gebhart/patrepeval huggingface dataset:
Motion in casual InfoVis and the interrelation between personality, performance, and preference (2009)

Abstract—Current real-world casual information visualization systems use motion to presumably increase system appeal and repeated use. Despite empirical evidence suggesting that motion is distracting and not particularly good for data encoding, its continued use may indicate benefits independent of traditional utility measures. We present two experiments designed to highlight differences and disparities between task performance, perceived system utility, and subject preference for static and moving glyphs. A music library visualization provided a casual, practical, nuanced, and pertinent domain application. Song glyphs represented beats per minute and beat strength using a line encircling the glyph. Beat encodings used one of four methods: a static sinusoidal pattern (static), an oscillating movement pattern (motion), an oscillating sinusoidal line (redundant), and a sinusoidal line that moves to the currently playing song (extraneous). Subjects first performed a pair-wise glyph comparison task to identify conditional differences in speed and accuracy. Then, a more realistic playlist generation task was performed using these beat encodings to explore opinions and behavioral patterns using a qualitative approach. Our results show clear performance decreases associated with motion use in the comparison task. Despite this, more than half the subjects preferred a moving glyph to the static encoding. We identified three groups of subjects (utility, fun, and intuitive) where subjects were consistent within groups but distinctly different between groups. This suggests that casual visualizations could be customizable based on high level groupings, where pragmatism can be emphasized for some users and aesthetics and style can be enhanced for others. Index Terms—Motion, casual InfoVis, qualitative analysis, music library 1
Nanoscale Terahertz Emission Microscopy (2017)

By utilizing plasmonic coupling to an AFM probe, we demonstrate Laser Terahertz Emission Nanoscopy (LTEN) with sub-20 nm resolution. We demonstrate the resolution by imaging a single gold nanorod on an InAs substrate.
Evaluation of Stable Resistance Expression in Self-pollinated Progenies of Bacterial Wilt Resistant Regenerants Obtained from Leaf Callus of Tomato. (1997)

The bacterial wilt resistant line LNSR-7 of tomato was isolated from self-pollinated progenies of leaf-callus derived regenerants by directly inoculating a bacterial wilt pathogen Pseudomonas solanacearum into injured roots of tested plants. The subsequent self-pollinated progenies of the line were examined for their fruit quality and resistance expression under natural cultivation conditions in a pathogen infested tomato field. During three generations of progenies, the tomato plants showing both the bacterial wilt resistance and the high fruit qualities comparable to the parental cultivar were selected in order to fix commercial characteristics of the line. The stable inheritance of the resistance in the subsequent self-pollinated progenies was further examined by directly inoculating the pathogen into the roots of test plants. Inoculated plants were planted in soil heavily infested with the pathogen to ensure exposure to the pathogen. Under these artificial inoculation conditions, the selected line was shown to be highly resistant to the disease. The resistance mechanism in the line was analyzed by examining multiplication and translocation of the pathogen in planta. The precise monitoring of infection behavior of the pathogen was successfully achieved using the genetically marked P. solanacearum. Consequently the present line LNSR-7 strictly limited secondary multiplication and translocation of the pathogen and suppressed the wilt induction by the pathogen.
Saying What You Mean (2018)

Specifying a problem and its solution is often viewed as dreary work. However, identifying the essential properties of a problem, and stating them clearly, is the heart of problem solving. Careful consideration of what a problem requires often leads to a solution, and clear and precise specification is necessary to determine whether a solution is correct. Formal specification is not only the necessary basis for any formal verification, but much of the work--and the most interesting work--of verification is in writing a specification, and iteratively adjusting it until it is suitable. In this talk, I will discuss the value of good specification, both formal and informal, some of its often overlooked benefits, and challenges in doing it well (and indeed, what constitutes doing it well). I will use anecdotes, drawn mostly from my experience in developing and verifying concurrent algorithms, to illustrate both positive and negative examples.
Photo‐Carrier Recombination in Polymer Solar Cells Based on P3HT and Silole‐Based Copolymer (2011)

Abstract Photo‐current loss in donor‐acceptor (DA) polymer‐fullerene bulk heterojunction solar cells was studied via carrier transport and recombination measurements. Focusing on the DA polymer poly((4,4‐dioctyldithieno (3,2‐b:2',3'‐d) silole)‐2,6‐diyl‐alt‐(2,1,3‐benzothiadiazole)‐4,7‐diyl) (DTS‐BTD) we found that the carrier transport is well‐balanced and attribute the loss mechanism in DTS‐BTD solar cells to carrier recombination. Using carrier extraction with linear increasing voltage (photo‐CELIV) and transient photo‐voltage (TPV), we show that carrier recombination plays an important role in photo‐current extraction at open circuit conditions due to increase in photo‐excited carrier concentration. Delay time dependent photo‐CELIV and temperature dependent transport studies suggest that the recombination rate is related to the degree of energetic disorder in the polymer: fullerene blends.
Pipelined adaptive filters (2002)

This paper examines methods for the design, implementation, and verification of pipelined adaptive filters in programmable logic. Pipelined adaptive filters can operate at far higher rates than non-pipelined types, but relaxations are required to realize these recursive structures. Design tools that automate the implementation of these filters are demonstrated, along with utilities that allow simulation of the completed system in both fixed and floating point formats. Finally, a communications channel equalization is designed and implemented.
Intestinal Akkermansia muciniphila predicts overall survival in advanced non-small cell lung cancer patients treated with anti-PD-1 antibodies: Results a phase II study. (2021)

9019 Background: The gut microbiome, most specifically centered on one of the most prevalent anaerobic bacterium Akkermansia muciniphila (Akk), has emerged as a potential hallmark of clinical benefit to ICI. The goal of this study was to validate the prognostic significance of Akk in advanced NSCLC patients amenable to ICI. Methods: The multicentric prospective observational study enrolled patients with advanced NSCLC amenable to single agent ICI in first and second line. Stool sample was collected at study entry. Primary end-point was investigator-assessed objective response rate (ORR). We considered that a meaningful clinical difference would correlate to a 10% ORR increase in the Akk-Pos group compared to the Akk-Neg group. At least 292 patients equally divided each in each group would be required for a power at 80% and a two-sided alpha level of 5%. Results: From Dec 2015 to Nov 2019, a total of 409 patients were screened and 311 patients enrolled across 12 academic centers in France and Canada. Median age was 64yr, 32% were female, 77% had non-squamous NSCLC and PD-L1 was ≥1% in 70% of the 213 assessable samples. Akk was detectable in 158 (51%) and absent in 153 (49%) patients. Baseline characteristics were well balanced between the two groups. When considering Akk-Pos vs Akk-Neg groups the primary endpoint ORR was 27% and 17% respectively ( p = 0.04). Rates of partial response, stable disease and progressive disease (PD) were 62%, 50% and 46% respectively in the Akk-Pos group compared to 38%, 50% and 54% in the Akk-Neg group ( p = 0.04). Moreover, 57% of patients were still alive after 12 months in the Akk-Pos group vs 43% in the Akk-Neg group ( p = 0.04). Microbiome profiling demonstrated that Akk-Pos group was associated with increase bacterial diversity and enrichment of Ruminococcus, Alistipes and Eubacterium. When considering the variations of the relative abundance of Akk within the Akk-Pos group, we obtained a large interval ranging from 0.0022% up to 64.78% with a 75 th percentile at 4.42%. The relative abundance of Akk within &gt; 0% to &lt; 4.42% range in stools at diagnosis was associated with increased ORR, overall survival (OS) in multivariate analysis, independent of PD-L1 expression and ECOG. This sub-group was associated with more inflamed tumors with upregulation of CD3e, IfngTH1 and Vcam-1. Conversely, patients with overrepresentation of Akk &gt; 4.42% experienced more PD and shorter OS. Antibiotic use was associated with a shift in favor of Gammaproteobacteria, enrichment of Akk ( &gt; 4.42%) and shorter OS. Conclusions: We validated the prognostic role of Akk in patients with NSCLC. Stratification based on Akk relative abundance represents a more accurate independent predictor than the binary modality. Our study provides the rationale to develop microbiome-based approach to study gut dysbiosis in routine clinical oncology care. Clinical trial information: NCT04567446.
Charge transport across pressure-laminated thin films of molecularly doped polymers (2006)

Discrete interfaces between successive layers in an organic semiconducting device simplify any examination of interface barriers for charge transport. To form discrete interfaces between organic layers we propose lamination as an alternate approach to physical vapor deposition. Transient photocurrent measurements as a function of pressure, thickness, and electric field were performed on cells of 1,1-bis[(di-4-tolylamino)phenyl]-cyclohexane (TAPC), N,N-bis(3,4-dimethylphenyl)-4-aminobiphenyl (DMPAB), and N,N’-diphenyl-N,N’-bis(3-methylphenyl)-[1,1’-biphenyl]-4,4’-diamine (TPD). It was found that, in the range 0.8–3.0 MPa, a pressure-laminated interface between two identical materials causes no measurable perturbation to charge transport. This justifies the use of pressure lamination to study interfaces between nonidentical layers.
Proteome-wide protein interaction measurements of bacterial proteins of unknown function (2012)

Despite the enormous proliferation of bacterial genome data, surprisingly persistent collections of bacterial proteins have resisted functional annotation. In a typical genome, roughly 30% of genes have no assigned function. Many of these proteins are conserved across a large number of bacterial genomes. To assign a putative function to these conserved proteins of unknown function, we created a physical interaction map by measuring biophysical interaction of these proteins. Binary protein--protein interactions in the model organism Streptococcus pneumoniae (TIGR4) are measured with a microfluidic high-throughput assay technology. In some cases, informatic analysis was used to restrict the space of potential binding partners. In other cases, we performed in vitro proteome-wide interaction screens. We were able to assign putative functions to 50 conserved proteins of unknown function that we studied with this approach.
Evaluating side-by-side diffusion models for studying drug supersaturation in an absorptive environment: a case example of fenofibrate and felodipine (2019)

The tested models were comparable; however, Caco-2 cell monolayers were considered too sensitive to be used to study drug supersaturation. Further studies are needed to evaluate the observed drug-dependent effects of absorption on drug supersaturation.
Precision optical navigation guidance system (2016)

We present the new precision optical navigation guidance system approach that provides continuous, high quality range and bearing data to fixed wing aircraft during landing approach to an aircraft carrier. The system uses infrared optical communications to measure range between ship and aircraft with accuracy and precision better than 1 meter at ranges more than 7.5 km. The innovative receiver design measures bearing from aircraft to ship with accuracy and precision better than 0.5 mRad. The system provides real-time range and bearing updates to multiple aircraft at rates up to several kHz, and duplex data transmission between ship and aircraft.
INNOVATIONS FORUM : Engineered Cementitious Composites for Structural Applications (1998)

In the last several years, the University of Michigan has been investigating a composite material known as Engineered Cementitious Composites (ECC). In many respects, this material has characteristics similar to medium- to high-strength concrete. However, the tensile strain capacity generally exceeds 1% with the most ductile composite in the 6-8% range. This article briefly reviews these emerging materials and also reports on some ongoing developmental application studies. The relatively small amount of fibers (less than or equal to 2%) utilized ensures economic feasibility in practical applications, whether in precast elements or on-site constructions. Results of the studies provide confidence in the widening use of ECC in a broad range of new and retrofitted concrete structures.
STI 28nm pitch guided DSA to enable the 450mm tools qualification and transition (2016)

One of the options to reduce the cost related to the next generation of devices in the semiconductor industry is the scale up of the wafer size from 300mm to 450mm. The 450mm transition requires the development and qualification of new tools and processes. G450C, a partnership between five international integrated circuit (IC) makers and CNSE (College of Nanoscale Science and Engineering), has been created to lead this transition. Patterned wafers are necessary to test and demonstrate these 450mm tools. The challenge has been to develop and validate a patterning process — capable of producing advanced-node-relevant features — in a timely manner to enable the process and tool demonstrations. Based on the provided and available 450mm processes and tools, a 28nm pitch STI (Shallow Trench Isolation) structure on a 450mm wafer was developed. This feature was made possible using a 193nm immersion lithography DSA (Directed Self Assembly) technique. This paper will update G450C program status and show process results obtained on 450mm wafers using an STI structure.
Supplementary Figure S1-S7 from Targeted Metabolomics Identifies the Cytochrome P450 Monooxygenase Eicosanoid Pathway as a Novel Therapeutic Target of Colon Tumorigenesis (2023)

&lt;p&gt;SF1: CYP monooxygenase expression in human colon cancer cells; SF2: gene expression of Cyp2e1 in the liver of Cyp2c+/+, Cyp2c+/-, and Cyp2c-/- mice; SF3: liver inflammation in Cyp2c+/+, Cyp2c+/-, and Cyp2c-/- mice; SF4: survival curve of the AOM/DSS-stimulated Cyp2c+/+, Cyp2c+/-, and Cyp2c-/- mice; SF5: pharmacological inhibition of CYP monooxygenases suppresses AOM/DSS-induced colon tumorigenesis in mice; SF6: effects of 12,13-EpOME on MC38 tumor growth in C57BL/6 mice; SF7: mRNA expression levels of CYP monooxygenases in control subjects and colon cancer patients&lt;/p&gt;
Barriers for guideline adherence in knee osteoarthritis care: A qualitative study from the patients' perspective (2016)

Patients indicate that both personal factors and factors related to health care professionals play an important role in nonadherence. An interview script, based on quality indicators, was a significant aid to structurally formulate barriers and facilitators in the perceived knee OA care. Future guideline implementation strategies should take the identified barriers and facilitators into account.
Humanized nucleosomes reshape replication initiation and rDNA/nucleolar integrity in yeast (2023)

Summary Eukaryotic DNA wraps around histone octamers forming nucleosomes, which modulate genome function by defining chromatin environments with distinct accessibility. These well-conserved properties allowed “humanization” of the nucleosome core particle (NCP) in Saccharomyces cerevisiae at high fitness costs. Here we studied nucleosome-humanized yeast-genomes to understand how species-specific chromatin affects nuclear organization and function. We found a size increase in human-NCP, linked to shorter free linker DNA, supporting decreased chromatin accessibility. 3-D humanized-genome maps showed increased chromatin compaction and defective centromere clustering, correlated with high chromosomal aneuploidy rate. Site-specific chromatin alterations were associated with lack of initiation of early origins of replication and dysregulation of the ribosomal (rDNA and rRNA) metabolism. This latter led to nucleolar fragmentation and rDNA-array instability, through a non-coding RNA dependent mechanism, leading to its extraordinary, but entirely reversible, intra-chromosomal expansion. Overall, our results reveal species-specific properties of the NCP that define epigenome function across vast evolutionary distances. Highlights Humanized nucleosomes wrap 10 additional nucleotides, shortening free linker length Histone-humanized nucleosomes have increased occupancy for DNA Humanized nucleosomes potentially decrease chromatin accessibility by blocking-out free linker DNA Nucleosome humanization impedes DNA replication by affecting chromatin structure at origins Humanized nucleosomes reversibly destabilize the ribosomal DNA array and leads to massive intrachromosomal rDNA locus expansion Histone humanization disrupts rDNA silencing and leads to nucleolar fragmentation
Infrared Laser Ablation Sample Transfer for MALDI Imaging (2012)

An infrared laser was used to ablate material from tissue sections under ambient conditions for direct collection on a matrix assisted laser desorption ionization (MALDI) target. A 10 μm thick tissue sample was placed on a microscope slide and was mounted tissue-side down between 70 and 450 μm from a second microscope slide. The two slides were mounted on a translation stage, and the tissue was scanned in two dimensions under a focused mid-infrared (IR) laser beam to transfer material to the target slide via ablation. After the material was transferred to the target slide, it was analyzed using MALDI imaging using a tandem time-of-flight mass spectrometer. Images were obtained from peptide standards for initial optimization of the system and from mouse brain tissue sections using deposition either onto a matrix precoated target or with matrix addition after sample transfer and compared with those from standard MALDI mass spectrometry imaging. The spatial resolution of the transferred material is approximately 400 μm. Laser ablation sample transfer provides several new capabilities not possible with conventional MALDI imaging including (1) ambient sampling for MALDI imaging, (2) area to spot concentration of ablated material, (3) collection of material for multiple imaging analyses, and (4) direct collection onto nanostructure assisted laser desorption ionization (NALDI) targets without blotting or ultrathin sections.
The effect of oligo(trimethylene carbonate) addition on the stiffness of acrylic bone cement (2016)

With the increasing elderly population an increase in the number of bony fractures associated to age-related diseases such as osteoporosis also follows. The relatively high stiffness of the acrylic bone cements used in these patients has been suggested to give raise to a suboptimal load distribution surrounding the cement in vivo, and hence contribute to clinical complications, such as additional fractures. The aim of this study was to develop a low-modulus bone cement, based on currently used, commercially available poly(methyl methacrylate) (PMMA) cements for vertebroplasty. To this end, acrylate end-functionalized oligo(trimethylene carbonate) (oTMC) was incorporated into the cements, and the resulting compressive mechanical properties were evaluated, as well as the cytotoxic and handling properties of selected formulations. Sixteen wt%oTMC was needed in the vertebroplastic cement Osteopal V to achieve an elastic modulus of 1063 MPa (SD 74), which gave a corresponding compressive strength of 46.1 MPa (SD 1.9). Cement extracts taken at 1 and 12 hours gave a reduced MG-63 cell viability in most cases, while extracts taken at 24 hours had no significant effect on cell behavior. The modification also gave an increase in setting time, from 14.7 min (SD 1.7) to 18.0 min (SD 0.9), and a decrease in maximum polymerization temperature, from 41.5°C (SD 3.4) to 30.7°C (SD 1.4). While further evaluation of other relevant properties, such as injectability and in vivo biocompatibility, remains to be done, the results presented herein are promising in terms of approaching clinically applicable bone cements with a lower stiffness.
Dual-phase argon ionization detector for measurement of coherent elastic neutrino scattering and medium-energy nuclear recoils (2007)

We propose to build and deploy a 10-kg dual-phase argon ionization detector for the detection of coherent neutrinonucleus scattering, which is described by the reaction; v + (Z,N) → v + (Z,N), where v is the scattering neutrino, and (Z,N) is the target nucleus of atomic number Z and neutron number N. Its detection would validate central tenets of the Standard Model. We have built a gas-phase argon ionization detector to determine the feasibility of measuring the small recoil energies (~ 1keV) predicted from coherent neutrino scattering, and to characterize the recoil spectrum of the argon nuclei induced by scattering from medium-energy neutrons. We present calibrations made with <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">55</sup> Fe, a low-energy X-ray source, and report on measurements to date of the recoil spectra from the 2-MeV LINAC Li-target neutron source at LLNL. A high signal-to-noise measurement of the recoil spectrum will not only serve as an important milestone in achieving the sensitivity necessary for measuring coherent neutrino-nucleus scattering, but will break new scientific ground on its own.
Cell-Based High-Throughput Luciferase Reporter Gene Assays for Identifying and Profiling Chemical Modulators of Endoplasmic Reticulum Signaling Protein, IRE1 (2015)

Endoplasmic reticulum (ER) stress activates three distinct signal transducers on the ER membrane. Inositol-requiring protein 1 (IRE1), the most conserved signal transducer, plays a key role in ER stress-mediated signaling. During ER stress, IRE1 initiates two discrete signaling cascades: the "adaptive" signaling cascade mediated by the XBP1 pathway and the "alarm" signaling cascade mediated by stress-activated protein kinase pathways. Fine-tuning of the balance between the adaptive and alarm signals contributes significantly to cellular fate under ER stress. Thus, we propose that the design of high-throughput screening (HTS) assays to selectively monitor IRE1 mediated-signaling would be desirable for drug discovery. To this end, we report the generation of stable human neural cell lines and development of cell-based HTS luciferase (Luc) reporter gene assays for the identification of pathway-specific chemical modulators of IRE1. We implemented a cell-based Luc assay using a chimeric CHOP-Gal4 transcription factor in 384-well format for monitoring IRE1 kinase-mediated p38MAPK activation and an unfolded response pathway element (URPE)-Luc cell-based assay in 1536-well format for monitoring IRE1's RNase-mediated activation of XBP1. Chemical library screening was successfully conducted with both the CHOP/Gal4-Luc cells and UPRE-Luc engineered cells. The studies demonstrate the feasibility of using these HTS assays for discovery of pathway-selective modulators of IRE1.