expand an atlas of genetic associations in non-European populations, we conducted 220 deep-phenotype GWASs (diseases, biomarkers, and medication usage) in BioBank Japan ( n =179,000), by incorporating past medical history and text-mining of electronic medical records. Meta-analyses with the UK Biobank and FinnGen ( n total =628,000) identified ∼5,000 novel loci, which improved the resolution of genomic map of human traits. This atlas elucidated landscape of pleiotropy as represented by MHC locus, where we conducted HLA fine-mapping. Finally, we performed statistical decomposition of matrices of phenome-wide summary statistics, and identified latent genetic components, which pinpointed responsible variants and biological mechanisms underlying current disease classifications across populations. The decomposed components enabled genetically-informed subtyping of similar diseases (e.g., allergic diseases). Our study suggests a potential avenue for hypothesis-free re-investigation of human diseases through genetics.
An opto-thermal study of high brightness 280 nm emission AlGaN micropixel light-emitting diode arrays (2020)

Abstract We present a study of the light output power and the thermal impedance of 281 nm emission AlGaN based micropixel LEDs. A modular interconnected micropixel array design is presented which enables dense packing with area and power scalability. We study 5–15 μ m diameter stand-alone devices and parallel-connected micropixel arrays with 5 μ m interpixel gaps. A standalone 5 μ m pixel emits 291 W cm −2 at 10.2 kA cm −2 DC-drive. A power as high as 23 mW (361 W cm −2 ) was measured at a pulsed-pump current of 800 mA (∼15 kA cm −2 ) for an interconnected array. These are the smallest and brightest DUV LEDs to date.
Large scale integration and reliability consideration of triple gate transistors (2005)

Large scale integration and reliability of triple gate FETs (TG-FETs) are investigated. The SRAM chip composed of TG-FETs demonstrated 20Mbits of working cells, and 45/spl deg/ rotated TG-FET is found to be superior from reliability perspective. Future TG-FET design is proposed, utilizing technologies including alternating phase shift mask lithography, local-interconnects and metal gate/undoped channel.