gebhart/patrepeval huggingface dataset:
M&A For Lithography Of Sparse Arrays Of Sub-Micrometer Features (1998)

Here, we overview the most recent advances in understanding the bacterial mechanisms that stay behind the reduction of tellurium oxyanions in both planktonic cells and biofilms. This is a topic of interest for basic and applied research because microorganisms are deeply involved in the transformation of metals and metalloids in the environment. In particular, the recent observation that toxic tellurite can be precipitated either inside or outside the cells being used as electron sink to support bacterial growth, opens new perspectives for both microbial physiologists and biotechnologists. As promising nanomaterials, tellurium based nanoparticles show unique electronic and optical properties due to quantum confinement effects to be used in the area of chemistry, electronics, medicine and environmental biotechnologies.
Direct imprinting of dielectric materials for dual damascene processing (2005)

Advanced microprocessors require several (eight or more) levels of wiring to carry signal and power from transistor to transistor and to the outside world. Each wiring level must make connection to the levels above and below it through via/contact layers. The dual damascene approach to fabricating these interconnected structures creates a wiring level and a via level simultaneously, thereby reducing the total number of processing steps. However, the dual damascene strategy (of which there are several variations) still requires around twenty process steps per wiring layer. In this work, an approach to damascene processing that is based on step-and-flash imprint lithography (SFIL) is discussed. This imprint damascene process requires fewer than half as many steps as the standard photolithographic dual damascene approach. By using an imprint template with two levels of patterning, a single imprint lithography step can replace two photolithography steps. Further efficiencies are possible if the imprint resist material is itself a functional dielectric material. This work is a demonstration of the compatibility of imprint lithography (specifically SFIL) with back-end-of-line processing using a dual damascene approach with functional materials.
The Role of the Estrogen Receptor Coactivator, Amplified in Breast Cancer 1 (AIB1), in Her2/neu-Initiated Mouse Mammary Carcinogenesis and Tamoxifen Resistance. (2008)

Amplified in Breast Cancer 1 (AIB1), a p160 nuclear receptor coactivator family member, is involved in steroid receptor-mediated transcription. The AIB1 gene is amplified in 5-10% of breast cancers, suggesting that AIB1 plays an important role in breast cancer progression. AIB1 directly interacts with estrogen receptor alpha (ERα) and enhances ER-dependent transcription in breast cancer cells. Overexpression of AIB1 in conjunction with Her2/neu overexpression has been shown to lead to resistance to therapy with the anti-estrogen, Tamoxifen. However, the roles AIB1 plays in breast cancer pathogenesis, estrogen signaling, and Tamoxifen resistance remain unclear. The purpose of this study was to determine the nature of the interaction between AIB1 and her2/neu in the mammary gland using a mouse model of her2-initiated mammary cancer. At four months of age mammary gland biopsy was performed on conditional transgenic mice overexpressing AIB1 with and without overexpression of her2/neu. Mammary gland morphology from the biopsy was examined by mammary gland whole mount and histological analyses and expression studies by RNA and protein analyses. Directly following the biopsy, a slow release Tamoxifen pellet was implanted under the skin of the mouse. After two months of exposure to Tamoxifen the other mammary glands were harvested for histological, mRNA and protein analyses. Mammary tissue was also examined using reflectance confocal microscopy (RCM) which yields unprocessed real-time imaging of mammary gland ductal epithelial cell morphology. Epithelial changes observed using RCM can be correlated with mammary gland histology and morphology after tissue fixation. Mammary gland morphology before and after Tamoxifen exposure will be compared to establish the presence of Tamoxifen resistance in AIB1 mice with and without overexpression of her2/neu. Differences in morphology, signaling pathways, growth, proliferation, apoptosis, and differentiation will be determined. We have examined whether targeted AIB1 overexpression collaborates with her2/neu in this model to stimulate proliferation and activate growth signaling pathways by studying mammary gland morphology changes by mammary gland whole mount and H&E analyses. We have observed that overexpression of AIB1 alone promotes the development of abnormal mammary ductal branching. We will examine further the hypothesis that overexpression of AIB1 can enhance the progression of carcinogenesis in mice with her2/neu overexpression. We will determine if overexpression of both AIB1 and her2/neu in the same mouse will lead to Tamoxifen sensitivity or resistance.
Abstract 4943: microRNAs as clinical biomarkers for lung cancer classification (2011)

Abstract Background: Lung cancers have traditionally been subdivided into two main groups: Small Cell Lung Cancer (SCLC) and Non Small Cell Lung Cancer (NSCLC). Due to limited tumor sample amounts and an abundance of poor quality samples, accurate subclassification of primary lung cancer using small pre-operative biopsies presents a diagnostic challenge using current tools (H&E and immunohistochemical stains). For patients with primary lung cancer, accurate determination of the tumor type significantly influences treatment decisions. Our previous studies have shown that microRNAs are differentially expressed in different subtypes of lung cancer; hence microRNA expression profiling holds a promising new strategy for the precise subclassification of lung cancers. Based on these findings, we present here the development of a microRNA-based qRT-PCR diagnostic assay that uses pathology and cytology samples in order to classify primary lung cancers into four subtypes: squamous, non-squamous, SCLC and carcinoid. Methods: FFPE tissue blocks and cell blocks from different histological subtypes of lung cancer, taken from primary lung cancer resection or pre-operative diagnostic procedures, were collected. High-quality RNA, including the well-preserved microRNA fraction, was extracted from the samples using proprietary protocols. Expression levels of potential microRNA biomarkers were profiled using a sensitive and specific qRT-PCR platform. Results: We find that combinations of a few microRNAs can successfully differentiate between different histological types of lung tumors. A classification algorithm was developed that reached high accuracy in the identification of the four main subtypes of lung tumors. Conclusion: We developed a highly accurate microRNA-based diagnostic assay that classifies primary lung cancer types with very high sensitivity and specificity. This assay is a simple and reliable diagnostic assay which will offer an accurate and standardized tool for primary lung cancer cytological samples, including those that presently fail pathological evaluation. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4943. doi:10.1158/1538-7445.AM2011-4943
Phase alignment transmit diversity for TDD systems (2002)

Phase alignment transmit diversity (PATD) is a novel technique for adjusting the phases of transmit adaptive antennas arrays based on joint optimisation of multiple users signals. This technique is equivalent to transmit adaptive antennas (TxAA) for the single user case. However, as the number of users jointly optimised increases, the gains remain significant but sub-optimal compared to TxAA gains. PATD uses a single parameter for all the users at the same time, minimising implementation complexity and costs. In the UMTS TDD mode case PATD is completely transparent to the MS receiver whereas TxAA requires modifications in the receiver structure (i.e. requires as many channel estimates as users sharing the same time slot). PATD can also be applied to broadcast PMR systems.
Aluminum Silicate Aerogels with High Temperature Stability (2009)

This chapter contains sections titled: Introduction Experimental Methods Characterization Methods Results XRD Analysis of Aerogels Conclusions
Analysis of genetic copy number changes in cervical disease progression (2010)

The application of a FISH assay comprised of chromosomal probes 8q24 and 3q26 to cervical cytology specimens confirms the positive correlation between increasing dysplasia and copy gains and shows promise as a marker in cervical disease progression.
Defining and Implementing Commutativity Conditions for Parallel Execution (2009)

Irregular applications, which manipulate complex, pointer-based data structures, are a promising target for parallelization. Recent studies have shown that these programs exhibit a kind of parallelism called amorphous data-parallelism. Prior approaches to parallelizing these applications, such as thread-level speculation and transactional memory, often obscure parallelism because they do not distinguish between the concrete representation of a data structure and its semantic state; they conflate metadata and data. Exploiting the semantic commutativity of methods in complex data structures is a promising approach to exposing more parallelism. Prior work has shown that abstract locks can be used to capture a subset of commutativity properties, however, abstract locks cannot uncover the parallelism in some complex data structures, such as kd-trees and union-find structures. In this paper, we propose a more flexible implementation of commutativity properties, called gatekeepers, which capture more complex commutativity conditions and thus expose more parallelism. We provide a formal definition of semantic commutativity and define conditions under which abstract locking can be applied and those under which gatekeeping is necessary. We present a quantitative study demonstrating the benefits of abstract locking and gatekeeping in amorphous data-parallel programs. We also present an efficient implementation of gatekeeping, which we evaluate on a real-world application. 1.
Test and testability techniques for open defects in RAM address decoders (1996)

It is a prevalent assumption that all RAM address decoder defects can be modelled as RAM array faults influencing one or more RAM cells. Therefore, can be implicitly detected by testing the RAM matrix with the march tests. Recently, we came across some failures in embedded SRAMs which were not detected by the march tests. The carried out analysis demonstrated the presence of open defects in address decoders that can not be modelled as the conventional coupling faults, therefore, are not detected by the march tests. In this article, we present the test and testability strategies for such hard to detect open defects.
Sporolactobacillus vineae sp. nov., a spore-forming lactic acid bacterium isolated from vineyard soil (2008)

Two spore-forming, facultatively anaerobic, lactic acid bacteria, strains SL153(T) and SL1153, were isolated from vineyard soil in Korea. Cells of both strains were slightly curved, Gram-positive, motile rods that measured between 1 and 4 mum in length and were approximately 0.5 mum in diameter. Strains SL153(T) and SL1153 fermented glucose, fructose, mannose and sorbitol, but were negative for nitrate reduction, catalase and oxidase. The predominant cellular fatty acids of the two isolates were iso-C(15 : 0), anteiso-C(15 : 0) and anteiso-C(17 : 0). meso-Diaminopimelic acid, glucose, mannose and galactose were determined in their whole-cell hydrolysates. 16S rRNA gene sequences from the two strains were almost identical (99.9 %) and they could be placed in the genus Sporolactobacillus according to phylogenetic analysis. The species most closely related to SL153(T) were Sporolactobacillus inulinus and Sporolactobacillus terrae with 16S rRNA gene similarities of 95.7 and 95.5 %, respectively, with the type strains. Levels of DNA-DNA relatedness between strain SL153(T) and the type strains of S. inulinus, S. terrae and Sporolactobacillus kofuensis were 18.5, 18.0 and 17.0 %, respectively. On the basis of the phylogenetic (16S rRNA gene), chemotaxonomic and phenotypic evidence given in this study, it is proposed that strains SL153(T) and SL1153 should be assigned to the genus Sporolactobacillus as representatives of the novel species Sporolactobacillus vineae sp. nov. The type strain is SL153(T) (=KCTC 5376(T)=JCM 14637(T)).
Simple method of light-shift suppression in optical pumping systems (2009)

We report a simple method to suppress the light shift in optical pumping systems. This method uses only frequency modulation of a radio frequency or microwave source, which is used to excite an atomic resonance, to simultaneously lock the source frequency to the atomic resonance and lock the pumping light frequency to suppress the light shift. We experimentally validate the method in a vapor-cell atomic clock and verify the results through numerical simulation. This technique can be applied to many optical pumping systems that experience light shifts. It is especially useful for atomic frequency standards because it improves long-term performance, reduces the influence of the laser, and requires less equipment than previous methods.
Daidzein–Estrogen Interaction in the Rat Uterus and Its Effect on Human Breast Cancer Cell Growth (2012)

Sex hormone replacement therapy provides several advantages in the quality of life for climacteric women. However, estrogen-induced cell proliferation in the uterus and mammary gland increases the risk of cancer development in these organs. The lower incidence of mammary cancer in Asian women as compared with Western women has been attributed to high intake of soy isoflavones, including genistein. We have previously shown that genistein induces an estradiol-like hypertrophy of uterine cells, but does not induce cell proliferation, uterine eosinophilia, or endometrial edema. It also inhibits estradiol-induced mitosis in uterine cells and hormone-induced uterine eosinophilia and endometrial edema. Nevertheless, genistein stimulates growth of human breast cancer cells in culture; therefore, it is not an ideal estrogen for use in hormone replacement therapy (HRD). The present study investigated the effect of another soy isoflavone, daidzein (subcutaneous, 0.066 mg/kg body weight), in the same animal model, and its effect on responses induced by subsequent treatment (1 h later) with estradiol-17β (E(2); subcutaneous, 0.33 mg/kg body weight). In addition, we investigated the effects of daidzein (1 μg/mL) or E(2) on the growth of human breast cancer cells in culture. Results indicate that daidzein stimulates growth of breast cancer cells and potentiates estrogen-induced cell proliferation in the uterus. We suggest caution for the use of daidzein or formulas containing this compound in HRD. Future research strategies should be addressed in the search for new phytoestrogens that selectively inhibit cell proliferation in the uterus and breast.
Breeding of blue chrysanthemums by genetic engineering (2019)

Breeding of blue flowers in commercially important ornamental plants, such as chrysanthemum and rose, is relatively difficult by conventional breeding techniques because there are no closely-related species with blue flowers. Therefore, the creation of novel blue flowers has been attempted in various ornamental plants by using biotechnology. As a result, bluish colored carnations and roses have been produced and successfully commercialized. Our research group has also succeeded in developing technology based on genetic engineering to confer the pure blue flower color trait to chrysanthemum (Chrysanthemum morifolium). The blue coloration of the chrysanthemum was accomplished by constructing functional genes producing flavonoid 3’,5’-hydroxylase and anthocyanin 3’,5’-O-glucosyltransferase. Accumulation of 3’,5’-O-glucosylated delphinidin-based anthocyanins synthesized by the transgenes led to the development of blue color via intermolecular copigmentation with flavone glycosides present in chrysanthemum petal. Subsequently, by introducing the two genes necessary for blue petal coloration, we succeeded in conferring the blue flower color trait to various chrysanthemums with different floral shapes and color shades. Successful commercialization of blue chrysanthemums should facilitate an expansion of flower color variation, increase potential flower value, and raise new possibilities and applications for chrysanthemums. Furthermore, in vitro experiments suggested that, in addition to flavone glycosides, flavonol glycosides might have an effect on 3’,5’-O-glucosylated delphinidin-based anthocyanins as blue-coloring copigments in planta. These results indicate that the method established in chrysanthemums for the blue color development of petals by hydroxylation and glucosylation of the B-ring of anthocyanins is likely to be applicable to other ornamental plants.
A process to enhance the specific surface area and capacitance of hydrothermally reduced graphene oxide (2016)

The impact of post-synthesis processing in reduced graphene oxide materials for supercapacitor electrodes has been analyzed. A comparative study of vacuum, freeze and critical point drying was carried out for hydrothermally reduced graphene oxide demonstrating that the optimization of the specific surface area and preservation of the porous network are critical to maximize its supercapacitance performance. As described below, using a supercritical fluid as the drying medium, unprecedented values of the specific surface area (364 m<sup>2</sup> g<sup>-1</sup>) and supercapacitance (441 F g<sup>-1</sup>) for this class of materials have been achieved.
Luciferases of Luminous Beetles: Evolution, Color Variation, and Applications. (1992)

Abstract : The biochemical basis of beetle luminescence is unrelated evolutionarily to other bioluminescent systems that have been characterized at a molecular level, such as of marine invertebrates (e.g. Aequorea or Varguia) or bacteria. To advance the study of the beetle system. cDNA's coding several luciferases have been cloned and expressed in Escherichia coli. Cells expressing the cDNA clones can be induced for luminescence when the substrate, luciferin, is supplied to the growth medium. The physical and enzymatic properties of the beetle luciferases synthesized in E. coli were found to be essentially identical with native enzymes extracted from beetle light organs. This equivalence of enzyme derived from native and recombinant sources indicates that beetle luciferases are homomeric enzymes without substantial covalent modification of the primary translation product (e.g. proteolytic cleaves or glycosylations).
Assays of type I procollagen domains and collagen fragments: Problems to be solved and future trends (1997)

The biochemical possibilities for developing specific assays for type I collagen metabolism are described. Type I collagen synthesis can be assessed either by the analysis of the carboxyterminal or aminoterminal propeptides, which are in principle produced in a molar ratio of 1:1. However, in clinical situations altered behaviour can be found, the reasons for which may be altered clearance or even the existence of variant forms of type I collagen. Type I collagen degradation can be specifically detected by analysis of either cross-linked carboxy- or aminoterminal telopeptides or by the cross-links themselves liberated during the degradation processes. The heterogeneity of the cross-links and the constituent chains of the cross-linked peptides in different tissues and possibly in different clinical situations introduce problems, which should be studied and resolved in the future.
Levitator for Containerless Processing (1982)

Objects are levitated by aerodynamic forces in an apparatus originally developed for space research but just as effective on Earth. New levitator is orientation-independent. Also works equally as well whether or not gravity is present. Apparatus supports a sphere by aerodynamic forces from gas flowing through convergent/divergent section. Concentric inner tube is moved along axis of cylindrical housing.
Leveraging the Trusted Clinician: Increasing Retention in Disease Management through Integrated Program Delivery (2008)

Disease management's (DM's) value largely depends on achieving and maintaining participation. Simply being enrolled in a program does not guarantee engaged participation by enrollees, a necessary factor to achieve the improved health outcomes and subsequent reduced health care costs that are the ultimate objective of DM. The objective of this study is to test the hypothesis that an integrated disease management (IDM) protocol (patent-pending), which combines telephonic-delivered disease management (TDM) with a worksite-based primary care center and pharmacy delivery, yields higher patient retention rates than traditional remote DM alone. An earlier study of the IDM protocol found that integrating a worksite-based primary care and pharmacy delivery system with traditional telephonic-based DM substantially increased contact, enrollment, and engagement rates compared to traditional stand-alone telephonic DM. This prospective cohort study tracks contact and enrollment rates for persons assigned to either IDM or traditional TDM protocols and compares participation rates at 6- and 12-month intervals as well as measures of continued retention in the DM program. The IDM protocol showed a significant improvement in participation persistence over traditional TDM. Integrating a worksite-based primary care and pharmacy delivery system led by "trusted clinicians at the workplace"trade mark with traditional telephonic-based DM not only increases contact and enrollment rates, but also results in higher patient engagement and retention. These improvements in participation are expected to result in improved outcomes for a larger proportion of the target population than traditional telephonic DM.
Fair Bayesian Optimization (2021)

Given the increasing importance of machine learning (ML) in our lives, several algorithmic fairness techniques have been proposed to mitigate biases in the outcomes of the ML models. However, most of these techniques are specialized to cater to a single family of ML models and a specific definition of fairness, limiting their adaptibility in practice. We introduce a general constrained Bayesian optimization (BO) framework to optimize the performance of any ML model while enforcing one or multiple fairness constraints. BO is a model-agnostic optimization method that has been successfully applied to automatically tune the hyperparameters of ML models. We apply BO with fairness constraints to a range of popular models, including random forests, gradient boosting, and neural networks, showing that we can obtain accurate and fair solutions by acting solely on the hyperparameters. We also show empirically that our approach is competitive with specialized techniques that enforce model-specific fairness constraints, and outperforms preprocessing methods that learn fair representations of the input data. Moreover, our method can be used in synergy with such specialized fairness techniques to tune their hyperparameters. Finally, we study the relationship between fairness and the hyperparameters selected by BO. We observe a correlation between regularization and unbiased models, explaining why acting on the hyperparameters leads to ML models that generalize well and are fair.