gebhart/patrepeval huggingface dataset:
Ultrasmooth, High Electron Mobility Amorphous In–Zn–O Films Grown by Atomic Layer Deposition (2013)

Ultrasmooth and highly conductive amorphous In–Zn–O (a-IZO) films are grown by atomic layer deposition (ALD). This opens a new pathway to highly transparent and conductive oxides with an extreme conformality. In this process, a-IZO films of various compositions are deposited by alternate stacking of ZnO and In2O3 atomic-layers at a temperature of 200 °C. The IZO films have an amorphous phase over a wide composition range, 43.2–91.5 at %, of In cation ratio. The In-rich a-IZO film (83.2 at % In) exhibits a very low resistivity of 3.9 × 10–4 Ω cm and extremely high electron mobility in excess of 50 cm2 V–1 s–1, one of the highest among the reported ALD-grown transparent conducting oxides. Moreover, it exhibits an ultrasmooth surface (∼0.2 nm in root-mean-square roughness), and can be conformally coated onto nanotrench structures (inlet size: 25 nm) with excellent step coverage of 96%.
Abstract 352: Up-regulation of CD44 in the development of metastasis, recurrence and drug resistance of ovarian cancer (2015)

Abstract Purpose: The clinical significance of Cluster of differentiation 44 (CD44) remains controversial in human ovarian cancer. The aim of this study is to evaluate the clinical significance of CD44 expression by using a unique tissue microarray, and then to determine the biological functions of CD44 in ovarian cancer. Experimental Design: A unique ovarian cancer tissue microarray (TMA) was constructed with paired primary, metastatic, and recurrent tumor tissues from 26 individual patients. CD44 expression in TMA was assessed by immunohistochemistry. Western blotting and Immunofluorescence assay determined the expression of CD44 and/or P-glycoprotein (Pgp) in ovarian cancer cell lines and the tumor tissues of a paclitaxel treated ovarian cancer xenograft mouse model. MTT assay, wound healing assay, and matrigel invasion assay were utilized to assess the proliferation, drug sensitivity, and migration/invasion ability, respectively. Results: Both the metastatic and recurrent ovarian cancer tissues expressed higher level of CD44 than the patient-matched primary tumor. A significant association has been shown between CD44 expression and both the disease free survival and overall survival. A strong increase of CD44 was found in the tumor recurrence of mouse model. Finally, when CD44 was knocked down, proliferation, migration/invasion activity, and spheroid formation were significantly suppressed, while drug sensitivity was enhanced. Conclusions: Up-regulation of CD44 represents a crucial event in the development of metastasis, recurrence, and drug resistance to current treatments in ovarian cancer. Developing strategies to target CD44 may prevent metastasis, recurrence, and drug resistance in ovarian cancer. Citation Format: Yan Gao, Rosemary Foster, Francis J. Hornicek, Mansoor M. Amiji, Zhenfeng Duan. Up-regulation of CD44 in the development of metastasis, recurrence and drug resistance of ovarian cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 352. doi:10.1158/1538-7445.AM2015-352
Check Points against Privacy Breaches in Android Applications (2012)

Summary The risk of privacy breaches by malicious programs has been increasing, and these programs have used more elaborate techniques to circumvent detection. Attacks using a collaboration of applications are especially difficult to find since distinct applications obtain privacy-sensitive data and send the data to the outside. Current mobile platforms have a security enforcement mechanism based on a sandbox to prevent direct data sharing between applications. Furthermore, several schemes have been proposed to improve the security against the attacks caused by two or more applications that communicate with each other. However, these schemes cannot monitor all the possible data-sharing methods. A security analysis that covers a wider range of possible data-sharing methods between applications is required for protecting leakage of privacy-sensitive information. In this paper, we present a detailed manual analysis regarding a wider range of possible methods for sharing data in the Android OS, and show how to detect actual privacy breaches using existing frameworks. Our analysis contributes to the enhancement for the security of the Android OS.
A 128Gb 3b/cell NAND flash design using 20nm planar-cell technology (2013)

The authors develop a 128Gb 3b/cell NAND Flash memory based on 20nm fully planar cell process technology. The planar cell allows the memory cell to be scaled in both the wordline (WL) and bitline (BL) directions, resulting in a small 3b/cell memory device. The sensing scheme is based on a ramping technique that allows the detection of hard and soft states in a single operation.
Comparaison between different simplified grain growth models using “full field” modelling method results (2012)

International audience
Comparative Sequence Analysis of the Symbiosis Island ofMesorhizobium lotiStrain R7A (2002)

The Mesorhizobium loti strain R7A symbiosis island is a 502-kb chromosomally integrated element which transfers to nonsymbiotic mesorhizobia in the environment, converting them to Lotus symbionts. It integrates into a phenylalanine tRNA gene in a process mediated by a P4-type integrase encoded at the left end of the element. We have determined the nucleotide sequence of the island and compared its deduced genetic complement with that reported for the 611-kb putative symbiosis island of M. loti strain MAFF303099. The two islands share 248 kb of DNA, with multiple deletions and insertions of up to 168 kb interrupting highly conserved colinear DNA regions in the two strains. The shared DNA regions contain all the genes likely to be required for Nod factor synthesis, nitrogen fixation, and island transfer. Transfer genes include a trb operon and a cluster of potential tra genes which are also present on the strain MAFF303099 plasmid pMLb. The island lacks plasmid replication genes, suggesting that it is a site-specific conjugative transposon. The R7A island encodes a type IV secretion system with strong similarity to the vir pilus from Agrobacterium tumefaciens that is deleted from MAFF303099, which in turn encodes a type III secretion system not found on the R7A island. The 414 genes on the R7A island also include putative regulatory genes, transport genes, and an array of metabolic genes. Most of the unique hypothetical genes on the R7A island are strain-specific and clustered, suggesting that they may represent other acquired genetic elements rather than symbiotically relevant DNA.
[Properdin mutations a risk factor for meningitis]. (2010)

Properdin deficiency is a rare X-chromosomal single gene immunological disorder that causes an increased risk for severe infectious diseases, especially for Neisseria meningitidis in males. Here we describe a Finnish family with a novel mutation in the properdin gene. The index-patient was diagnosed to have meningococcal meningitis and severe properdin deficiency that was caused by a nonsense mutation in exon 9 (c.1164G > A; W377X). The mutation was inherited from his mother and was also detected in his brother, two maternal aunts, one female cousin and her son. Vaccinations and preventive antibiotics were given to all males at risk.
TinyML for Ubiquitous Edge AI (2021)

TinyML is a fast-growing multidisciplinary field at the intersection of machine learning, hardware, and software, that focuses on enabling deep learning algorithms on embedded (microcontroller powered) devices operating at extremely low power range (mW range and below). TinyML addresses the challenges in designing power-efficient, compact deep neural network models, supporting software framework, and embedded hardware that will enable a wide range of customized, ubiquitous inference applications on battery-operated, resource-constrained devices. In this report, we discuss the major challenges and technological enablers that direct this field's expansion. TinyML will open the door to the new types of edge services and applications that do not rely on cloud processing but thrive on distributed edge inference and autonomous reasoning.
Metal organic cluster photoresists: new metal oxide systems (2019)

Extreme ultraviolet (EUV) lithography, using 13.5 nm radiation, is a prominent candidate for next generation manufacturing. Our main effort has recently focused on metal organic cluster photoresists, including both Zr and Hf metal oxides, both relatively low EUV absorbing metals. However, integration of high EUV absorption elements is now considered to be a more promising route to further improve lithographic performance under EUV radiation. Here, we report lithography of zinc oxide-based metal organic cluster photoresists, and EUV patterning below 15 nm. The lithographic performance of this and other metal oxides is described and etch characteristics discussed.
Radiation sterilization compatibility of medical packaging materials (1998)

Abstract We have examined gamma sterilization compatibility for many of medical packaging materials. Techniques used include thermal analysis, physical testing, optical property evaluations, and failure analysis. For a variety of PVC formulations, gamma radiation often leads to discoloration. This results from conjugated poly‐ene sequences formed through dehydrohalogenation degradation during ionizing radiation. In addition to unacceptable color formation, excessive pH shifts and high extractables are often observed. For most polylefins, radiations was found to deplete the antioxidant package and lead to discoloration and/or mechanical failures. For polypropylenes, the degradation can lead to the well‐publicized catastrophic failures during post radiation shelf life storage. These examples and methods to ensure radiation compatibility and shelf‐life stability are presented.
African American race as a risk factor associated with a second primary lung cancer after initial primary head and neck cancer (2022)

We show that AA race is associated with an increased risk of SPLC after IPHNC; reasons of this increased risk warrant further investigation.
A degenerate alpha satellite probe, detecting a centromeric deletion on chromosome 21 in an apparently normal human male, shows limitations of the use of satellite DNA probes for interphase ploidy analysis. (1992)

A degenerate alpha satellite DNA probe specific for a repeated sequence on human chromosomes 13 and 21 was synthesized using the polymerase chain reaction (PCR). Fluorescence in situ hybridization (FISH) with this probe to normal metaphase spreads revealed strong probe binding to the centromeric regions of human chromosomes 13 and 21 with negligible cross-hybridization with other chromosomes. FISH to normal interphase cell nuclei showed four distinct domains of probe binding. However, hybridization with probe to interphase and metaphase preparations from one apparently normal human male resulted in only three major binding domains. Metaphase chromosome analysis revealed a centromeric deletion on one chromosome 21 that caused greatly reduced probe binding. The result suggest caution in the interpretation of interphase ploidy studies performed with chromosome-specific alphoid DNA probes.
A Markov Random Field Model for Network-based Differential Expression Analysis of Single-cell RNA-seq Data (2020)

Abstract Background: Recent development of single cell sequencing technologies has made it possible to identify genes with different expression (DE) levels at the cell type level between different groups of samples. However, the often-low sample size of single cell data limits the statistical power to identify DE genes. In this article, we propose to borrow information through known biological networks. Results: We develop MRFscRNAseq, which is based on a Markov Random Field (MRF) model to appropriately accommodate gene network information as well as dependencies among cell types to identify cell-type specific DE genes. We implement an Expectation-Maximization (EM) algorithm with mean field-like approximation to estimate model parameters and a Gibbs sampler to infer DE status. Simulation study shows that our method has better power to detect cell-type specific DE genes than conventional methods while appropriately controlling type I error rate. The usefulness of our method is demonstrated through its application to study the pathogenesis and biological processes of idiopathic pulmonary fibrosis (IPF) using a single-cell RNA-sequencing (scRNA-seq) data set, which contains 18,150 protein-coding genes across 38 cell types on lung tissues from 32 IPF patients and 28 normal controls.Conclusions: The proposed MRF model is implemented in the R package MRFscRNAseq available on GitHub. By utilizing gene-gene and cell-cell networks, our method provides differential expression analysis for scRNA-seq data with increased statistical power.
ChemInform Abstract: Structural Characterization of the Product of Oxidation of a Macrocyclic Cobalt(II) Complex in Pyridine Solution. (1988)

Abstract The title reaction gives the Co(III) complexes (II) isolated as their BF 4 salts.
Phosphonylated Acyclic Guanosine Analogues with the 1,2,3-Triazole Linker (2015)

A novel series of {4-[(2-amino-6-chloro-9H-purin-9-yl)methyl]-1H-1,2,3-triazol-1-yl}alkylphosphonates and {4-[(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)methyl]-1H-1,2,3-triazol-1-yl}alkylphosphonates as acyclic analogues of guanosine were synthesized and assessed for antiviral activity against a broad range of DNA and RNA viruses and for their cytostatic activity toward three cancerous cell lines (HeLa, L1210 and CEM). They were devoid of antiviral activity; however, several phosphonates were found slightly cytostatic against HeLa cells at an IC50 in the 80-210 µM range. Compounds (1R,2S)-17k and (1S,2S)-17k showed the highest inhibitory effects (IC50=15-30 µM) against the proliferation of murine leukemia (L1210) and human T-lymphocyte (CEM) cell lines.
Abstract 768: Identification of signal transduction pathways specific for mutant KRas-dependent tumors (2018)

Abstract Targeting KRas directly has proven difficult. Therefore, identifying vulnerabilities specific for mutant KRas tumors is an important alternative approach to target mutant KRas-driven tumors. Towards this goal, we used phosphoproteomics to dissect key differences in signaling pathways between mutant KRas-dependent and mutant KRas-independent human cancer cells. Mass spectrometry analysis led to the identification of 25 proteins with significantly higher (up to 410 fold) phosphorylation levels in mutant KRas-dependent cells. Among these, 25 proteins- 8, 8 and 3 were tyrosine (Y), Serine (S) and Threonine (T) phosphorylated, and 6 were phosphorylated on both S and T. Presently, CRISPR-Cas9 knockout and siRNA depletion studies are ongoing to identify which of these 25 hits are required for the survival of mutant KRas-dependent human cancer cells. These studies can lead to identifying signaling circuits that can be targeted to treat mutant KRas-driven cancers. Citation Format: Oorvashi Roy Puli, Hua Yang, Bin Fang, Hong Yuan (Rays) Jiang, John Koomen, Said M. Sebti. Identification of signal transduction pathways specific for mutant KRas-dependent tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 768.
Photochemically Crushable and Regenerative Metal–Organic Framework (2020)

A photochemically crushable and regenerative metal-organic framework (<sup><b>DTE</b></sup><b>MOF</b>) was developed by complexation of photochromic ligand <sup><b>Py</b></sup><b>DTE</b><sub><b>open</b></sub> and 5-nitroisophthalate (nip<sup>2-</sup>) with Cd<sup>2+</sup> in DMF/MeOH. <sup><b>DTE</b></sup><b>MOF</b> ([Cd(nip)(<sup><b>Py</b></sup><b>DTE</b><sub><b>open</b></sub>)(H<sub>2</sub>O)(DMF)<sub>2</sub>]<sub><i>n</i></sub>) was obtained as colorless crystals. Its crystal structure revealed that <sup><b>DTE</b></sup><b>MOF</b> adopts a tubular structure with interlocked coordination networks and can accommodate guest molecules in its one-dimensional pores. When <sup><b>DTE</b></sup><b>MOF</b> suspended in DMF/MeOH was exposed to UV light, its crystalline network, though thermally stable up to 260 °C, was readily crushed to afford a homogeneous blue-colored solution, via ring-closing isomerization of the constituent <sup><b>Py</b></sup><b>DTE</b><sub><b>open</b></sub> ligand into <sup><b>Py</b></sup><b>DTE</b><sub><b>closed</b></sub>. Upon successive exposure of this solution to visible light, colorless MOF crystals identical to those of <sup><b>DTE</b></sup><b>MOF</b> were regenerated. Light-responsive <sup><b>DTE</b></sup><b>MOF</b> enabled highly efficient on-demand guest release.
Triacetic acid lactone production in industrial Saccharomyces yeast strains (2015)

Triacetic acid lactone (TAL) is a potential platform chemical that can be produced in yeast. To evaluate the potential for industrial yeast strains to produce TAL, the g2ps1 gene encoding 2-pyrone synthase was transformed into 13 industrial yeast strains of varied genetic background. TAL production varied 63-fold between strains when compared in batch culture with glucose. Ethanol, acetate, and glycerol were also tested as potential carbon sources. Batch cultures with ethanol medium produced the highest titers. Therefore, fed-batch cultivation with ethanol feed was assayed for TAL production in bioreactors, producing our highest TAL titer, 5.2 g/L. Higher feed rates resulted in a loss of TAL and subsequent production of additional TAL side products. Finally, TAL efflux was measured and TAL is actively exported from S. cerevisiae cells. Percent yield for all strains was low, indicating that further metabolic engineering of the strains is required.
Comparison of extraction techniques and modeling of accelerated solvent extraction for the authentication of natural vanilla flavors (2009)

Accelerated solvent extraction (ASE) of vanilla beans has been optimized using ethanol as a solvent. A theoretical model is proposed to account for this multistep extraction. This allows the determination, for the first time, of the total amount of analytes initially present in the beans and thus the calculation of recoveries using ASE or any other extraction technique. As a result, ASE and Soxhlet extractions have been determined to be efficient methods, whereas recoveries are modest for maceration techniques and depend on the solvent used. Because industrial extracts are obtained by many different procedures, including maceration in various solvents, authenticating vanilla extracts using quantitative ratios between the amounts of vanilla flavor constituents appears to be unreliable. When authentication techniques based on isotopic ratios are used, ASE is a valid sample preparation technique because it does not induce isotopic fractionation.
ChemInform Abstract: Fluorescence Micro(spectro)scopy as a Tool to Study Catalytic Materials in Action (2011)

Abstract Review: 82 refs.
Are Realistic Training Data Necessary for Depth-from-Defocus Networks? (2022)

Image-based depth estimation is one of the important tasks in computer vision. Depth-from-defocus (DfD) methods estimate the scene depth from a single or multiple defocused images by exploiting depth-dependent defocus blur cues. Because of the difficulty in obtaining a real-world dataset with ground-truth scene depth, most deep-learning-based DfD methods rely on a synthetic training dataset, where more realistic scene rendering is considered desirable for more accurate depth estimation. In this paper, we consider if realistic 3D objects are really necessary for training DfD networks. To investigate this, we design a very simple and fast synthetic training data generation method for DfD using only two front-parallel texture planes in one scene and compare it with a widely-applied path-tracing method using a common 3D object dataset. Through real-world experiments, we show that the 2-plane method provides comparable and even slightly better performance than the path-tracing method and can be considered as an alternative method for simple and practical DfD network training.
<title>Hybrid refractive/diffractive elements in lenses for staring focal-plane arrays</title> (1992)

Much has been written in the past four to five years on the application of hybrid refractive/diffractive elements in infrared optical design. We are now beginning to see several excellent examples of actual systems which utilize such components. Little has been written, however, on the use of hybrid elements in lens systems for staring focal plane arrays which require 100% cold stop efficiency (CSE). Most designs presented in the literature have been for uncooled staring arrays. The purpose of this paper is to examine the requirements that present MWIR focal plane arrays (FPAs) place on the objective, and to investigate the role hybrid diffractive optical elements (DOEs) play in the solution of this imaging problem. We briefly examine the requirements imposed by the next generation MWIR FPAs to show that hybrids can play a role in compact, lightweight systems of the future. In addition, we illustrate areas of future design activity such as passively athermal IR objectives and wide angle IR lenses.
The Rearrangements of Naphthylnitrenes:  UV/Vis and IR Spectra of Azirines, Cyclic Ketenimines, and Cyclic Nitrile Ylides (2003)

Ar matrix photolysis of 1- and 2-naphthyl azides 3 and 4 at 313 nm initially affords the singlet naphthyl nitrenes, (1)()1 and (1)()2. Relaxation to the corresponding lower energy, persistent triplet nitrenes (3)()1 and (3)()2 competes with cyclization to the azirines 15 and 18, which can also be formed photochemically from the triplet nitrenes. On prolonged irradiation, the azirines can be converted to the seven-membered cyclic ketenimines 10 and 13, respectively, as described earlier by Dunkin and Thomson. However, instead of the o-quinoid ketenimines 16 and 19, which are the expected primary ring-opening products of azirines 15 and 18, respectively, we observed their novel bond-shift isomers 17 and 20, which may be formally regarded as cyclic nitrile ylides. The existence of such ylidic heterocumulenes has been predicted previously, but this work provides the first experimental observation of such species. The factors which are responsible for the special stability of the ylidic species 17 and 20 are discussed.
Possible Benefits of Faecalibacterium prausnitzii for Obesity-Associated Gut Disorders (2021)

Metabolic disorders are an increasing concern in the industrialized world. Current research has shown a direct link between the composition of the gut microbiota and the pathogenesis of obesity and diabetes. In only a few weeks, an obesity-inducing diet can lead to increased gut permeability and microbial dysbiosis, which contributes to chronic inflammation in the gut and adipose tissues, and to the development of insulin resistance. In this review, we examine the interplay between gut inflammation, insulin resistance, and the gut microbiota, and discuss how some probiotic species can be used to modulate gut homeostasis. We focus primarily on <i>Faecalibacterium prausnitzii</i>, a highly abundant butyrate-producing bacterium that has been proposed both as a biomarker for the development of different gut pathologies and as a potential treatment due to its production of anti-inflammatory metabolites.
ChemInform Abstract: 2‐Fluoromalonate Esters: Fluoroaliphatic Building Blocks for the Life Sciences (2014)

Abstract Review: 120 refs.