gebhart/patrepeval huggingface dataset:
Rolling Circle Amplification and Circle-to-circle Amplification of a Specific Gene Integrated with Electrophoretic Analysis on a Single Chip (2008)

We have developed an integrated platform for rolling circle amplification (RCA) and circle-to-circle amplification (C2CA) of circular probe (padlock probe) and subsequent microchip electrophoretic detection of a specific gene on a poly(methyl methacrylate) microchip. RCA and C2CA were successfully carried out at a steady temperature of 37 degrees C in the sample well of the microchip, and their respective product was detected on the same channel of the microchip, which was prefilled with a polymer separation matrix and fluorescent dye. Using a species-specific padlock probe for bacterial pathogen V. cholerae, a 25-ng bacterial genomic DNA could be detected in less than 65 min (including RCA and microchip electrophoresis) by this platform. Stable dsDNA C2CA product of genomic DNA for V. cholerae can be detected with the introduced integrated platform. Furthermore, the usefulness of this technique for the monitoring of RCA was demonstrated. This integrated platform provides a sensitive, fast, high-throughput, and reproducible method for signal amplification and detection of the padlock probes in the same microchip and is a promising tool for highly specific gene detection strategies.
Language Differences and Metadata Features on Twitter (2010)

In the past several years, microblogging services like Twitter and Facebook have become a popular method of communication, allowing users to disseminate and gather information to and from hundreds or thousands (or even millions) of people, often in real-time. As much of the content on microblogging services is publicly accessible, we have recently seen many secondary services being built atop them, including services that perform signicant content analysis, such as real-time search engines and trend analysis services. With the eventual goal of building more accurate and less expensive models of microblog streams, this paper investigates the degree to which language variance is related to the metadata of microblog content. We hypothesize that if a strong relationship exists between metadata features and language then we will be able to use this metadata as a trivial classier to match individual messages with specialized, more accurate language models. To investigate the validity of this hypothesis, we analyze a corpus of over 72M Twitter messages, building language models conditioned on a variety of available message metadata.
Photon scanning tunneling microscope study of optical waveguides (1990)

A novel technique, photon scanning microscopy, is shown to probe directly the evanescent field outside a planar and a channel waveguide. The decay lengths for these evanescent fields were measured and correspond well to the decay lengths of the evanescent fields calculated for each structure. Two-dimensional scanning at constant intensity or constant height reveals lateral variations in these fields due to topographic changes, index of refraction inhomogeneities, or modal variations within the waveguide.
Further Investigation of Slurry Additives for Selective Polishing of SiO2Films over Si3N4Using Ceria Dispersions (2015)

Following our earlier analysis of amino acids, we investigated the effectiveness of acetic acid, pyridine, and sorbitol that were chosen to represent carboxylic acid, amine and alcohol functional group families, respectively, as additives in ceria dispersions for polishing SiO2 and Si3N4 films. By comparing the speciation of the additives available and the material removal rates with respect to pH, we identified that the removal rates of nitride, but not oxide, are suppressed to <1 nm/min in the pH range where the additive species containing a protonated amino group or a neutral carboxylic group or a neutral hydroxyl group are dominant. All of these species are strong hydrogen bond donors and can form strong hydrogen bonds with Si3N4 surface while their corresponding bonding on SiO2 surface sites is weaker. The stronger hydrogen bonding hinders Si3N4 hydrolysis and suppresses Si3N4 removal. In contrast, the weakly bound additive species are easily removed from the SiO2 surface by the polishing pad and the ceria abrasives, leading to high SiO2 to Si3N4 removal rate selectivity. Similar results were also obtained with valeric acid, imidazole, glucose, sucrose, and mannitol, confirming the importance of a strong hydrogen bond formation in a broader class of additives.
Supplemental Material from Toward Personalized Lymphoma Immunotherapy: Identification of Common Driver Mutations Recognized by Patient CD8<sup>+</sup> T Cells (2023)

&lt;p&gt;Supplemental Methods. Table S1. Frequency of hematopoietic subsets in PBMC at all time points for patient samples used for in vitro immunogenicity experiments Table S2: Clinical characteristics of follicular lymphoma cohorts Table S3. Amino acid changes encoded by somatic mutations identified in candidate genes in follicular lymphoma cohort Table S4. Patient HLA class I alleles for in vitro immunogenicity cohort Figure S1. The number of mutant peptides predicted to bind patient-specific HLA class I molecules in the sequencing cohort. Figure S2. Clinical timeline for 13-patient cohort selected for in vitro immunogenicity studies. Figure S3. CD8 status of mutant peptide-reactive T cells.&lt;/p&gt;
Magneto-structural correlations in binuclear copper(ii) compounds bridged by a ferrocenecarboxylato(–1) and an hydroxo- or methoxo-ligands (2005)

The syntheses, characterization and X-ray crystal structures of the first two examples of asymmetrically bridged dinuclear copper(ii) complexes containing a ferrocenecarboxylato ligand and a methoxo group in [{Cu(dmen)}2(micro-OMe){micro-O2C(eta5-C5H4)Fe(eta5-C5H5)}](ClO4)2, 1, (dmen=N,N-dimethylethylenediamine) or an hydroxo group in [{Cu(tmen)}2(micro-OH){micro-O2C(eta5-C5H4)Fe(eta5-C5H5)}](ClO4)2, 2 , (tmen=N,N,N'N'-tetramethylethylenediamine) are reported. Magneto-chemical studies revealed that 1 and 2 exhibit opposite superexchange interactions between the two Cu(II) paramagnetic centers: an antiferromagnetic coupling (J = -11 cm(-1)) in 1 and a ferromagnetic interaction (J = +29 cm(-1)) in 2. The results obtained from these studies suggest that the weak interactions between the Cu(II) ions and the perchlorate anions detected in the crystal structures are important to introduce significant distortions in the heterobridged [Cu2(micro-OR){micro-O2C(eta5-C5H4)Fe(eta5-C5H5)}]2+ cores of 1 and 2, which clearly affect the nature and strength of the superexchange interactions. Computational studies based on density functional theory and ab initio multiconfigurational second-order perturbation theory (CASPT2) calculations have also been performed in order to rationalize the magnetic behaviour of 1 and 2. The magneto-structural correlations for complexes containing the [Cu(micro-OR)(micro-O2CR')Cu] core are discussed, and the relevance of the out-of-plane angle of the R group with the Cu(micro-OR)Cu plane established.
Reversible Lithium‐Ion Insertion in Molybdenum Oxide Nanoparticles (2008)

Li-ion battery anodes fabricated from crystalline MoO3 nanoparticles display an anomalous reversible capacity of 630 mAhg−1 when cycled at high rate. The nanoparticle anodes show no degradation in capacity for 150 cycles, where micron sized MoO3 particles are shown to fail after several cycles. Theoretical calculations elucidate the Li-ion intercalation mechanism and explain the reversible capacity. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2089/2008/adma200800999_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Fundamental variability limits of filament-based RRAM (2016)

While Resistive RAM (RRAM) are seen as an alternative to NAND Flash, their variability and cycling understanding remain a major roadblock. Extensive characterizations of multi-kbits RRAM arrays during Forming, Set, Reset and cycling operations are presented allowing the quantification of the intrinsic variability factors. As a result, the fundamental variability limits of filament-based RRAM in the full resistance range are identified.
Status of the EU FP7 HERCULES Project: What Is the Potential of n-Type Silicon Solar Cells in Europe? (2016)

The concept proposed by the HERCULES project is to develop innovative n-type monocrystalline c-Si device structures based on both sides’ contacted silicon heterojunction (SHJ) solar cells, on interdigitated back-contact (IBC) solar cells with alternative junction formation, as well as on hybrid concepts (homo-heterojunction). These concepts are the most promising technologies to reach ultra-high efficiencies with industrially relevant processes. The HERCULES strategy is to transfer the developed processes to industrial scale by considering all major cost drivers of the entire manufacturing process chain. The final objective is to obtain both high-efficiency solar cells and modules, based on adequately simple process sequences. It requires strong expertise and equipment mastering in order to provide a commercially viable technology that can be implemented by the European PV industry. To this end, the HERCULES consortium takes advantage of its leading European expertise in both research and production. In this paper, major results are presented concerning the first 30 months in material, solar cell development, module integration and pilot line activity. The strong improvements achieved in all the value chain demonstrate the strong need of collaboration within all partners to reach very ambitious objectives from the optimization of n-type solar cells &amp; modules up to production level.
Rapid Determination of Thioglycolic Acid Lignin for Various Biomass Samples (2019)

非木質材料を含む多種多検体バイオマス試料の迅速なリグニン量評価に向け，本研究ではチオグリコール酸（TGA）法を迅速化した。迅速TGA（rTGA）法は既存法の，1M NaOHでのTGAリグニン抽出時間を16hから1hに，濃塩酸滴下後のTGAリグニン沈殿操作を4℃4hから転倒混和のみに短縮した方法である。rTGA法で得たリグニン量は，様々な試料で従来法と有意差が無かった。さらに，rTGA法で得たTGAリグニン沈殿を凍結乾燥し秤量することでリグニン量を求める，迅速TGA重量（grTGA）法を考案した。木部試料のリグニン含有量はクラソン法とgrTGA法どちらの手法でもおよそ同等であったが，スギ葉のリグニン含有量はクラソン法よりもgrTGA法の方がかなり低かった。組織化学的解析でスギ葉の木化細胞がわずかであったことから，葉のリグニン定量はgrTGA法がクラソン法よりも適することが示唆された。
Alteration of Cellular and Humoral Immunity by Mutant p53 Protein and Processed Mutant Peptide in Head and Neck Cancer (2007)

Our results support the hypothesis that mutated p53 neoantigens can bind to specific HLA class II molecules, leading to a break in tolerance. This may lead to skewing of the CD4(+) T lymphocyte response toward a tumor-permissive T helper type 2 profile in head and neck cancer patients, as manifested by seropositivity for p53.
ChemInform Abstract: Ring Enlargement of Diaziridinone: Reactions with Bifunctionalized Carbanions Leading to Functionalized Pyrazolines or Novel Spiroheterocycles. (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Topology of the lateral visual system: The fundus of the superior temporal sulcus and parietal area H connect nonvisual cerebrum to the lateral occipital lobe (2023)

FST and PH are two hub-like areas that demonstrate extensive functional coactivation and structural connections to nonvisual cerebrum. Their structural interconnectedness with language cortices along with the abnormal activation of areas commonly located in the temporo-occipital region in dyslexic individuals suggests possible important roles of FST and PH in the integration of information related to language and reading. Future studies should refine our model by examining the functional roles of these hub areas and their clinical significance.
Transmission Over 608 km of Standard Single-Mode Fiber Using a 10.709-Gb/s Chirp Managed Laser and Electronic Dispersion Precompensation (2012)

An electronic dispersion precompensation scheme for a chirp-managed directly modulated laser is described and experimentally demonstrated for transmission at 10.709 Gb/s. A single look-up-table (LUT) for the drive current is designed to mitigate the effects of fiber dispersion and the intrinsic nonlinear modulation response of the laser. Experimental results show that an 11-bit LUT can compensate the dispersion of 608 km of a standard single-mode fiber with a required optical-signal-to-noise ratio of 14.5 dB at a bit-error ratio of 3.8 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> .
Reading Between the Lines: Modeling User Behavior and Costs in AI-Assisted Programming (2022)

Code-recommendation systems, such as Copilot and CodeWhisperer, have the potential to improve programmer productivity by suggesting and auto-completing code. However, to fully realize their potential, we must understand how programmers interact with these systems and identify ways to improve that interaction. To seek insights about human-AI collaboration with code recommendations systems, we studied GitHub Copilot, a code-recommendation system used by millions of programmers daily. We developed CUPS, a taxonomy of common programmer activities when interacting with Copilot. Our study of 21 programmers, who completed coding tasks and retrospectively labeled their sessions with CUPS, showed that CUPS can help us understand how programmers interact with code-recommendation systems, revealing inefficiencies and time costs. Our insights reveal how programmers interact with Copilot and motivate new interface designs and metrics.
CD229 CAR T cells eliminate multiple myeloma and tumor propagating cells without fratricide (2020)

Multiple myeloma (MM) is a plasma cell malignancy and most patients eventually succumb to the disease. Chimeric antigen receptor (CAR) T cells targeting B-Cell Maturation Antigen (BCMA) on MM cells have shown high-response rates, but limited durability. CD229/LY9 is a cell surface receptor present on B and T lymphocytes that is universally and strongly expressed on MM plasma cells. Here, we develop CD229 CAR T cells that are highly active in vitro and in vivo against MM plasma cells, memory B cells, and MM-propagating cells. We do not observe fratricide during CD229 CAR T cell production, as CD229 is downregulated in T cells during activation. In addition, while CD229 CAR T cells target normal CD229<sup>high</sup> T cells, they spare functional CD229<sup>neg/low</sup> T cells. These findings indicate that CD229 CAR T cells may be an effective treatment for patients with MM.
Ultrahigh resolution optical coherence tomography in the visible and 1300 nm wavelength region (2003)

Ultrahigh axial resolution OCT is demonstrated in human cells and other human biopsies for two fiber broadened femtosecond light sources, achieving 0.5µm axial resolution in the visible and 1.4µm in the in the 1300nm wavelength region.
Data from Early Detection of Lung Cancer Using DNA Promoter Hypermethylation in Plasma and Sputum (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; CT screening can reduce death from lung cancer. We sought to improve the diagnostic accuracy of lung cancer screening using ultrasensitive methods and a lung cancer–specific gene panel to detect DNA methylation in sputum and plasma.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; This is a case–control study of subjects with suspicious nodules on CT imaging. Plasma and sputum were obtained preoperatively. Cases (&lt;i&gt;n&lt;/i&gt; = 150) had pathologic confirmation of node-negative (stages I and IIA) non–small cell lung cancer. Controls (&lt;i&gt;n&lt;/i&gt; = 60) had non-cancer diagnoses. We detected promoter methylation using quantitative methylation-specific real-time PCR and methylation-on-beads for cancer-specific genes (&lt;i&gt;SOX17, TAC1, HOXA7, CDO1, HOXA9&lt;/i&gt;, and &lt;i&gt;ZFP42&lt;/i&gt;).&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; DNA methylation was detected in plasma and sputum more frequently in people with cancer compared with controls (&lt;i&gt;P&lt;/i&gt; &lt; 0.001) for five of six genes. The sensitivity and specificity for lung cancer diagnosis using the best individual genes was 63% to 86% and 75% to 92% in sputum, respectively, and 65% to 76% and 74% to 84% in plasma, respectively. A three-gene combination of the best individual genes has sensitivity and specificity of 98% and 71% using sputum and 93% and 62% using plasma. Area under the receiver operating curve for this panel was 0.89 [95% confidence interval (CI), 0.80–0.98] in sputum and 0.77 (95% CI, 0.68–0.86) in plasma. Independent blinded random forest prediction models combining gene methylation with clinical information correctly predicted lung cancer in 91% of subjects using sputum detection and 85% of subjects using plasma detection.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; High diagnostic accuracy for early-stage lung cancer can be obtained using methylated promoter detection in sputum or plasma. &lt;i&gt;Clin Cancer Res; 23(8); 1998–2005. ©2016 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Realistic Full Wave Modeling of Focal Plane Array Pixels (2017)

Here, we investigate full-wave simulations of realistic implementations of multifunctional nanoantenna enabled detectors (NEDs). We focus on a 2x2 pixelated array structure that supports two wavelengths of operation. We design each resonating structure independently using full-wave simulations with periodic boundary conditions mimicking the whole infinite array. We then construct a supercell made of a 2x2 pixelated array with periodic boundary conditions mimicking the full NED; in this case, however, each pixel comprises 10-20 antennas per side. In this way, the cross-talk between contiguous pixels is accounted for in our simulations. We observe that, even though there are finite extent effects, the pixels work as designed, each responding at the respective wavelength of operation. This allows us to stress that realistic simulations of multifunctional NEDs need to be performed to verify the design functionality by taking into account finite extent and cross-talk effects.
A Marked Point Process of Rectangles and Segments for Automatic Analysis of Digital Elevation Models (2007)

This work presents a framework for automatic feature extraction from images using stochastic geometry. Features in images are modeled as realizations of a spatial point process of geometrical shapes. This framework allows the incorporation of a priori knowledge on the spatial repartition of features. More specifically, we present a model based on the superposition of a process of segments and a process of rectangles. The former is dedicated to the detection of linear networks of discontinuities, while the latter aims at segmenting homogeneous areas. An energy is defined, favoring connections of segments, alignments of rectangles, as well as a relevant interaction between both types of objects. The estimation is performed by minimizing the energy using a simulated annealing algorithm. The proposed model is applied to the analysis of Digital Elevation Models (DEMs). These images are raster data representing the altimetry of a dense urban area. We present results on real data provided by the IGN (French National Geographic Institute) consisting in low quality DEMs of various types.
The Electronic Absorption Spectra of Some N-Substituted Pyrroles—Molecular Orbital Calculations (1982)

The electronic absorption spectra of N-phenylpyrrole and some of its parasubstituted derivatives have been investigated in polar and nonpolar solvents. Such an investigation could predict the extent of resonance interaction between the pyrryl and phenyl moieties of the composite molecule. The direction and polarization of the electronic transitions were predicted. Molecular orbital calculations using the SCF-CI procedures were performed on N-phenylpyrrole and some of its p-substituted derivatives. The state functions and energies were computed. The weight of each configuration was evidence for the direction of the electronic transition. The correspondence between the theoretical and experimental results is satisfactory.
Target tracking with distributed sensors: the focus of attention problem (2004)

In this paper, we investigate data fusion techniques for target tracking using distributed sensors. Specifically, we are interested in how pairs of bearing or range sensors can be best assigned to targets in order to minimize the expected error in the estimates. We refer to this as the focus of attention (FOA) problem. In its general form, FOA is NP-hard and not well approximable. However, for specific geometries we obtain significant approximation results: a 2-approximation algorithm for stereo cameras on a line, a PTAS for when the cameras are equidistant, and a 1.42 approximation for equally spaced range sensors on a circle. By reposing as a maximization problem - where the goal is to maximize the number of tracks with bounded error - we are able to leverage results from maximum set-packing to render the problem approximable. We demonstrate the results in simulation for a target tracking task, and for localizing a team of mobile agents in a sensor network. These results provide insights into sensor/target assignment strategies, as well as sensor placement in a distributed network.
Spatial, Spectral, and Polarization Multiplexed Ptychography (2015)

We demonstrate ptychographic imaging of multiple areas of a sample simultaneously with no loss of resolution, by using different wavelengths or polarizations to collect independent diffraction patterns in parallel. This significantly reduces imaging times.
Post‐dialysis recovery time in ESRD patients receiving more frequent hemodialysis in skilled nursing facilities (2022)

SNF dialysis patients receiving 5x per week MFD report rapid recovery time ≤2 h in 92% of dialyses despite advanced age, frailty, and comorbidities. Future studies will assess the practical ramifications of rapid DRT perception/experience on nursing home rehabilitation programs, which could impact patient health beyond the nursing home stay.