gebhart/patrepeval huggingface dataset:
Synergy between methionine stress and chemotherapy in the treatment of brain tumor xenografts in athymic mice. (2001)

This study describes a novel approach to the treatment of brain tumors with the combination of recombinant L-methionine-alpha-deamino-gamma-lyase and chemotherapeutic regimens that are currently used against such tumors. The growth of Daoy, SWB77, and D-54 xenografts in athymic mice was arrested after the depletion of mouse plasma methionine (MET) with a combination of a MET- and choline-free diet and recombinant L-methionine-alpha-deamino-gamma-lyase. The treated tumor-bearing mice were rescued from the toxic effects of MET withdrawal with daily i.p. homocystine. This regimen suppressed plasma MET to levels below 5 microM for several days, with no treatment-related deaths. MET depletion for 10-12 days induced mitotic and cell cycle arrest, apoptotic death, and widespread necrosis in tumors but did not prevent tumor regrowth after cessation of the regimen. However, when a single dose of 35 mg/m(2) of N,N'-bis(2-chloroethyl)-N-nitrosourea (BCNU), which was otherwise ineffective as a single therapy in any of the tumors tested, was given at the end of the MET depletion regimen, a more than 80-day growth delay was observed for Daoy and D-54, whereas the growth of SWB77 was delayed by 20 days. MET-depleting regimens also trebled the efficacy of temozolomide (TMZ) against SWB77 when TMZ was given to animals as a single dose of 180 mg/m(2) at the end of a 10-day period of MET depletion. The enhanced responses of both Daoy and SWB77 to DNA alkylating agents such as BCNU and TMZ could be attributed to the down-regulation of O(6)-methylguanine-DNA methyltransferase activity. However, the synergy of MET depletion and BCNU observed with D-54 tumors, which do not express measurable O(6)-methylguanine-DNA methyltransferase protein, is probably mediated by a different mechanism. MET depletion specifically sensitizes tumors to alkylating agents and does not significantly lower the toxicity of either BCNU or TMZ for the host. In this regard, the combination approach of MET depletion and genotoxic chemotherapy demonstrates significant promise for clinical evaluation.
A bipolar 4:1 time division multiplexer IC operating up to 5.5Gb/s (1986)

A 4:1 multiplexer, composed of three 2:1 multiplexers, operating up to 5.5Gb/s will be reported. To attain this speed, internal voltage swings were limited to 0.4V differential, and a fast output buffer was employed. An IC was fabricated in a 2μm oxide-isolated bipolar process.
‘Silly Novels’? Gender and the Westminster Review at Mid-century (2001)

Cultural criticism of our own period often takes ‘gender’ to denote ‘women’ and the woman question in the nineteenth century. I shall argue here that the ‘contraband’ contents of the Westminster Review between 1850 and 1865 address the subject of gender at its most inclusive. I suggest that this is only in part due to the Westminster’s well-known affiliations with progressives such as the Philosophical Radicals, and that its adherence to the topical — the domestic, political ‘news’ of the day, in which gender figured repeatedly2 — is the other principal factor, irrespective of any characteristic ‘set pattern’ of kinds of articles successive issues reproduce.3 In a period in which gender is inscribed in a telling variety of discourses in print culture generally — from In Memoriam to Men and Women, homosocial to straight, the Westminster is no exception: where articles on ‘Prostitution’ and ‘Enfranchisement of Women’ appear in the early 1850s, those on Aurora Leigh and the Divorce Bill appear later in the decade.
Compressible area fill synthesis (2005)

Control of variability and performance in the back end of the VLSI manufacturing line has become extremely difficult with the introduction of new materials such as copper and low-k dielectrics. To improve manufacturability, and in particular to enable more uniform chemical-mechanical planarization (CMP), it is necessary to insert area fill features into low-density layout regions. Because area fill feature sizes are very small compared to the large empty layout areas that need to be filled, the filling process can increase the size of the resulting layout data file by an order of magnitude or more. To reduce file transfer times, and to accommodate future maskless lithography regimes, data compression becomes a significant requirement for fill synthesis. In this paper, we make the following contributions. First, we define two complementary strategies for fill data volume reduction corresponding to two different points in the design-to-manufacturing flow: compressible filling and post-fill compression . Second, we compare compressible filling methods in the fixed-dissection regime when two different sets of compression operators are used: the traditional GDSII array reference (AREF) construct, and the new Open Artwork System Interchange Standard (OASIS) repetitions. We apply greedy techniques to find practical compressible filling solutions and compare them with optimal integer linear programming solutions. Third, for the post-fill data compression problem, we propose two greedy heuristics, an exhaustive search-based method, and a smart spatial regularity search technique. We utilize an optimal bipartite matching algorithm to apply OASIS repetition operators to irregular fill patterns. Our experimental results indicate that both fill data compression methodologies can achieve significant data compression ratios, and that they outperform industry tools such as Calibre V8.8 from Mentor Graphics. Our experiments also highlight the advantages of the new OASIS compression operators over the GDSII AREF construct.
Phenotypic Characterization of Toxic Compound Effects on Liver Spheroids Derived from iPSC Using Confocal Imaging and Three-Dimensional Image Analysis (2016)

Cell models are becoming more complex to better mimic the in vivo environment and provide greater predictivity for compound efficacy and toxicity. There is an increasing interest in exploring the use of three-dimensional (3D) spheroids for modeling developmental and tissue biology with the goal of accelerating translational research in these areas. Accordingly, the development of high-throughput quantitative assays using 3D cultures is an active area of investigation. In this study, we have developed and optimized methods for the formation of 3D liver spheroids derived from human iPS cells and used those for toxicity assessment. We used confocal imaging and 3D image analysis to characterize cellular information from a 3D matrix to enable a multi-parametric comparison of different spheroid phenotypes. The assay enables characterization of compound toxicities by spheroid size (volume) and shape, cell number and spatial distribution, nuclear characterization, number and distribution of cells expressing viability, apoptosis, mitochondrial potential, and viability marker intensities. In addition, changes in the content of live, dead, and apoptotic cells as a consequence of compound exposure were characterized. We tested 48 compounds and compared induced pluripotent stem cell (iPSC)-derived hepatocytes and HepG2 cells in both two-dimensional (2D) and 3D cultures. We observed significant differences in the pharmacological effects of compounds across the two cell types and between the different culture conditions. Our results indicate that a phenotypic assay using 3D model systems formed with human iPSC-derived hepatocytes is suitable for high-throughput screening and can be used for hepatotoxicity assessment in vitro.
The in vitro biological activities of synthetic 18-O-methyl mycalamide B, 10-epi-18-O-methyl mycalamide B and pederin. (1997)

Mycalamides A and B, which were originally isolated from a marine sponge, show close structural similarity to the insect toxin pederin, and exhibit potent cytotoxicity and antitumour activity. Detailed investigation of the clinical potential of these compounds has been hampered because they are available in only minute quantities from natural sources. We now describe the biological activities of 18-O-methyl mycalamide B, 10-epi-18-O-methyl mycalamide and pederin, all prepared by total synthesis. The activities of 18-O-methyl mycalamide B and pederin were virtually indistinguishable when evaluated in DNA or protein synthesis assays, and in cytotoxicity assays using human carcinoma cell lines (IC50s 0.2-0.6 nM). In all assays, 10-epi-18-O-methyl mycalamide B was 10(3) times less toxic than its diastereoisomer, demonstrating that the cytotoxicity of 18-O-methyl mycalamide B is inseparable from its ability to inhibit protein synthesis. Short-term exposure of squamous carcinoma cells to 18-O-methyl mycalamide B or pederin caused an irreversible inhibition of cellular proliferation and induced cellular necrosis. In contrast, the antiproliferative effects of the compounds on human fibroblasts were reversible and there was no evidence of necrosis. Demonstration that 18-O-methyl mycalamide B and the synthetically less complex molecule, pederin, show some tumour cell toxicity indicates that this novel class of compounds should be subjected to preclinical evaluation.
Building Pipelines for Heterogeneous Execution Environments for Big Data Processing (2016)

Many real-world data analysis scenarios require pipelining and integration of multiple (big) data-processing and data-analytics jobs, which often execute in heterogeneous environments, such as MapReduce; Spark; or R, Python, or Bash scripts. Such a pipeline requires much glue code to get data across environments. Maintaining and evolving these pipelines are difficult. Pipeline frameworks that try to solve such problems are usually built on top of a single environment. They might require rewriting the original job to take into account a new API or paradigm. The Pipeline61 framework supports the building of data pipelines involving heterogeneous execution environments. It reuses the existing code of the deployed jobs in different environments and provides version control and dependency management that deals with typical software engineering issues. A real-world case study shows its effectiveness. This article is part of a special issue on Software Engineering for Big Data Systems.
AN INTEGRATED SPATIAL INDEXING OF HUGE POINT IMAGE MODEL (2012)

Abstract. In order to manage point image model easier and build the point cloud model on the basis of the need and improve the query efficiency, a 2D&amp;3D integrated spatial index of large point image model is proposed in this paper. Point image is managed by 2D quad tree and 3D MBB. Point image model constituted by point image are indexed by 3D-R tree. Finally the organized hierarchical model and other attribute data are stored in commercial database. The storage, management and visualization of large point image model are verified on the ordinary PCs. The experiment data are derived from the representative ancient buildings in Forbidden City. Experimental results show that the algorithm is able to manage more than 10G-level data and one billion valid points with satisfactory rendering efficiency.
Genome-wide identification and annotation of HIF-1α binding sites in two cell lines using massively parallel sequencing (2010)

The online version of this article (doi:10.1007/s11568-011-9150-9) contains supplementary material, which is available to authorized users.
RamB, a Novel Transcriptional Regulator of Genes Involved in Acetate Metabolism of <i>Corynebacterium glutamicum</i> (2004)

The adaptation of Corynebacterium glutamicum to acetate as a carbon and energy source involves transcriptional regulation of the pta-ack operon coding for the acetate-activating enzymes phosphotransacetylase and acetate kinase and of the aceA and aceB genes coding for the glyoxylate cycle enzymes isocitrate lyase and malate synthase, respectively. Deletion and mutation analysis of the respective promoter regions led to the identification of highly conserved 13-bp motifs (AA/GAACTTTGCAAA) as cis-regulatory elements for expression of the pta-ack operon and the aceA and aceB genes. By use of DNA affinity chromatography, a 53-kDa protein specifically binding to the promoter/operator region of the pta-ack operon was purified. Mass spectrometry and peptide mass fingerprinting identified the protein as a putative transcriptional regulator (which was designated RamB). Purified His-tagged RamB protein was shown to bind specifically to both the pta-ack and the aceA/aceB promoter/operator regions. Directed deletion of the ramB gene in the genome of C. glutamicum resulted in mutant strain RG1. Whereas the wild type of C. glutamicum showed high-level specific activities of acetate kinase, phosphotransacetylase, isocitrate lyase, and malate synthase when grown on acetate and low-level specific activities when grown on glucose as sole carbon and energy sources, mutant RG1 showed high-level specific activities with all four enzymes irrespective of the substrate. Comparative transcriptional cat fusion experiments revealed that this deregulation takes place at the level of transcription. The results indicate that RamB is a negative transcriptional regulator of genes involved in acetate metabolism of C. glutamicum.
Infectious diarrhea: when to test and when to treat (2010)

Acute gastrointestinal illness is common. An estimated 1.3 episodes per person occur each year in Canada, which translates to more than 40 million incidents at an estimated cost of $3.7 billion annually.[1][1] Acute diarrhea is the second most common reason travellers returning from developing
Oxidation of Proline by Plant Mitochondria (1978)

Mitochondria isolated from etiolated shoots of corn (Zea mays), wheat (Triticum aestivum), barley (Hordeum vulgare), soybean (Glycine max L. Merr.), and mung bean (Phaseolus aureus) exhibited a proline-dependent O(2) uptake subject to respiratory control. ADP/O ratios with proline as substrate were intermediate between ratios obtained with exogenous NADH and malate + pyruvate as substrates. Isotope studies showed proline metabolism to be dependent on O(2), but not NAD. The major ninhydrin-positive product formed via Delta(1)-pyrroline-5-carboxylic acid was glutamate. Mitochondria were capable of further metabolism of glutamate, as radioactive CO(2), organic acids, and aspartate were recovered after [(14)C]proline feeding experiments. These results demonstrate the mitochondrial association and O(2) dependence of plant proline metabolism.
Orthogonal chip mount - A 3D hybrid wafer scale integration technology (1987)

In the last decade, device scaling in the integrated circuit technology has permitted a drastic improvement in the density of electronic systems. This trend will continue in the next decade. However, submicron feature sizes involved will demand escalating investment in manufacturing equipment and facilities. MOS technology will also reach its fundamental scaling limit at around 0.2 µm. At this time it is necessary that alternative schemes of system density improvement, which are more cost-effective, be explored. Three-dimensional (3D) hybrid wafer scale integration technologies offer this possibility. Such a novel approach, called Orthogonal Chip Mount (OCM), is introduced and described in this paper.
Nuclear reprogramming (2013)

There is currently particular interest in the field of nuclear reprogramming, a process by which the identity of specialised cells may be changed, typically to an embryonic-like state. Reprogramming procedures provide insight into many mechanisms of fundamental cell biology and have several promising applications, most notably in healthcare through the development of human disease models and patient-specific tissue-replacement therapies. Here, we introduce the field of nuclear reprogramming and briefly discuss six of the procedures by which reprogramming may be experimentally performed: nuclear transfer to eggs or oocytes, cell fusion, extract treatment, direct reprogramming to pluripotency and transdifferentiation.
<i>In Situ</i> Prepared Transparent Polyaniline Electrode and Its Application in Bifacial Dye-Sensitized Solar Cells (2011)

Highly uniform and transparent polyaniline (PANI) electrodes that can be used as counter electrodes in dye-sensitized solar cells (DSSCs) were prepared by a facile in situ polymerization method. They were used to fabricate a novel bifacially active transparent DSSC, which showed conversion efficiencies of 6.54 and 4.26% corresponding to front- and rear-side illumination, respectively. Meanwhile, the efficiency of the same photoanode employing a Pt counter electrode was 6.69%. Compared to conventional Pt-based DSSCs, the design of the bifacial DSSC fabricated in this work would help to bring down the cost of energy production due to the lower cost of the materials and the higher power-generating efficiency of such devices for their capabilities of utilizing the light from both sides. These promising results highlight the potential application of PANI in cost-effective, transparent DSSCs.
Further studies on the feasibility of one-day Salmonella detection by enzyme-linked immunosorbent assay (1993)

A model system previously developed for the rapid detection of Salmonella typhimurium in foods was improved and extended to many other Salmonella serotypes. The original protocol, which consisted of an overnight nonselective culture followed by a specific enzyme-linked immunosorbent assay (ELISA), was modified and improved. A sandwich ELISA which used polyclonal antibodies for the capture stage and a cocktail of monoclonal antibodies for the detector stage was developed. The assay recognized a wide range of Salmonella serotypes; S. enteritidis, the most important serotype in the United Kingdom had a detection limit in the ELISA of about 4 x 10(2) cells ml-1. The cultural stage prior to the ELISA was either a single nonselective broth (incubated for 28 h) or a preenrichment broth (incubated for 7 h) plus a selective broth (incubated for 21 h). Antibodies which bind to cells grown in the unfavorable conditions of a selective medium were selected. It was concluded that, in the future, the shortened protocols for the detection of Salmonella spp. in foods described here will be of considerable value.
Treatment of early Rheumatoid Arthritis with minocycline or placebo. Results of a Randomized, double‐blind, placebo‐controlled trial (1997)

In patients with early seropositive RA, therapy with minocycline is superior to placebo.
Scattered data modeling (1993)

A variety of methods for modeling scattered data are discussed, with an emphasis on two types of data: volumetric and spherical. To demonstrate the performance of the various methods, results from an empirical study using trivariate scattered data are presented. The author's objective is to provide information to aid in selecting a type of method or to form the basis for customizing a method for a particular application.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Buprenorphine Treatment of Refractory Depression (1995)

Opiates were used to treat major depression until the mid-1950s. The advent of opioids with mixed agonist-antagonist or partial agonist activity, with reduced dependence and abuse liabilities, has made possible the reevaluation of opioids for this indication. This is of potential importance for the population of depressed patients who are unresponsive to or intolerant of conventional antidepressant agents. Ten subjects with treatment-refractory, unipolar, nonpsychotic, major depression were treated with the opioid partial agonist buprenorphine in an open-label study. Three subjects were unable to tolerate more than two doses because of side effects including malaise, nausea, and dysphoria. The remaining seven completed 4 to 6 weeks of treatment and as a group showed clinically striking improvement in both subjective and objective measures of depression. Much of this improvement was observed by the end of 1 week of treatment and persisted throughout the trial. Four subjects achieved complete remission of symptoms by the end of the trial (Hamilton Rating Scale for Depression scores < or = 6), two were moderately improved, and one deteriorated. These findings suggest a possible role for buprenorphine in treating refractory depression.
Silicon nitride transmission X-ray mirrors (2008)

Transmission X-ray mirrors have been fabricated from 300-400 nm-thick low-stress silicon nitride windows of size 0.6 mm x 85 mm. The windows act as a high-pass energy filter at grazing incidence in an X-ray beam for the beam transmitted through the window. The energy cut-off can be selected by adjusting the incidence angle of the transmission mirror, because the energy cut-off is a function of the angle of the window with respect to the beam. With the transmission mirror at the target angle of 0.22 degrees , a 0.3 mm x 0.3 mm X-ray beam was allowed to pass through the mirror with a cut-off energy of 10 keV at the Cornell High Energy Synchrotron Source. The energy cut-off can be adjusted from 8 to 12 keV at an angle of 0.26 degrees to 0.18 degrees , respectively. The observed mirror transmittance was above 80% for a 300 nm-thick film.
A Turn‐on Fluorescent Sensor for Imaging Labile Fe<sup>3+</sup> in Live Neuronal Cells at Subcellular Resolution (2012)

An eye for an iron: A highly sensitive, selective and reversible turn-on Fe(3+) sensor for imaging labile Fe(3+) in live cells at subcellular resolution is reported. The sensor can respond to changes in intracellular Fe(3+) levels and was used to image endogenous chelatable Fe(3+) in live human neuroblastoma SH-SY5Y cells, with two Fe(3+) pools being identified in mitochondria and endosomes/ lysosomes for the first time.
Direct electrospinning of highly twisted, continuous nanofiber yarns (2010)

Yarns are key building blocks to construct complicated fibrous structures for diverse applications. Although carbon nanotube yarns have been fabricated by a few novel techniques, challenges still remain in processing other nano fibrous materials into yarns, especially during the fiber fabricating process. In this paper, we report a simple but efficient and versatile method to prepare well‐twisted continuous nanofiber yarns directly through an electrospinning process. The yarn electrospinning process used two oppositely charged electrospinning nozzles to generate a hollow nanofiber “cone” on an intermediate funnel collector. Continuous nanofiber yarns can be directly withdrawn from the “cone” apex, with up to 7400 turns per meter of twists inserted through the rotation of the funnel. The maximum yarn production rate is 5 m/min, and the yarn twist level and fiber orientation can be controlled by the funnel rotating speed and yarn withdrawal rate. The yarn tensile properties showed dependence on the twist level.