gebhart/patrepeval huggingface dataset:
Fundamental scaling laws for the direct-write chemical vapor deposition of nanoscale features: modeling mass transport around a translating nanonozzle (2019)

The nanometer placement of nanomaterials, such as nanoribbons and nanotubes, at a specific pitch and orientation on a surface, remains an unsolved fundamental problem in nanotechnology. In this work, we introduce and analyze the concept of a direct-write chemical vapor deposition (CVD) system that enables the in-place synthesis of such structures with control over orientation and characteristic features. A nanometer scale pore or conduit, called the nanonozzle, delivers precursor gases for CVD locally on a substrate, with spatial translation of either the nozzle or the substrate to enable a novel direct write (DW) tool. We analyze the nozzle under conditions where it delivers reactants to a substrate while translating at a constant velocity over the surface at a fixed reaction temperature. We formulate and solve a multi-phase three-dimensional reaction and diffusion model of the direct-write operation, and evaluate specific analytically-solvable limits to determine the allowable operating conditions, including pore dimensions, reactant flow rates, and nozzle translation speed. A Buckingham Π analysis identifies six dimensionless quantities crucial for the design and operation of the direct-write synthesis process. Importantly, we derive and validate what we call the ribbon extension inequality that brackets the allowable nozzle velocity relative to the CVD growth rate - a key constraint to enabling direct-write operation. Lastly, we include a practical analysis using attainable values towards the experimental design of such a system, building the nozzle around a commercially available near-field scanning optical microscopy (NSOM) tip as a feasible example.
A ring-shaped EMG measurement system for applying to user interface (2004)

This paper proposes a ring-shaped EMG measurement system to be worn on one or more fingers for a new user interface that relies on EMG measurements. A preamplifier is mounted on each electrode to suppress the effect of noise. The system is truly wearable since the main amplifier is designed to be worn on the wrist. The proposed EMG measurement system is implemented and evaluated. The experiments confirm that the proposed electrode is superior to conventional electrodes in terms of stability and usability while offering excellent long term performance. The effectiveness of the proposed electrode system is confirmed by the test in which the interface realizes highly accurate speech recognition via EMG.
Gel Robots : Turning over Motion Generation of Electroactive Polymer Gel by Translation of Spatially Varying Electric Fields (2003)

アレイ状に配置する複数電極に電圧を印加して空間的に分布する電場を生成し, 負の電極の真下に短冊状ゲルを配置すると, ゲルは凸向きに屈曲する。生成電場をタイミングよく平行移動することで, 反転運動を生成する手法を提案する。
Therapeutic Guide for mTOuRing through the Braided Kidney Cancer Genomic River (2016)

mTORC1 inhibitors were first approved for the use in metastatic kidney cancer. However, observed treatment benefit was highly heterogeneous among patients. Through case-based cancer genomic sequencing of therapeutic outliers, we can begin to appreciate the convergent evolution of given cancer pathways/phenotypes beyond genes in kidney cancer, like a braided river. Clin Cancer Res; 22(10); 2320-2. ©2016 AACRSee related article by Kwiatkowski et al., p. 2445.
Snapshots used in "Correlator Convolutional Neural Networks: An Interpretable Architecture for Image-like Quantum Matter Data" (2021)

Snapshots used to train the models examined in the main text and supplementary material of "Correlator Convolutional Neural Networks: An Interpretable Architecture for Image-like Quantum Matter Data".
Novel RNA m <sup>6</sup> A methyltransferase METTL16 inhibitors (2023)

Abstract The overexpression of RNA 6-N-methyladenosine (m 6 A) methyltransferase METTL16 has oncogenic role in the case of several cancer types, including leukemia, but efficient small-molecule inhibitors are not available. Initially identified by high-throughput virtual screening of the ZINC15 database in vivo subset, but then confirmed by measuring catalytic activity, two nanomolar-active METTL16 inhibitors, compounds 1 (IC 50 = 25.82 ± 17.19 nM) and 2 (IC 50 = 60.91 ± 2.75 nM) were found. The inhibitory activity of the compounds was measured using the m 6 A antibody-based ELISA assay. We also present the results on the effect of these inhibitors on the viability of promyeloblast HL-60 and lymphoblast CCRF-CEM leukemia cell lines. In unstressed growth conditions, both identified METTL16 inhibitors reduced the viability of HL-60 cells by up to 40%. The effect on the viability of CCRF-CEM cells was smaller with no dose dependency observed. In parallel, the level of the m 6 A as compared to unmodified adenosine in the HL-60 cell mRNAs was significantly reduced by the inhibitor 1 . Collectively, we herein demonstrate novel METTL16 inhibitors that exert tumor cell-lineage-selective antiproliferative effects.
Illustration of microengraving. (2015)

&lt;p&gt;Arrays of nanowells with dimensions of 50 µm×50 µm×50 µm were used for microengraving. Spleen or cervical lymph nodes cells were loaded in the nanowells. Cells in the nanowells were imaged using an automated epifluorescence microscope. Micrograving is performed by hybridizing nanowells with capture slides containing anti-mouse Ig for 2 hrs at 37°C with 5% CO&lt;sub&gt;2&lt;/sub&gt;. After incubation, nanowells containing intact live cells and capture slides were separated. A mixture of antibodies containing IgG1-Alexa Fluor 488, B6 SG lysate-Alexa Fluor 594 and &lt;i&gt;Aec1Aec2&lt;/i&gt; SG lysate-Alexa Fluor 555 were added to the capture slides. Micrographs of microarrays were generating by scanning using a Genepix 4200AL microarray scanner.&lt;/p&gt;
Once daily clarithromycin extended-release vs twice-daily amoxicillin/clavulanate in patients with acute bacterial sinusitis: a randomized, investigator-blinded study (2004)

In this multinational population of patients with acute bacterial sinusitis, clarithromycin ER was comparable, and for selected measures superior, to amoxicillin/clavulanate based on clinical, bacteriological, and radiological responses as well as quality of life measures, satisfaction with antibiotic therapy, and health care resource utilization.
Comparison among different insulin sensitivity indices in obese patients (2003)

Indices of IS based on fasting glucose and insulin show a greater association with diabetes, but not with other abnormalities related to insulin resistance, when compared with fasting insulin levels. Indices based on post-load glucose and insulin do not offer any advantage over those based on fasting values.
Bitvector-aware Query Optimization for Decision Support Queries (2020)

Bitvector filtering is an important query processing technique that can significantly reduce the cost of execution, especially for complex decision support queries with multiple joins. Despite its wide application, however, its implication to query optimization is not well understood. In this work, we study how bitvector filters impact query optimization. We show that incorporating bitvector filters into query optimization straightforwardly can increase the plan space complexity by an exponential factor in the number of relations in the query. We analyze the plans with bitvector filters for star and snowflake queries in the plan space of right deep trees without cross products. Surprisingly, with some simplifying assumptions, we prove that, the plan of the minimal cost with bitvector filters can be found from a linear number of plans in the number of relations in the query. This greatly reduces the plan space complexity for such queries from exponential to linear. Motivated by our analysis, we propose an algorithm that accounts for the impact of bitvector filters in query optimization. Our algorithm optimizes the join order for an arbitrary decision support query by choosing from a linear number of candidate plans in the number of relations in the query. We implement our algorithm in a commercial database DBMS-X as a transformation rule. Our evaluation on both industry standard benchmarks and customer workload shows that, compared with DBMS-X, our technique reduces the total CPU execution time by 22%-64% for the workloads, with up to two orders of magnitude reduction in CPU execution time for individual queries.
Identification of a Human Airway Epithelial Cell Subpopulation with Altered Biophysical, Molecular, and Metastatic Properties (2017)

Lung cancers are documented to have remarkable intratumoral genetic heterogeneity. However, little is known about the heterogeneity of biophysical properties, such as cell motility, and its relationship to early disease pathogenesis and micrometastatic dissemination. In this study, we identified and selected a subpopulation of highly migratory premalignant airway epithelial cells that were observed to migrate through microscale constrictions at up to 100-fold the rate of the unselected immortalized epithelial cell lines. This enhanced migratory capacity was found to be Rac1-dependent and heritable, as evidenced by maintenance of the phenotype through multiple cell divisions continuing more than 8 weeks after selection. The morphology of this lung epithelial subpopulation was characterized by increased cell protrusion intensity. In a murine model of micrometastatic seeding and pulmonary colonization, the motility-selected premalignant cells exhibit both enhanced survival in short-term assays and enhanced outgrowth of premalignant lesions in longer-term assays, thus overcoming important aspects of "metastatic inefficiency." Overall, our findings indicate that among immortalized premalignant airway epithelial cell lines, subpopulations with heritable motility-related biophysical properties exist, and these may explain micrometastatic seeding occurring early in the pathogenesis of lung cancer. Understanding, targeting, and preventing these critical biophysical traits and their underlying molecular mechanisms may provide a new approach to prevent metastatic behavior. <i>Cancer Prev Res; 10(9); 514-24. ©2017 AACR</i><i>See related editorial by Hynds and Janes, p. 491</i>.
Blood and Urine Markers for Ovarian Cancer: A Comprehensive Review (2004)

Kathryn L. Terrya, Patrick M. Slussb, Steven J. Skatesc,d, Samuel C. Mokd, Bin Yed, Allison F. Vitonisa and Daniel W. Cramera Ob-Gyn Center Epidemiology Center, Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women’s Hospital, Boston, MA, USA Reproductive Endocrinology Unit Laboratory, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA Biostatistics Center, Massachusetts General Hospital, Boston, MA, USA Laboratory of Gynecologic Oncology, Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women’s Hospital, Boston, MA, USA
&lt;title&gt;Integrated, dynamic machine vision system with virtual high resolution&lt;/title&gt; (1993)

A novel active vision system for CIM production and inspection applications has been developed in the framework of ESPRIT II project No. 5194 (CIVIS). The system consists of a unique, integrated combination of novel components: camera head, data acquisition electronics, a custom digital image processor, control hardware and a commercial framestore, all under the direction of control and processing software on a PC-486 platform. The camera head incorporates a fast zoom lens in combination with a pan/tilt mirror system, allowing region-of-interest acquisition. The special 256 X 256 MOS image sensor offers programmable resolution and random pixel access. The unique combination of optics, optomechanics and versatile image sensor has a high `virtual resolution,' corresponding to more than 1k X 1k pixels but without the overhead of a high pixel transfer rate. The fast computation of the algorithm employed for the fractal inspection of surfaces is realized with an unusual combination of an electrically switchable hologram (for performing all linear operations at the speed of light in the optical domain), a module-based digital processor and the host computer. In this way, active vision for the inspection of concrete tile surfaces has been implemented by acquiring only relevant image data and elegantly processing them in the most appropriate domain.
HDTV scan converter (2005)

A hardware implementation of the video scan converter for a Grand Alliance high definition television (GA-HDTV) system is described.
Entangling one polariton with a photon: effect of interactions on a single-polariton quantum state (2016)

Polaritons are quasi-particles originating from the coupling of light with matter that demonstrated quantum phenomena at the many-particle mesoscopic level, such as BEC and superfluidity. A highly sought and long-time missing feature of polaritons is a genuine quantum manifestation of their dynamics at the single-particle level. Although they are conceptually perceived as entangled states and theoretical proposals abound for an explicit manifestation of their single-particle properties, so far their behaviour has remained fully accountable for by classical and mean-field theories. In this Article, we report the first experimental demonstration of a genuinely-quantum manifestation of microcavity polaritons, by swapping, in a two-photon entangled state generated by parametric down-conversion, a photon for a polariton. Furthermore, we show how single polaritons are affected by polariton-polariton interactions in a propaedeutic demonstration of their qualities for quantum information applications.
Integrated polymer photonic RF phase shifters for optically controlled beam forming systems (2003)

We have demonstrated integrated polymer photonic RF phase shifter arrays with a novel balanced design, new symmetric mode configurations and a simplified fabrication procedure, which is capable of removing conventional drawbacks in this type of phase shifter architecture. These devices showed four independent highly linear RF phase outputs and negligible RF power fluctuation at the modulation frequency of 20 GHz.
What is it like to program with artificial intelligence? (2022)

Large language models, such as OpenAI's codex and Deepmind's AlphaCode, can generate code to solve a variety of problems expressed in natural language. This technology has already been commercialised in at least one widely-used programming editor extension: GitHub Copilot. In this paper, we explore how programming with large language models (LLM-assisted programming) is similar to, and differs from, prior conceptualisations of programmer assistance. We draw upon publicly available experience reports of LLM-assisted programming, as well as prior usability and design studies. We find that while LLM-assisted programming shares some properties of compilation, pair programming, and programming via search and reuse, there are fundamental differences both in the technical possibilities as well as the practical experience. Thus, LLM-assisted programming ought to be viewed as a new way of programming with its own distinct properties and challenges. Finally, we draw upon observations from a user study in which non-expert end user programmers use LLM-assisted tools for solving data tasks in spreadsheets. We discuss the issues that might arise, and open research challenges, in applying large language models to end-user programming, particularly with users who have little or no programming expertise.
Supplementary data and materials from Reprogramming of Glucose Metabolism by Zerumbone Suppresses Hepatocarcinogenesis (2023)

&lt;p&gt;Fig. S1-S11, Tables S1-S2 and primer sequences&lt;/p&gt;
Skeletal cell YAP and TAZ combinatorially promote bone development (2018)

The functions of the paralogous transcriptional coactivators Yes-associated protein (YAP) and transcriptional coactivator with PDZ-binding motif (TAZ) in bone are controversial. Each has been observed to promote or inhibit osteogenesis in vitro, with reports of both equivalent and divergent functions. Their combinatorial roles in bone physiology are unknown. We report that combinatorial YAP/TAZ deletion from skeletal lineage cells, using Osterix-Cre, caused an osteogenesis imperfecta-like phenotype with severity dependent on allele dose and greater phenotypic expressivity with homozygous TAZ vs. YAP ablation. YAP/TAZ deletion decreased bone accrual and reduced intrinsic bone material properties through impaired collagen content and organization. These structural and material defects produced spontaneous fractures, particularly in mice with homozygous TAZ deletion and caused neonatal lethality in dual homozygous knockouts. At the cellular level in vivo, YAP/TAZ ablation reduced osteoblast activity and increased osteoclast activity, in an allele dose-dependent manner, impairing bone accrual and remodeling. Transcriptionally, YAP/TAZ deletion and small-molecule inhibition of YAP/TAZ interaction with the transcriptional coeffector TEAD reduced osteogenic and collagen-related gene expression, both in vivo and in vitro. These data demonstrate that YAP and TAZ combinatorially promote bone development through regulation of osteoblast activity, matrix quality, and osteoclastic remodeling.-Kegelman, C. D., Mason, D. E., Dawahare, J. H., Horan, D. J., Vigil, G. D., Howard, S. S., Robling, A. G., Bellido, T. M., Boerckel, J. D. Skeletal cell YAP and TAZ combinatorially promote bone development.
Understanding a Value Chain in Health Care (2015)

As the US health care system transitions toward a value-based system, providers and health care organizations will have to closely scrutinize their current processes of care. To do this, a value chain analysis can be performed to ensure that only the most efficient steps are followed in patient care. Ultimately this will produce a higher quality or equal quality product for less cost by eliminating wasteful steps along the way.
Comparison between CFG filtering techniques for LTAG and HPSG (2003)

An empirical comparison of CFG filtering techniques for LTAG and HPSG is presented. We demonstrate that an approximation of HPSG produces a more effective CFG filter than that of LTAG. We also investigate the reason for that difference.
Host Microarray Molecular Signature and Serologic Evaluation of Stages of <i>Pseudomonas aeruginosa</i> Infection in Cystic Fibrosis (2014)

Background: Cystic fibrosis (CF) is a genetic disorder caused by mutations in the CF transmembrane regulator gene (CFTR); lung disease is characterized by chronic infection by Pseudomonas aeruginosa, the major cause of morbidity and mortality in patients with CF. However, oropharyngeal cultures for P. aeruginosa in young children result in poor specificity for lower airway infection. We used a novel approach to generate genomewide expression profiles to identify markers for P. aeruginosa infection and CF disease severity. Transcription was induced in healthy unrelated peripheral blood mononuclear cells through coculture with autologous serum (self-baseline control), allogeneic serums (healthy unrelated controls), and serums from patients with CF.

Methodology: All CF diagnoses included sweat chloride levels greater than or equal to 60 mEq/L and/or two CFTR mutations. We performed various ELISAs against 192 serum samples (43 individuals sampled over 15 years) and comparative cultures. Concurrently, we completed expression profiling of RNA (HU133 plus 2.0 array; Affymetrix, Santa Clara, CA) from coculture of peripheral blood mononuclear cells with the serum of patients with CF, who possessed increasing degrees of colonization with P. aeruginosa. Differentially expressed probe sets were defined as those possessing a false discovery rate less than 10% and |log2 ratio| greater than 0.5 among comparison groups.

Results: Our ELISA data indicated that the host response to P. aeruginosa infection increased over time, suggesting that serology to P. aeruginosa may help determine initial airway pathology. Comparison of array signatures performed before and after seroconversion identified several hundred unique genes; the most significant differences in gene expression included host genes involved with airway defense, antigen presentation, and transcription.

Conclusions: Our methodology consistently identified a small number of genes that were unique to patients with CF or to patients with CF with initial P. aeruginosa infection conversion. These genes merit investigation as active participants in the function of the lung microbiome and may serve as therapeutic targets for P. aeruginosa infection in CF.
Water Oxidation Catalyst via Heterogenization of Iridium Oxides on Silica: A Polyamine-Mediated Route To Achieve Activity and Stability (2016)

Heterogenization of nanostructured iridium-based catalysts to simultaneously achieve activity and stability in the catalytic water oxidation with cerium ammonium nitrate (CAN) as the oxidant is reported herein. We demonstrate that a polyamine-mediated assembly process to disperse iridium species on mesoporous silica spheres facilitates the fabrication of nanosized iridium oxides under optimal thermal treatment. From comprehensive morphological and electronic structure studies including electron microscopy, UV–vis spectroscopy, XANES, and EXAFS, we show that the influence of polyamine is crucial in stabilizing catalytically active iridium oxides in the mesoporous silica matrix. While the functionalization of the silica surface with polyamine facilitates interaction with the negatively charged iridium precursor, the presence of polyamine further enables control of the dispersion and crystallization of the generated iridium oxides during the thermal treatment at 573 K. As a consequence, the catalyst exhibits enhanced activity with higher TON along with desirable stability to allow it to be recycled while keeping the activity intact. The activity and stability of the synthesized catalyst in comparison with those of IrCl3 and IrO2 reveal that balancing between the dispersion and crystallization of iridium oxides is crucial in heterogenization of the catalyst.