gebhart/patrepeval huggingface dataset:
TAPETUM DETERMINANT1 Is Required for Cell Specialization in the Arabidopsis Anther (2003)

In flowering plants, pollen formation depends on the differentiation and interaction of two cell types in the anther: the reproductive cells, called microsporocytes, and somatic cells that form the tapetum. The microsporocytes generate microspores, whereas the tapetal cells support the development of microspores into mature pollen grains. Despite their importance to plant reproduction, little is known about the underlying genetic mechanisms that regulate the differentiation and interaction of these highly specialized cells in the anther. Here, we report the identification and characterization of a novel tapetum determinant1 (TPD1) gene that is required for the specialization of tapetal cells in the Arabidopsis anther. Analysis of the male-sterile mutant, tpd1, showed that functional interruption of TPD1 caused the precursors of tapetal cells to differentiate and develop into microsporocytes instead of tapetum. As a results, extra microsporocytes were formed and tapetum was absent in developing tpd1 anthers. Molecular cloning of TPD1 revealed that it encodes a small protein of 176 amino acids. In addition, tpd1 was phenotypically similar to excess microsporocytes1/extra sporogenous cells (ems1/exs) single and tpd1 ems1/exs double mutants. These data suggest that the TPD1 product plays an important role in the differentiation of tapetal cells, possibly in coordination with the EMS1/EXS gene product, a Leu-rich repeat receptor protein kinase.
Effect of Fibroblast Donor Cell Age and Cell Cycle on Development of Bovine Nuclear Transfer Embryos In Vitro1 (2001)

The effects of cell cycle stage and the age of the cell donor animal on in vitro development of bovine nuclear transfer embryos were investigated. Cultures of primary bovine fibroblasts were established from animals of various ages, and the in vitro life span of these cell lines was analyzed. Fibroblasts from both fetuses and calves had similar in vitro life spans of approximately 30 population doublings (PDs) compared with 20 PDs in fibroblasts obtained from adult animals. When fibroblasts from both fetuses and adult animals were cultured as a population, the percentage of cells in G1 increased linearly with time, whereas the percentage of S-phase cells decreased proportionately. Furthermore, the percentage of cells in G1 at a given time was higher in adult fibroblasts than in fetal fibroblasts. To study the individual cells from a population, a shake-off method was developed to isolate cells in G1 stage of the cell cycle and evaluate the cell cycle characteristics of both fetal and adult fibroblasts from either 25% or 100% confluent cultures. Irrespective of the age, the mean cell cycle length in isolated cells was shorter (9.6-15.5 h) than that observed for cells cultured as a population. Likewise, the length of the G1 stage in these isolated cells, as indicated by 5-bromo-deoxyuridine labeling, lasted only about 2-3 h. There were no differences in either the number of cells in blastocysts or the percentage of blastocysts between the embryos reconstructed with G1 cells from 25% or 100% confluent cultures of fetal or adult cell lines. This study suggests that there are substantial differences in cell cycle characteristics in cells derived from animals of different ages or cultured at different levels of confluence. However, these factors had no effect on in vitro development of nuclear transfer embryos.
Questions in Fluid Mechanics: Understanding Foams and Foaming (1997)

Technical Forum Questions in Fluid Mechanics: Understanding Foams and Foaming D. D. Joseph D. D. Joseph Aerospace Engineering and Mechanics, University of Minnesota, 107 Akerman Hall, 110 Union St. SE, Minneapolis, MN 55455 Search for other works by this author on: This Site PubMed Google Scholar Author and Article Information D. D. Joseph Aerospace Engineering and Mechanics, University of Minnesota, 107 Akerman Hall, 110 Union St. SE, Minneapolis, MN 55455 J. Fluids Eng. Sep 1997, 119(3): 497-498 (2 pages) https://doi.org/10.1115/1.2819270 Published Online: September 1, 1997 Article history Online: December 4, 2007
Optical security system with Fourier plane encoding (1998)

We propose a new technique for security verification of personal documents and other forms of personal identifications such as ID cards, passports, or credit cards. In this technique a primary pattern that might be a phase-encoded image is convolved by a random code. The information is phase encoded on the personal document. Therefore the information cannot be reproduced by an intensity detector such as a CCD camera. An optical processor based on the nonlinear joint transform correlator is used to perform the verification and the validation of documents with this technique. By verification of the biometrics information and the random code simultaneously, the proposed optical system determines whether a card is authentic or is being used by an authorized person. We tested the performance of the optical system for security and validation in the presence of input noise and in the presence of distortion of the information on the card. The performance of the proposed method is evaluated by use of a number of metrics. Statistical analysis of the system is performed to investigate the noise tolerance and the discrimination against false inputs for security verification.
COSMO: a new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient (1993)

Starting from the screening in conductors, an algorithm for the accurate calculation of dielectric screening effects in solvents is presented, which leads to rather simple explicit expressions for the screening energy and its analytic gradient with respect to the solute coordinates. Thus geometry optimization of a solute within a realistic dielectric continuum model becomes practicable for the first time. The algorithm is suited for molecular mechanics as well as for any molecular orbital algorithm. The implementation into MOPAC and some example applications are reported.
Synthesis of thiocoumarins from acrylic and propiolic ortho esters and benzenethiols (1982)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of thiocoumarins from acrylic and propiolic ortho esters and benzenethiolsJill A. Panetta and Henry RapoportCite this: J. Org. Chem. 1982, 47, 13, 2626–2628Publication Date (Print):June 1, 1982Publication History Published online1 May 2002Published inissue 1 June 1982https://pubs.acs.org/doi/10.1021/jo00134a022https://doi.org/10.1021/jo00134a022research-articleACS PublicationsRequest reuse permissionsArticle Views815Altmetric-Citations13LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Learning to Diagnose: Assimilating Clinical Narratives using Deep Reinforcement Learning (2017)

Clinical diagnosis is a critical and non-trivial aspect of patient care which often requires significant medical research and investigation based on an underlying clinical scenario. This paper proposes a novel approach by formulating clinical diagnosis as a reinforcement learning problem. During training, the reinforcement learning agent mimics the clinician’s cognitive process and learns the optimal policy to obtain the most appropriate diagnoses for a clinical narrative. This is achieved through an iterative search for candidate diagnoses from external knowledge sources via a sentence-by-sentence analysis of the inherent clinical context. A deep Q-network architecture is trained to optimize a reward function that measures the accuracy of the candidate diagnoses. Experiments on the TREC CDS datasets demonstrate the effectiveness of our system over various non-reinforcement learning-based systems.
Compiling high performance Fortran for distributed-memory systems (1995)

a language for writing parallel programs. The compiler generates code for distributed-memory machines consisting of interconnected workstations or servers powered by Digital’s Alpha microprocessors. The DEC Fortran 90 compiler efficiently implements the features of Fortran 90 and HPF that support parallelism. HPF programs compiled with Digital’s compiler yield performance that scales linearly or even superlinearly on significant applications on both distributedmemory and shared-memory architectures.
Formal Intramolecular [5 + 2] Photocycloaddition Reactions of Maleimides:  A Novel Approach to the CDE Ring Skeleton of (−)-Cephalotaxine (2001)

A concise approach to the cephalotaxine CDE ring skeleton based on the intramolecular formal [5 + 2] photocycloaddition of cyclopentenyl-substituted maleimides is described. An investigation of the diastereoselectivity afforded by various protected alkoxy groups demonstrated that the best selectivity (3.5:1) was afforded by the free hydroxyl group, strongly suggesting a hydrogen-bonded excited state. Reaction: see text.
Effect of surface re-emission on the surface roughness of film growth in low pressure chemical vapor deposition (1993)

For films deposited by low pressure chemical vapor deposition (LPCVD) the effect of roughness in the underlying substrate on film microstructure is investigated by computer simulation. Previous workers have assumed a normal surface velocity related to the local surface curvature; however, transport in many LPCVD systems has been shown to be governed by surface re-emission of the deposition precursors with a single sticking coefficient. In this article, the dependence of film profile evolution on both the sticking coefficient of the precursors, as well as the wave number of the underlying roughness is demonstrated. All wave numbers are shown to grow in the small time regime, for all values of the sticking coefficient except zero. At longer times, the mechanism of cusp formation is shown to arrest this growth for small but finite values of the sticking coefficient. In the limit that the sticking coefficient approaches zero, a simple geometric model for profile evolution is developed to accurately predict both the time required for cusp formation, as well as the maximum rate of decay of roughness. All wave numbers grow for large values of the sticking coefficient, eventually leading to the formation of a columnar microstructure with voids. For the sticking coefficient equal to unity, small geometric perturbations on the starting surface are shown to grow into asymptotic columns. Pair interactions between adjacent, unequal perturbations are studied, and larger columns are found to ‘‘shadow’’ smaller columns. For low values of the sticking coefficient, these interactions result in slowing down the decay of surface roughness by an effective halving of the wave number. The conclusions obtained from simulating deposition on periodic, sinusoidal surfaces are shown to be useful in understanding deposition on statistically rough surfaces.
Transforming system operations' interactions into a design class diagram (2007)

This work reports the results of the development of a model transformation realized in Kermeta. This transformation accepts a Domain Model and a set of Communication Diagrams containing the design of system operations corresponding to the same use-case. The result is a Design Class Diagram expressing the class structure that part of a system should logically exhibit in order to enable the occurrence of the interactions specified in the Communication Diagrams. To that end, along with specific meta-models for input models and for the output model, an executable model for the transformation was defined. This paper reviews the elements involved in the development of this transformation, and describes the design of its structure and behavior. The transformation was applied to a case study taken from the bibliography and the results are presented and discussed.
Optomechanical Coupling in a Two-Dimensional Photonic Crystal Defect Cavity (2011)

Periodically structured materials can sustain both optical and mechanical modes. Here we investigate and observe experimentally the optomechanical properties of a conventional two-dimensional suspended photonic crystal defect cavity with a mode volume of ~3(λ/n)³. Two families of mechanical modes are observed: flexural modes, associated to the motion of the whole suspended membrane, and localized modes with frequencies in the GHz regime corresponding to localized phonons in the optical defect cavity of diffraction-limited size. We demonstrate direct measurements of the optomechanical vacuum coupling rate using a frequency calibration technique. The highest measured values exceed 80 kHz, demonstrating high coupling of optical and mechanical modes in such structures.
Comparison of the Promoter Region of the Human and Porcine Choline Acetyltransferase Genes: Localization of an Important Enhancer Region (1993)

Genomic clones of human and porcine choline acetyltransferase were obtained by screening genomic libraries with synthetic oligonucleotides. The human and porcine genes exhibit significant conservation of both their intron/exon structure and the nucleotide sequence in their 5' flanking regions. However, the two genes differ in several respects, including the absence of a "TATA" box in the human gene and differences in the position of the methionine start codon. Analysis of the promoter region of the two genes has led to the localization of an enhancer element that appears necessary for efficient transcription of the gene.
ATM polymorphisms as risk factors for prostate cancer development (2004)

The risk of prostate cancer is known to be elevated in carriers of germline mutations in BRCA2, and possibly also in carriers of BRCA1 and CHEK2 mutations. These genes are components of the ATM-dependent DNA damage signalling pathways. To evaluate the hypothesis that variants in ATM itself might be associated with prostate cancer risk, we genotyped five ATM variants in DNA from 637 prostate cancer patients and 445 controls with no family history of cancer. No significant differences in the frequency of the variant alleles at 5557G>A (D1853N), 5558A>T (D1853V), ivs38-8t>c and ivs38-15g>c were found between the cases and controls. The 3161G (P1054R) variant allele was, however, significantly associated with an increased risk of developing prostate cancer (any G vs CC OR 2.13, 95% CI 1.17-3.87, P=0.016). A lymphoblastoid cell line carrying both the 3161G and the 2572C (858L) variant in the homozygote state shows a cell cycle progression profile after exposure to ionising radiation that is significantly different to that seen in cell lines carrying a wild-type ATM gene. These results provide evidence that the presence of common variants in the ATM gene, may confer an altered cellular phenotype, and that the ATM 3161C>G variant might be associated with prostate cancer risk.
Pyrosequencing Analysis of Bacterial Diversity in 14 Wastewater Treatment Systems in China (2012)

To determine if there is a core microbial community in the microbial populations of different wastewater treatment plants (WWTPs) and to investigate the effects of wastewater characteristics, operational parameters, and geographic locations on microbial communities, activated sludge samples were collected from 14 wastewater treatment systems located in 4 cities in China. High-throughput pyrosequencing was used to examine the 16S rRNA genes of bacteria in the wastewater treatment systems. Our results showed that there were 60 genera of bacterial populations commonly shared by all 14 samples, including Ferruginibacter, Prosthecobacter, Zoogloea, Subdivision 3 genera incertae sedis, Gp4, Gp6, etc., indicating that there is a core microbial community in the microbial populations of WWTPs at different geographic locations. The canonical correspondence analysis (CCA) results showed that the bacterial community variance correlated most strongly with water temperature, conductivity, pH, and dissolved oxygen (DO) content. Variance partitioning analyses suggested that wastewater characteristics had the greatest contribution to the bacterial community variance, explaining 25.7% of the variance of bacterial communities independently, followed by operational parameters (23.9%) and geographic location (14.7%). Results of this study provided insights into the bacterial community structure and diversity in geographically distributed WWTPs and discerned the relationships between bacterial community and environmental variables in WWTPs.
The control of IL-4 gene expression in activated murine T lymphocytes: a novel role for neu-1 sialidase (1997)

IL-4 is important in controlling the development of immune responses. Following activation with anti-CD3epsilon under serum-free conditions, splenocytes from most normal (neu-1b) mouse strains directly produced IL-4 and other T cell cytokines. However, splenic T cells from SM/J and B10.SM (H-2v, neu-1a) strain mice, deficient in neu-1 sialidase activity, failed to produce IL-4 but produced normal levels of IL-2 following activation. Moreover, sialidase-deficient mice produced markedly less IgE and IgG1 Abs following immunization with protein Ags than did mouse strains with normal neu-1 sialidase activity. Enriched T cells from neu-1a mice failed to be effectively primed with exogenous murine IL-4 to become IL-4-producing cells. Treatment of splenocytes or enriched T cells from neu-1a mice with bacterial sialidase prior to activation or IL-4 priming promoted their subsequent capacity to produce IL-4. In contrast, activation of T cells from neu-1b mice in the presence of a sialidase inhibitor almost completely blocked subsequent IL-4 production. The presence of IL-4 during priming enhanced T cell expression of neu-1-specific sialidase activity and increased the membrane expression of asialo-G(M1) compared with T cells activated without IL-4. These results suggest that T cell-associated neu-1 sialidase is required for early IL-4 production by splenic T cells and is involved in the IL-4 priming process of conventional T cells to become active IL-4 producers.
Synthesis of Combs, Centipedes, and Barbwires:  Poly(isoprene-graft-styrene) Regular Multigraft Copolymers with Trifunctional, Tetrafunctional, and Hexafunctional Branch Points (2002)

The synthesis of poly(isoprene-graft-styrene) copolymers with multiple, regularly spaced branch points is reported. The synthetic strategy employs classical anionic polymerization techniques and utilizes a modular approach in which polystyryllithium and α,ω-poly(1,4-)isoprenyldilithium are sequentially incorporated into chlorosilane linking centers. Previous syntheses employing this basic strategy have yielded graft copolymers with trifunctional (“combs”) and tetrafunctional (“centipedes”) branch points. Here we further develop and extend this methodology to include a novel regular multigraft material with hexafunctional branch points (“barbwires”); these materials possess polystyrene side chains of uniform length attached in clusters of four at regularly spaced points along a narrow molecular weight distribution polyisoprene main chain. In the synthesis of barbwires, PSLi is added first to 1,6-bis(trichlorosilyl)hexane, in an incremental fashion, until 4 equiv has been incorporated into the linking silane; LiPILi is next added in a slight stoichiometric excess, resulting in a condensation between macromolecular dinucleophiles and dielectrophiles. Homogeneous multigraft samples of all three architectures were synthesized, with a polydispersity index of about 1.2, through fractionation of the raw condensation products.
Tumorigenicity and metastasis of human breast carcinoma cell lines in nude mice. (1990)

There are few reports describing experimental models of the growth and metastasis of human breast carcinomas. This article discusses the tumorigenic and metastatic properties of two estrogen receptor-negative breast carcinomas injected into nude mice. Tumor growth in the mammary fatpad (m.f.p.) and the subcutis was compared in female nude mice. The injection of 10(5) viable cells of two human breast carcinoma cell lines (MDA-MB-231 and MDA-MB-435) gave a 100% tumor take rate in the m.f.p., whereas only 40% of the s.c. injections produced tumors and these occurred several weeks after the appearance of the m.f.p. tumors. Thus, the m.f.p. of nude mice is a favorable site for the growth of human breast carcinomas. MDA-MB-435 tumors produced distant metastases in 80% to 100% of recipients. The most common sites for metastasis were the lymph nodes and lungs, with a lower incidence of metastases in muscle (chest wall and thigh), heart, and brain. New variant cell lines were isolated from metastases in the lungs, brain, and heart. All the cell lines were tumorigenic in the m.f.p., and the lung- and heart-derived metastasis lines produced slightly more lung metastases than the original cell line. However, the brain metastasis variant produced significantly fewer lung metastases. Intravenous inoculation of the spontaneous metastasis-derived cell lines produced few lung colonies. Only cell variants isolated from experimental lung metastases showed enhanced lung colonization potential when reinjected i.v. Our results suggest that the estrogen receptor-negative MDA-MB-435 cell line injected in the m.f.p. of nude mice could be a valuable tool for analysis of the cellular and molecular basis of the metastasis of advanced breast cancer.
Lipoprotein-Associated Phospholipase A 2 and C-Reactive Protein for Risk-Stratification of Patients With TIA (2009)

Many patients with TIA have a high-risk mechanism (large vessel stenosis or cardioembolism) or will experience stroke/death within 90 days. In contrast to CRP, both Lp-PLA(2) mass and activity were associated with this composite end point, and LpPLA(2)-A appears to provide additional prognostic information beyond the ABCD(2) clinical risk score alone.
Long-Term Sustainable Aluminum Precursor Solution for Highly Conductive Thin Films on Rigid and Flexible Substrates (2014)

To fabricate the highly conductive Al film via a solution process, AlH3 etherates have been a unique Al source despite their chemical instability in solvents and thus lack of long-term sustainability. Herein, we suggest an innovative solution process to overcome the aforementioned drawbacks in AlH3 etherates; AlH3 aminates powder, which can be stored in low temperature surroundings and redissolved in solvents whenever it is needed. Since refrigeration of AlH3 aminates, AlH3{N(CH3)3}, was very effective to prevent its chemical degradation, Al film with excellence and uniformity in electrical and mechanical properties was successfully fabricated even by the 180-day stored AlH3{N(CH3)3} dissolved in solvents. Moreover, the applicability of long-term stored AlH3{N(CH3)3} to electronic devices was experimentally demonstrated by the successful operation of LED lamps connected to the Al pattern films on glass, PET, and paper substrates.