gebhart/patrepeval huggingface dataset:
Feasibility and safety of sequential research-related tumor core biopsies in clinical trials with anti-angiogenic and targeted therapies. (2012)

2545 Background: There has been increasing interest in serial/paired research biopsies (bx) in studies of molecularly targeted therapies. Definition of optimal target tissue and patient characteristics for safe and feasible research tumor bx in the era of anti-angiogenic and targeted therapies is needed. Methods: IRB-approved review of retrospective clinical data including patient demographics, pre-and post-procedure and recovery notes, and radiographic bx images. The cohort consisted of 142 pts scheduled for serial bx enrolled in phase 1 (5) and phase 2 (1) studies. Tumor core bx were obtained percutaneously under local anesthesia using a 16 or 18g needles under US or CT visualization by interventional radiologists. Results: Paired tumor core bx were collected in 96 pts (68%) and baseline only in 42 pts (32%). Bx were aborted in 4 pts due to cystic mass (3) and safety (1). 132 pts were female and 10 pts were male, median age 56 yrs (27-78), median BMI 25.8 (14.4-46.2), ECOG PS 0-2, and normal end-organ function. All pts had recurrent metastatic cancers (gynecologic 121, breast 6, sarcoma 5, melanoma 4, colon 2, adrenal 1, mesothelioma 1, RCC 1, papillary thyroid ca 1). 67 pts (51%) were on bevacizumab (bev)-based therapy at the time of their 2 nd /3 rd bx (bev + sorafenib; bev + dasatinib); others received gefitinib (27), imatinib (23), vandetinib (9), or olaparib + carboplatin (16). Median tumor size was 2.7cm (1-14.5cm). Bx sites were abd/pelvic masses 42, liver 40, lymph nodes 42, abd/chest wall 12, lung 4 (3 pleural, 1 parenchymal), and psoas muscle 1. Minor complications were observed in four pts (3%; uncomplicated liver subcapsular hematoma [1]; vasovagal syncope responding to fluids [2]; uncomplicated pneumothorax without intervention [1]) and there were no major complications. The median number of tumor cores was 3 (1-6) at the baseline, 2 nd (during or at the end of the first cycle) and 3 rd time point (during cycle 2). Conclusions: Core needle bx of deep internal lesions such as intra-abdominal masses and retroperitoneal lymph nodes can be obtained percutaneously under imaging guidance. Sequential tumor bx are feasible and safe for pts on anti-angiogenic and chemotherapeutic agents.
Novel protein-altering variants associated with serum apolipoprotein and lipid levels (2021)

Abstract Dyslipidemia is a major risk factor for cardiovascular disease. While common genetic variants are known to modestly affect the serum lipid concentrations, rare genetic mutations can cause monogenic forms of hypercholesteremia and other genetic disorders of lipid metabolism. Aiming to identify low-frequency protein-altering variants (PAVs) affecting lipoprotein and lipid traits, we analyzed whole-exome and whole-genome sequencing data of 481 and 573 individuals with type 1 diabetes, respectively. The phenotypic data consisted of 97 serum lipid, apolipoprotein, or other metabolic phenotypes obtained with clinical laboratory measurements and nuclear magnetic resonance (NMR) technology. Single variant analysis identified a novel association between LIPC p.Thr405Met (rs113298164) and serum apolipoprotein-A1 levels (p=7.8×10 −8 ). In the APOB gene, we identified novel associations at two protein-truncating variants (PTVs) resulting in lower serum apolipoprotein B levels (p=5.6×10 −4 ). The burden of PAVs was significantly associated with lipid phenotypes in LIPC, RBM47, TRMT5 , and GTF3C5 (p&lt;2.9×10 −6 ). The RBM47 gene is required for apolipoprotein-B post-translational modifications, and in our data, the association between RBM47 and apolipoprotein C-III levels was led by a rare 21 base pair Ala496-Ala502 deletion; as replication, the burden of rare deleterious variants in RBM47 was associated with TG-to-HDLC ratio in WES of 20,917 individuals (p=0.0093). Two PAVs in GTF3C5 were highly Finnish-enriched and associated with cardiovascular phenotypes in external data, whereby the TRMT5 p.Ser185Cys lead variant was associated with stroke phenotypes. Altogether, we identified both novel variant associations in known lipid genes, as well as novel genes implicated in lipoprotein metabolism.
Low-Temperature Polycrystalline Silicon Thin-Film Flash Memory With Hafnium Silicate (2007)

In this paper, we have successfully fabricated poly-Si-oxide-nitride-oxide-silicon (SONOS)-type poly-Si-thin-film transistor (TFT) memories employing hafnium silicate as the trapping layer with low-thermal budget processing (les600degC). It was demonstrated that the fabricated memories exhibited good performance in terms of relatively large memory window, high program/erase speed (1 ms/10 ms), long retention time (>10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sup> s for 20% charge loss), and 2-bit operation. Interestingly, we found that these memories depicted very unique disturbance behaviors, which are obviously distinct from those observed in the conventional SONOS-type Flash memories. We thought these specific characteristics are closely related to the presence of the inherent defects along the grain boundaries. Therefore, the elimination of the traps along the grain boundaries in the channel is an important factor for achieving high performance of the SONOS-type poly-Si-TFT Flash memory
Metal–Organic Frameworks with Low‐Valent Metal Nodes (2022)

Metal-organic frameworks (MOFs) are crystalline, 2- and 3-dimensional coordination polymers formed by bonding interactions between metals and multitopic organic ligands. These are typically formed using hard Lewis basic organic ligands with high oxidation state metal ions. The use of low-valent metals as structural elements in MOFs is far less common, despite the widespread use of such metals for catalysis, luminescence, and other applications. This Minireview focuses on recent advances in the field of low-valent MOFs and offers a perspective on the future development of these materials.
Genetic Analysis of Variation in Gene Expression inArabidopsis thaliana (2005)

In Arabidopsis thaliana, significant efforts to determine the extent of genomic variation between phenotypically divergent accessions are under way, but virtually nothing is known about variation at the transcription level. We used microarrays to examine variation in transcript abundance among three inbred lines and two pairs of reciprocal F1 hybrids of the highly self-fertilizing species Arabidopsis. Composite additive genetic effects for gene expression were estimated from pairwise comparisons of the three accessions Columbia (Col), Landsberg erecta (Ler), and Cape Verde Islands (Cvi). For the pair Col and Ler, 27.0% of the 4876 genes exhibited additive genetic effects in their expression (alpha = 0.001) vs. 32.2 and 37.5% for Cvi with Ler and Col, respectively. Significant differential expression ranged from 32.45 down to 1.10 in fold change and typically differed by a factor of 1.56. Maternal or paternal transmission affected only a few genes, suggesting that the reciprocal effects observed in the two crosses analyzed were minimal. Dominance effects were estimated from the comparisons of hybrids with the corresponding midparent value. The percentage of genes showing dominance at the expression level in the F1 hybrids ranged from 6.4 to 21.1% (alpha = 0.001). Breakdown of these numbers of genes according to the magnitude of the dominance ratio revealed heterosis for expression for on average 9% of the genes. Further advances in the genetic analysis of gene expression variation may contribute to a better understanding of its role in affecting quantitative trait variation at the phenotypic level.
Variation in fiber spreading from the human corpus callosum: a statistical study on DT-MRI data (2002)

LTS5
Colorfulness adaptation for real surfaces under wide color gamut illumination (2019)

In the colorfulness adaptation effect, a scene appears desaturated after adapting to the scene rendered with high color-gamut lighting or vice versa. Previous studies have demonstrated this effect for simple stimuli and natural images on a monitor (Mizokami et al., 2012, Ilic et al., 2017). We examined whether the effect also occurs when observing a real object under real illumination. A set of objects were viewed in a light booth equipped with a spectrally tunable light. The illuminant was varied in steps from a blackbody spectrum to a wide gamut spectrum while keeping the mean illuminant color (the chromaticity for a white surface) constant. Observers chose the illuminant so that the color of the objects appeared most natural, after adapting to either the blackbody or the wide-gamut illuminant. Objects included red tomato, a blue doll, a yellow banana, and green adhesive tape. Horizontal illuminance was 150 lx on a desk where the objects were placed. Ten observers with normal color vision were tested. Adaptation to each illuminant caused the objects to appear more natural when the test illumination was shifted toward the adapting spectrum, consistent with a normalization for the adapting spectrum. Similar effects also occurred for objects viewed under real illumination. Our results suggest that color perception can rapidly adapt to changes in the color gamut produced by artificial lighting.
Overview of the Status and Global Strategy for Neonicotinoids (2010)

In recent years, neonicotinoid insecticides have been the fastest growing class of insecticides in modern crop protection, with widespread use against a broad spectrum of sucking and certain chewing pests. As potent agonists, they act selectively on insect nicotinic acetylcholine receptors (nAChRs), their molecular target site. The discovery of neonicotinoids can be considered as a milestone in insecticide research and greatly facilitates the understanding of functional properties of the insect nAChRs. In this context, the crystal structure of the acetylcholine-binding proteins provides the theoretical foundation for designing homology models of the corresponding receptor ligand binding domains within the nAChRs, a useful basis for virtual screening of chemical libraries and rational design of novel insecticides acting on these practically relevant channels. Because of the relatively low risk for nontarget organisms and the environment, the high target specificity of neonicotinoid insecticides, and their versatility in application methods, this important class has to be maintained globally for integrated pest management strategies and insect resistance management programs. Innovative concepts for life-cycle management, jointly with the introduction of generic products, have made neonicotinoids the most important chemical class for the insecticide market.
Ultrasensitive version of nucleic acid sequence-based amplification (NASBA) utilizing a nicking and extension chain reaction system (2021)

Nucleic acid sequence-based amplification (NASBA) is a transcription-based isothermal amplification technique especially designed for the detection of RNA targets. The NASBA basically relies on the linear production of T7 RNA promoter-containing double-stranded DNA (T7DNA), and thus the final amplification efficiency is not sufficiently high enough to achieve ultrasensitive detection. We herein ingeniously integrate a nicking and extension chain reaction system into the NASBA to establish an ultrasensitive version of NASBA, termed Nicking and Extension chain reaction System-Based Amplification (NESBA). By employing a NESBA primer set designed to contain an additional nicking site at the 5' end of a NASBA primer set, the T7DNA is exponentially amplified through continuously repeated nicking and extension chain reaction by the combined activities of nicking endonuclease (NE) and reverse transcriptase (RT). As a consequence, a much larger number of RNA amplicons would be produced through the transcription of the amplified T7DNA, greatly enhancing the final fluorescence signal from the molecular beacon (MB) probe binding to the RNA amplicon. Based on this unique design principle, we successfully identified the target respiratory syncytial virus A (RSV A) genomic RNA (gRNA) down to 1 aM under isothermal conditions, which is 100-fold more sensitive than regular NASBA.
Steps Towards a Theory of Visual Information: Active Perception,\n Signal-to-Symbol Conversion and the Interplay Between Sensing and Control (2011)

This manuscript describes the elements of a theory of information tailored to\ncontrol and decision tasks and specifically to visual data. The concept of\nActionable Information is described, that relates to a notion of information\nchampioned by J. Gibson, and a notion of "complete information" that relates to\nthe minimal sufficient statistics of a complete representation. It is shown\nthat the "actionable information gap" between the two can be reduced by\nexercising control on the sensing process. Thus, senging, control and\ninformation are inextricably tied. This has consequences in the so-called\n"signal-to-symbol barrier" problem, as well as in the analysis and design of\nactive sensing systems. It has ramifications in vision-based control,\nnavigation, 3-D reconstruction and rendering, as well as detection,\nlocalization, recognition and categorization of objects and scenes in live\nvideo.\n This manuscript has been developed from a set of lecture notes for a summer\ncourse at the First International Computer Vision Summer School (ICVSS) in\nScicli, Italy, in July of 2008. They were later expanded and amended for\nsubsequent lectures in the same School in July 2009. Starting on November 1,\n2009, they were further expanded for a special topics course, CS269, taught at\nUCLA in the Spring term of 2010.\n
The energy efficiency of IRAM architectures (1997)

Portable systems demand energy efficiency in order to maximize battery life. IRAM architectures, which combine DRAM and a processor on the same chip in a DRAM process, are more energy efficient than conventional systems. The high density of DRAM permits a much larger amount of memory on-chip than a traditional SRAM cache design in a logic process. This allows most or all IRAM memory accesses to be satisfied on-chip. Thus there is much less need to drive high-capacitance off-chip buses, which contribute significantly to the energy consumption of a system. To quantify this advantage we apply models of energy consumption in DRAM and SRAM memories to results from cache simulations of applications reflective of personal productivity tasks on low power systems. We find that IRAM memory hierarchies consume as little as 22% of the energy consumed by a conventional memory hierarchy for memory-intensive applications, while delivering comparable performance. Furthermore, the energy consumed by a system consisting of an IRAM memory hierarchy combined with an energy efficient CPU core is as little as 40% of that of the same CPU core with a traditional memory hierarchy.
Synthese von Pyridinderivaten aus Perchlorpentadiensäurenitril und Grignard‐Verbindungen (1966)

Abstract In 2‐Stellung alkyl‐ oder arylsubstituierte Tetrachlorpyridine 2 werden aus Perchlor‐pentadien‐(1.3)‐säure‐(5)‐nitril 1 und Grignard‐Verbindungen synthetisiert. Die Oxydation des 2‐Methyl‐ und des 2‐Phenyl‐Derivates liefert Tetrachlor‐α‐picolinsäure 4 .
Estrogen and raloxifene stimulate transforming growth factor-beta 3 gene expression in rat bone: a potential mechanism for estrogen- or raloxifene-mediated bone maintenance. (1996)

Estrogen or raloxifene (LY156758) prevent estrogen deficiency-induced bone loss in animals and humans. We demonstrated in the rat that a 22% reduction in bone mineral density generated by ovariectomy was associated with a 2-fold reduction of transforming growth factor-beta 3 (TGF beta 3) messenger RNA expression in the femur. Administration of 17 beta-estradiol or raloxifene to ovariectomized rats restored both bone mineral density and TGF beta 3 messenger RNA expression in the femur to levels measured in intact animals. In transient transfection assays, the promoter sequence from -38 to + 110 of the human TGF beta 3 gene, which contains no palindromic estrogen response element, was sufficient to mediate 17 beta-estradiol or raloxifene induced-reporter gene expression in presence of the estrogen receptor. Raloxifene activated TGF beta 3 promoter as a full agonist at nanomolar concentrations. In the same cellular system, raloxifene inhibited the estrogen response element-containing vitellogenin promoter expression as a pure estrogen antagonist. In two well characterized osteoclast differentiation models, TGF beta 3 significantly inhibited the differentiation and bone-resorptive activities of murine and avian osteoclasts. These findings suggest that regulation of TGF beta 3 gene expression by raloxifene or estrogen in bone may be an important target to mediate bone maintenance.
Prettier concurrency (2011)

This article presents an extension to the work of Launchbury and Peyton-Jones on the ST monad. Using a novel model for concurrency, called concurrent revisions [3,5], we show how we can use concurrency together with imperative mutable variables, while still being able to safely convert such computations (in the Rev monad) into pure values again. In contrast to many other transaction models, like software transactional memory (STM), concurrent revisions never use rollback and always deterministically resolve conflicts. As a consequence, concurrent revisions integrate well with side-effecting I/O operations. Using deterministic conflict resolution, concurrent revisions can deal well with situations where there are many conflicts between different threads that modify a shared data structure. We demonstrate this by describing a concurrent game with conflicting concurrent tasks.
Improving the robustness of wavelet transform for epoch detection (2002)

This paper investigates (1) the robustness of epoch detection (i.e. identification of glottal closure) by the wavelet transform and (2) the methods to improve its robustness. We achieved a similar identification performance (2% error rate) to earlier investigation using the spline wavelet transform, under Gaussian noise degradation. However, the performance under other types of noise degradation, such as periodic noise (e.g. traffic lights) and short noise (e.g. keyboard noise), is not as robust as before. The scale matching technique could not secure good performance because the spline wavelet has poor recall performance. We explored the use of the Gaussian wavelet transform. Instead of scale matching, a single level is used and the recall of epochs associated with the nearest laryngograph differences by the Gaussian wavelet is about 30% more than by the spline wavelet, across different types of noise degradation. However, the spline wavelet has less false alarm (29% on average) in identification and the peaks correspond well to epoch positions (with less [standard] deviation). We evaluated detection schemes using both scalograms of Gaussian and spline wavelets and achieved improvement of recall (26%), with a relative position consistency of 1.4 ms.
Evaluation of Time Constants Governing the Cathodic Reaction in SOFCs (2006)

The need for power sources has created a lot of interest in fuel cells. SOFCs with LSM and LSCF cathodes and YSZ electrolytes are materials of interest; however, the processes governing the cathodic reactions are not well understood. Impedance spectroscopy is used to evaluate the RC time constant behavior of the various electrochemical steps contributing to the cathodic reaction. This evaluation typically involves separating the various contributions using a circuit element type model. The focus of this work is to use the model parameters to determine kinetic behavior, particularly the time constants for each of the process steps contributing to the overall cathodic reaction. The determined time constants are compared for the various cathode materials tested with the goal of generating a common understanding of the kinetic behavior of the cathodic SOFC reaction.
Monte Carlo studies of directional pair ordering in disordered binary and ternary ferromagnetic BCC crystalline alloys (2007)

Magnetic field annealing can be used to induce uniaxial magnetic anisotropy in ferromagnetic alloys, which is often desirable, for example, to reduce core losses in materials of interest for high frequency inductive components in power conversion applications. An understanding of the compositional dependence of the uniaxial induced anisotropy constant KU is important to develop materials for such applications. In this work, Monte Carlo studies of directional pair ordering in bcc crystalline alloys using the Néel pair model and a Metropolis-type algorithm are reported. The compositional dependence of KU in disordered binary alloys is compared with analytical results and extended to the calculation of KU for ternary alloys. An approximate XB2(1−XB)2 functional dependence of KU is observed for binary alloys, where XB is the atomic fraction of one of the atomic species. For ternary alloys a more complicated functional dependence is observed. These results are used to critically evaluate the potential for increasing KU through ternary alloying additions to binary ferromagnetic alloys.
Structural Analysis of the Effect of a Dual-FLAG Tag on Transthyretin (2020)

Recombinant proteins have increased our knowledge regarding the physiological role of proteins; however, affinity purification tags are often not cleaved prior to analysis, and their effects on protein structure, stability and assembly are often overlooked. In this study, the stabilizing effects of an N-terminus dual-FLAG (FT<sub>2</sub>) tag fusion to transthyretin (TTR), a construct used in previous studies, are investigated using native ion mobility-mass spectrometry (IM-MS). A combination of collision-induced unfolding and variable-temperature electrospray ionization is used to compare gas- and solution-phase stabilities of FT<sub>2</sub>-TTR to wild-type and C-terminal tagged TTR. Despite an increased stability of both gas- and solution-phase FT<sub>2</sub>-TTR, thermal degradation of FT<sub>2</sub>-TTR was observed at elevated temperatures, viz., backbone cleavage occurring between Lys9 and Cys10. This cleavage reaction is consistent with previously reported metalloprotease activity of TTR [Liz et al. 2009] and is suppressed by either metal chelation or excess zinc. This study brings to the fore the effect of affinity tag stabilization of TTR and emphasizes unprecedented detail afforded by native IM-MS to assess structural discrepancies of recombinant proteins from their wild-type counterparts.
Coupling Metal Centers with Linearly Bridging, Delocalized, π‐Bonded Ligands: p‐Phenylenediimido Dimolybdenum Complexes (1988)

Complex fragments having metal centers in high oxidation states can be coupled with the linearly bridging p-phenylenediimido ligand. This is demonstrated by the Mo complex 1, which could be prepared from [MoCl4(thf)2] and p-phenylene diazide. Complex 1 can be reduced stepwise to isolable Mo, Mo, and Mo complexes. Of special interest in connection with the synthesis of new conducting materials is a Mo complex.