gebhart/patrepeval huggingface dataset:
Update in Lung Cancer 2014 (2015)

In the past 2 years, lung cancer research and clinical care have advanced significantly. Advancements in the field have improved outcomes and promise to lead to further reductions in deaths from lung cancer, the leading cause of cancer death worldwide. These advances include identification of new molecular targets for personalized targeted therapy, validation of molecular signatures of lung cancer risk in smokers, progress in lung tumor immunotherapy, and implementation of population-based lung cancer screening with chest computed tomography in the United States. In this review, we highlight recent research in these areas and challenges for the future.
TableMaker: An ad hoc Query Tool for Relational Databases (2008)

This paper discusses an ad hoc query tool for relational databases. Most Web servers hosting biological data limit users to a defined set of search options and output formats that are short of the whole range of options available to users with direct database access. However, to make full use of the wealth of data in the database resource, it is desirable to have an intermediate solution that provides a broad range of flexible query and output options through a Web portal.
Manganese intoxication in the rhesus monkey (1996)

We gave three adult rhesus monkeys seven IV injections of manganese chloride at approximately 1-week intervals. We evaluated neurologic status by serial clinical examinations and performed a levodopa test if the animal developed features of basal ganglia dysfunction. After the animals were killed, we performed neuropathologic, neurochemical, and laser microprobe mass analysis (LAMMA) studies. Two of three animals developed a parkinsonian syndrome characterized by bradykinesia, rigidity, and facial grimacing suggestive of dystonia but not tremor. Neither animal responded to levodopa. Autopsy demonstrated gliosis primarily confined to the globus pallidus (GP) and the substantia nigra pars reticularis (SNr). We detected focal mineral deposits throughout the GP and SNr, particularly in a perivascular distribution. LAMMA studies noted that mineral deposits were primarily comprised of iron and aluminum. The severity of pathologic change correlated with the degree of clinical dysfunction. These studies demonstrate that, in contrast to Parkinson's disease (PD) and MPTP-induced parkinsonism, manganese primarily damages the GP and SNr and relatively spares the nigrostriatal dopaminergic system. Further, the results suggest that Mn-induced parkinsonism can be differentiated from PD and MPTP-induced parkinsonism by the clinical syndrome and response to levodopa. The accumulation of iron and aluminum suggests that iron/aluminum-induced oxidant stress may contribute to the damage associated with Mn toxicity.
Supplementary Methods from The G Protein–Coupled Receptor GPR30 Inhibits Proliferation of Estrogen Receptor–Positive Breast Cancer Cells (2023)

Supplementary Methods from The G Protein–Coupled Receptor GPR30 Inhibits Proliferation of Estrogen Receptor–Positive Breast Cancer Cells
Scatter and attenuation correction in technetium-99m brain SPECT. (1997)

This method was clinically practical and cost-effective for reconstructing quantitative 99mTc brain SPECT images.
Real-Time Adaptive Control of Flow-Induced Cavity Tones (2004)

An adaptive generalized predictive control (GPC) algorithm was formulated and applied to the cavity flow-tone problem. The algorithm employs gradient descent to update the GPC coefficients at each time step. The adaptive control algorithm demonstrated multiple Rossiter mode suppression at fixed Mach numbers ranging from 0.275 to 0.38. The algorithm was also able t o maintain suppression of multiple cavity tones as the freestream Mach number was varied over a modest range (0.275 to 0.29). Controller performance was evaluated with a measure of output disturbance rejection and an input sensitivity transfer function. The results suggest that disturbances entering the cavity flow are colocated with the control input at the cavity leading edge. In that case, only tonal components of the cavity wall-pressure fluctuations can be suppressed and arbitrary broadband pressure reduction is not possible. In the control-algorithm development, the cavity dynamics are treated as linear and time invariant (LTI) for a fixed Mach number. The experimental results lend support this treatment.
Investigation of processing performance and requirements for next generation lithography cluster tools (2011)

In this paper we summarize our investigations into processing capability on the CLEAN TRACK<sup>TM</sup> LITHIUS Pro<sup>TM</sup> -<i>i</i> & TWINSCAN<sup>TM</sup> NXT:1950i litho cluster. Process performance with regards to critical dimension (CD) uniformity and defectivity are investigated to confirm adherence to ITRS<sup>1</sup> roadmaps specifications. Additionally, a study of wafer backside particle contamination is performed to understand the implications towards processing. As wafer stage chuck cleaning on the scanner will require considerable down time, this study is necessary to understand the requirements for manufacturability. Previous work from our collaboration succeeded in a processing improvement of over 80% in across wafer CD variation by implementing the newest post exposure bake (PEB) plate design<sup>2</sup> and optimized developer process. With regards to defectivity, the use of the advanced defect reduction (ADR) process with an optimized bevel cut of the resist allowed the use of a high contact angle material process which is required for optimal immersion hood performance. In this work, further optimization of the process with consideration of the design concept of the TWINSCAN<sup>TM</sup> NXT:1950i and hardware modifications on the CLEAN TRACK<sup>TM</sup> LITHIUS Pro<sup>TM</sup> -<i>i</i> will be performed. From this investigation, it is expected to understand the process capability of 38nm CD uniformity using novel developer hardware. Additionally, the defectivity challenges for processing with higher scan speeds in combination with the hydrophobicity of the coating materials and edge cut strategy will be clarified. Initial evaluation results are analyzed to understand the correlation of various types and densities of contaminates on the backside of the wafer to the formation of wafer stage chuck focus spots (FS). Focus spots are a localized irregular focus and leveling height.
Development of “L-Shaped” Rotary Voice Coil Motor Actuator for Ultra Slim Optical Disk Drive Using Integrated Design Method based on Coupled-Field Analysis (2007)

In this paper, we propose an "L-shaped" rotary voice coil motor (VCM) actuator for an ultra slim optical disk drive (ODD) with a CF II card size using the integrated design method that integrates coupled-field analysis and design methods.
Covering All the Bases: Complementary MR1 Antigen Presentation Pathways Sample Diverse Antigens and Intracellular Compartments (2020)

The ubiquitously expressed, monomorphic MHC class Ib molecule MHC class I-related protein 1 (MR1) presents microbial metabolites to mucosal-associated invariant T (MAIT) cells. However, recent work demonstrates that both the ligands bound by MR1 and the T cells restricted by it are more diverse than originally thought. It is becoming increasingly clear that MR1 is capable of presenting a remarkable variety of both microbial and non-microbial small molecule antigens to a diverse group of MR1-restricted T cells (MR1Ts) and that the antigen presentation pathway differs between exogenously delivered antigen and intracellular microbial infection. These distinct antigen presentation pathways suggest that MR1 shares features of both MHC class I and MHC class II antigen presentation, enabling it to sample diverse intracellular compartments and capture antigen of both intracellular and extracellular origin. Here, we review recent developments and new insights into the cellular mechanisms of MR1-dependent antigen presentation with a focus on microbial MR1T cell antigens.
(Invited) Chemically Modified Two-Dimensional Nanoelectronic Heterostructures (2016)

The outstanding properties of graphene have been established on pristine samples in idealized conditions. However, for most applications, graphene needs to be chemically functionalized in a manner that either preserves its intrinsic properties or modifies its properties in a manner that enhances functionality. Towards these ends, several noncovalent chemistries have been demonstrated and characterized at the molecular scale with ultra-high vacuum scanning tunneling microscopy including 3,4,9,10-perylenetetracarboxylic dianhydride and 10,12 pentacosadiynoic acid. These self-assembled monolayers are shown to be effective atomic layer deposition seeding layers for dielectrics (e.g., Al 2 O 3 , HfO 2 , and ZnO), which allows for substantial improvements in the uniformity and reliability of metal-oxide-graphene electronic devices. On the other hand, covalent modification schemes based on free radical chemistries allow for more fundamental changes to the electronic and chemical properties of graphene. In particular, atomic oxygen has been established as an effective method for homogeneously and reversibly functionalizing graphene with epoxide groups. In addition to chemically doping graphene, epoxidation yields local modification of the graphene bandstructure and provides pathways for further chemical functionalization, thereby expanding the suite of chemically modified graphene heterostructures. Finally, this talk will conclude with ongoing work in our laboratory to extend the chemical modification strategies for graphene to other two-dimensional materials including ultrathin silicon [1,2], black phosphorus [3,4], and transition metal dichalcogenides [5]. [1] A. J. Mannix, B. Kiraly, B. L. Fisher, M. C. Hersam, and N. P. Guisinger, “Silicon growth at the two-dimensional limit on Ag(111),” ACS Nano , 8 , 7538 (2014). [2] B. Kiraly, A. J. Mannix, M. C. Hersam, and N. P. Guisinger, “Graphene-silicon heterostructures at the two-dimensional limit,” Chem. Mater. , 27 , 6085 (2015). [3] J. D. Wood, S. A. Wells, D. Jariwala, K.-S. Chen, E. Cho, V. K. Sangwan, X. Liu, L. J. Lauhon, T. J. Marks, and M. C. Hersam, “Effective passivation of exfoliated black phosphorus transistors against ambient degradation,” Nano Lett. , 14 , 6964 (2014). [4] X. Liu, J. D. Wood, K.-S. Chen, E. Cho, and M. C. Hersam, “In situ thermal decomposition of exfoliated two-dimensional black phosphorus,” J. Phys. Chem. Lett. , 6 , 773 (2015). [5] X. Liu, I. Balla, H. Bergeron, G. P. Campbell, M. J. Bedzyk, and M. C. Hersam, “Rotationally commensurate growth of MoS 2 on epitaxial graphene,” ACS Nano , DOI: 10.1021/acsnano.5b06398 (2015).
Behaviours and attitudes influencing treatment decisions for menopausal symptoms in five European countries (2016)

Menopausal symptoms are common, persistent, and bothersome, but many fail to seek treatment. Sources and types of treatment vary among age groups and countries. Education regarding women's attitudes toward treatment should be provided to those physicians who treat menopausal symptoms in each country.
Neural Network Segmentation of Cell Ultrastructure Using Incomplete\n Annotation (2020)

The Pancreatic beta cell is an important target in diabetes research. For\nscalable modeling of beta cell ultrastructure, we investigate automatic\nsegmentation of whole cell imaging data acquired through soft X-ray tomography.\nDuring the course of the study, both complete and partial ultrastructure\nannotations were produced manually for different subsets of the data. To more\neffectively use existing annotations, we propose a method that enables the\napplication of partially labeled data for full label segmentation. For\nexperimental validation, we apply our method to train a convolutional neural\nnetwork with a set of 12 fully annotated data and 12 partially annotated data\nand show promising improvement over standard training that uses fully annotated\ndata alone.\n
Pre‐ and postoperative MR brain imaging with automatic planning and scanning software in tumor patients: An intraindividual comparative study at 3 Tesla (2009)

Automatic planning and scanning before and after brain surgery yields robust results in most of the patients with substantial shape deviations. The dimensions of necessary geometry corrections are predominantly small. These results are promising to minimize interscan variability in longitudinal studies.
Gate oxide thickness dependence of edge charge trapping in nmos transistors caused by charge injection under constant-current stress (2003)

This brief reports a study of charge injection-induced edge charge trapping in the gate oxide overlapping the drain extension which has an impact on the drain leakage current. The edge charge trapping is determined for the gate oxide thickness of 6.5, 3.9, and 2.0 nm by using a simple approach to analyze the change of the band-to-band tunneling current measured with a three-terminal gate-controlled-diode configuration. The edge charge trapping has a strong dependence on the gate oxide thickness, and it is different from the charge trapping in the oxide over the channel. A plausible explanation for both the oxide thickness dependence of the edge charge trapping and the difference between the edge charge trapping and the charge trapping over the channel is presented.
An experimental and computational study of blunt carotid artery injury. (2006)

A carotid artery dissection begins as a tear or defect of the intimal lining of the artery, and can lead to luminal occlusion and ultimately cerebral ischemia. Our aim is to conduct an organ level validation of a finite element model of the carotid artery using an experiment designed to elicit internal layer failure within fluid-filled carotid artery samples. A 2.4-kg beveled guillotine is dropped from three heights (0.3, 0.5 and 0.7 m) onto fluid-filled porcine carotid arteries and resulting damage is recorded. These events are modeled using finite element analysis. Stress, strain and strain rate are correlated to experimental outcome. Internal layer damage is reported in half of the experiments, with damage occurring with 100% frequency at a drop height of 0.7 m. Simulations of this experiment result in maximum principal stress and strain values of 1.43 MPa and 46.2% respectively. The strain level predicted by the model for this impact scenario approaches the strain to intimal failure level for porcine arteries found in the literature. The results of this study represent an important step in validating this finite element carotid artery model at the organ level.
Structure-Based Discovery of Inhibitors of the SARS-CoV-2 Nsp14 N7-Methyltransferase (2023)

An under-explored target for SARS-CoV-2 is the <i>S</i>-adenosyl methionine (SAM)-dependent methyltransferase Nsp14, which methylates the N7-guanosine of viral RNA at the 5'-end, allowing the virus to evade host immune response. We sought new Nsp14 inhibitors with three large library docking strategies. First, up to 1.1 billion lead-like molecules were docked against the enzyme's SAM site, leading to three inhibitors with IC<sub>50</sub> values from 6 to 50 μM. Second, docking a library of 16 million fragments revealed 9 new inhibitors with IC<sub>50</sub> values from 12 to 341 μM. Third, docking a library of 25 million electrophiles to covalently modify Cys387 revealed 7 inhibitors with IC<sub>50</sub> values from 3.5 to 39 μM. Overall, 32 inhibitors encompassing 11 chemotypes had IC<sub>50</sub> values < 50 μM and 5 inhibitors in 4 chemotypes had IC<sub>50</sub> values < 10 μM. These molecules are among the first non-SAM-like inhibitors of Nsp14, providing starting points for future optimization.
Analysis of telomere lengths in human corneal endothelial cells from donors of different ages. (1998)

Human corneal endothelial cells have long telomeres throughout life. Their limited replicative ability does not appear to result from critically short telomere lengths.
Z-Ion (2016)

This document contains recommendations for terminology in mass spectrometry. Development of standard terms dates back to 1974 when the IUPAC Commission on Analytical Nomenclature issued recommendations on mass spectrometry terms and definitions. In 1978, the IUPAC Commission on Molecular Structure and Spectroscopy updated and extended the recommendations and made further recommendations regarding symbols, acronyms, and abbreviations. The IUPAC Physical Chemistry Division Commission on Molecular Structure and Spectroscopy’s Subcommittee on Mass Spectroscopy revised the recommended terms in 1991 and appended terms relating to vacuum technology. Some additional terms related to tandem mass spectrometry were added in 1993 and accelerator mass spectrometry in 1994. Owing to the rapid expansion of the field in the intervening years, particularly in mass spectrometry of biomolecules, a further revision of the recommendations has become necessary. This document contains a comprehensive revision of mass spectrometry terminology that represents the current consensus of the mass spectrometry community.
The APP300 access network processor (2006)

This article consists of a collection of slides from the author's conference presentation on Agere's APP300 Access Network Processor. Some of the specific topics discussed include: targeted markets for the processor line; data communications capabilities of the APP300 processor; the company approach to marketing the product line; APP300 block diagram; unified memory architecture; classifier and policing engines, features versus benefits; traffic management capabilities; scheduling hierarchies; and processing subsystems.
Author response: GREB1 amplifies androgen receptor output in human prostate cancer and contributes to antiandrogen resistance (2018)

Prostate cancer cells maintain heterogeneous androgen receptor transcriptional activity through upregulation of AR-regulated coactivator GREB1, and cells with high activity rapidly develop resistance to antiandrogen therapy in a GREB1-dependent manner.
Similarity search in high-dimensional datasets (2005)

The problem of finding "similar" multimedia objects is a central one, and a popular approach is to represent objects as vectors in a high-dimensional space, and to build a spatial index over a collection of such vectors in order to retrieve the "nearest neighbors" of a query object. There are some fundamental assumptions involved here. First, that the user's notion of similarity can be captured by distance in the space that the vectors are embedded, and second, that nearest neighbors can be efficiently retrieved. In this talk, we discuss these assumptions, based on our experience with the PiQ image database project, carried out at the University of Wisconsin-Madison, and some subsequent work.We will first present a brief overview of the PiQ system and its goal of identifying the DBMS infrastructure required to support image databases, and discuss the role of similarity and nearest-neighbor queries in content-based querying. Next, we consider when the notion of "nearest neighbor" is well-defined in high-dimensional spaces, and when efficient indexing is feasible. The goal is not to suggest that indexing high-dimensional data is impossible, although our results here are mainly negative. Rather, we seek to identify the conditions under which effective indexing and retrieval techniques are feasible, and to identify the key difficulties that must be overcome. Finally, we present some indexing techniques to retrieve nearest neighbors under appropriate conditions, highlighting the role played by redundancy and approximation.
Abstract 41: Synthesis And Pharmacological Validation Of Novel Neuroprotective Purinergic Receptor P2X4 Antagonists For The Treatment Of Ischemic Stroke (2023)

Background and Purpose: Identification of a novel treatment for ischemic stroke is urgently needed. We previously showed that genetic deletion as well as short term pharmacological inhibition of P2X4R, a purinergic receptor for adenosine triphosphate ATP, provides acute neuroprotection and thus can be potential drug targets to treat ischemic stroke. Here we synthesized and pharmacologically validated those experimental drugs for the treatment of ischemic stroke. Methods: We first performed the P2X4 receptor structure activity (SAR) relationship based on known heterocyclic antagonist P2X4 antagonists including NP-1815-PX Following extensive modification of the reported synthetic route, we synthesized several analogues that maintained or enhanced antagonist affinity. We used [Ca 2+ ] i influx assay in P2X4R overexpressing human HEK cells to identify potent and specific P2X4R antagonist. Two most potent leads (MRS4719 and 4596 given subcutaneously for 3 days post stroke) were then tested for their neuroprotective activity using middle cerebral artery occlusion (MCAo) model of ischemic stroke (60 min MCAo followed by 3 days of reperfusion) using both sexes of young and aged mice. MRS4719 was also tested in human primary monocyte derived macrophage obtained from the blood of de-identified aged healthy subjects (55±10 years). Results: Analogues MRS 4719 and MRS4596 were most potent at human (h) P2X4R (IC 50 0.503 and 1.38 μM, respectively), and were highly selective versus hP2X1R, hP2X2/3R, hP2X3R). Both MRS 4719 and MRS 4596 showed neuroprotective effects after 3 days of ischemic stroke in a dose dependent manner in young mice (8-12 weeks old). Optimal dose of MRS4719 (1.5 mg/kg/day) also significantly reduced infarct volume (59.6±5.3 vs. 27.47±10.23 mm 3 ; p&lt;0.05) in middle-aged mice (11-12 months). MRS 4719 showed learning and memory enhancing activity when measured after 4 weeks of stroke. MRS 4719 inhibited ATP-induced [Ca 2+ ] i influx in primary human monocyte-derived macrophages, consistent with its blocking effect at endogenously expressed P2X4R. Conclusions: This study indicates MRS4719 is a potent P2X4R antagonist and has translational potential for the treating of ischemic stroke across the age.
Degradation of Ursolic Acid, a Major Component of Apple Wax, by a Pseudomonad Isolated from Soil (1969)

SUMMARY A Pseudomonas sp. isolated from orchard soil utilized ursolic acid (C30H48O3), a major component of apple wax, as a sole source of carbon. It evolved 14CO2 from [14C]ursolic acid and incorporated the label into all usual cell constituents; it formed a labelled polar metabolite of ursolic acid. Orchard soil thus contains at least one organism which is able to degrade the terpenes of the cuticular wax of plants.
Synthesis and characterization of a stable poly(iminomethylene) with pendant phenoxyl radicals (1991)

Poly(4-hydroxy-3,5-diphenyl isocyanide) was prepd. and oxidized to give the corresponding stable 4-oxyl radical. Magnetic susceptibility measurements indicated no evidence for ferromagnetism or any other short-range ordering among unpaired spins at 77-320 K for the polymer radical. A spin d. of 0.8 spin/repeating unit was measured. ESR spectroscopy indicated that the radical was a paramagnet at both 4 and 320 K. [on SciFinder (R)]