gebhart/patrepeval huggingface dataset:
Genetic Engineering of <i>Zymobacter palmae</i> for Production of Ethanol from Xylose (2007)

Its metabolic characteristics suggest that Zymobacter palmae gen. nov., sp. nov. could serve as a useful new ethanol-fermenting bacterium, but its biotechnological exploitation will require certain genetic modifications. We therefore engineered Z. palmae so as to broaden the range of its fermentable sugar substrates to include the pentose sugar xylose. The Escherichia coli genes encoding the xylose catabolic enzymes xylose isomerase, xylulokinase, transaldolase, and transketolase were introduced into Z. palmae, where their expression was driven by the Zymomonas mobilis glyceraldehyde-3-phosphate dehydrogenase promoter. When cultured with 40 g/liter xylose, the recombinant Z. palmae strain was able to ferment 16.4 g/liter xylose within 5 days, producing 91% of the theoretical yield of ethanol with no accumulation of organic acids as metabolic by-products. Notably, xylose acclimation enhanced both the expression of xylose catabolic enzymes and the rate of xylose uptake into recombinant Z. palmae, which enabled the acclimated organism to completely and simultaneously ferment a mixture of 40 g/liter glucose and 40 g/liter xylose within 8 h, producing 95% of the theoretical yield of ethanol. Thus, efficient fermentation of a mixture of glucose and xylose to ethanol can be accomplished by using Z. palmae expressing E. coli xylose catabolic enzymes.
Special Purpose Nuclear Reactor (5 MW) for Reliable Power at Remote Sites Assessment Report (2017)

The Phenomena Identification and Ranking Table (PIRT) technique was conducted on the Special Purpose Reactor nuclear plant design. The PIRT is a structured process to identify safety-relevant/safety-significant phenomena and assess the importance and knowledge base by ranking the phenomena. The Special Purpose Reactor is currently in the conceptual design stage. The candidate reactor has a solid monolithic stainless steel core with an array of heat pipes and fuel pellets embedded in the monolith. The heat pipes are used to remove heat from the core using simple, reliable, and well-characterized physics (capillarity, boiling, and condensation). In the initial design, one heat exchanger is used for the working fluid that produces energy, and a second heat exchanger is used to remove decay heat in emergency or shutdown conditions. In addition, a power conversion cycle such as an open-air Brayton system is available as an option for power conversion and process heat. This report summarizes and documents the process and scope of the four PIRT reviews, noting the major activities and conclusions. The identified phenomena, analyses, rationales, and associated ratings are presented along with a summary of the findings from the four individual PIRTs, namely (1) Reactor Accident and Normal Operations, (2) Heat Pipes, (3) Materials, and (4) Power Conversion. The PIRT reports for these four major system areas evaluated are attached as appendixes to this report and provide considerably more detail about each assessment as well as a more complete listing of the phenomena that were evaluated.
Rapid assay processing by integration of dual-color fluorescence cross-correlation spectroscopy: High throughput screening for enzyme activity (1998)

Dual-color fluorescence cross-correlation spectroscopy (dual-color FCS) has previously been shown to be a suitable tool not only for binding but also for catalytic rate studies. In this work, its application as a rapid method for high-throughput screening (HTS) and evolutionary biotechnology is described. This application is called RAPID FCS (rapid assay processing by integration of dual-color FCS) and does not depend on the characterization of diffusion parameters that is the prerequisite for conventional fluorescence correlation spectroscopy. Dual-color FCS parameters were optimized to achieve the shortest analysis times. A simulated HTS with homogeneous assays for different restriction endonucleases ( Eco RI, Bam HI, Ssp I, and Hin dIII) achieved precise yes-or-no decisions within analysis times of about 1 s per sample. RAPID FCS combines these short analysis times with the development of fast and flexible assays resulting in sensitive, homogeneous fluorescence-based assays, where a chemical linkage between different fluorophores is either cleaved or formed, or where differently labeled molecules interact by noncovalent binding. In principle, assay volumes can be reduced to submicroliters without decreasing the signal strength, making RAPID FCS an ideal tool for ultra-HTS when combined with nanotechnology. RAPID FCS can accurately probe 10 4 to 10 5 samples per day, and possibly more. In addition, this method has the potential to be an efficient tool for selection strategies in evolutionary biotechnology, where rare and specific binding or catalytic properties have to be screened in large numbers of samples.
Developing a prediction model for customer churn from electronic banking services using data mining (2016)

Given the importance of customers as the most valuable assets of organizations, customer retention seems to be an essential, basic requirement for any organization. Banks are no exception to this rule. The competitive atmosphere within which electronic banking services are provided by different banks increases the necessity of customer retention. Being based on existing information technologies which allow one to collect data from organizations’ databases, data mining introduces a powerful tool for the extraction of knowledge from huge amounts of data. In this research, the decision tree technique was applied to build a model incorporating this knowledge. The results represent the characteristics of churned customers. Bank managers can identify churners in future using the results of decision tree. They should be provide some strategies for customers whose features are getting more likely to churner’s features.
The effect of thymosin application upon radiation sickness in mice. (1976)

The mechanism of thymosin effect upon radiation sickness was analyzed in mice. Thymosin (fraction 5) applied before and after a whole-body radiation exposure increased the LD 50/30 of treated animals by 250R. In mice exposed to 500R, thymosin treatment resulted in a faster recovery of haemopoiesis and lymphopoiesis, as indicated by higher bone marrow cellularity, higher lymph node, thymus and spleen weights, and greater 59Fe uptake in the spleen and femur and 125IUdR uptake in the spleens, femur and thymus. The results provide an indication that thymus and its humoral factor markedly influence the haemopoietic stem cells in the population surviving the sublethal irradiation of an organism. They further suggest the existence of feed-back mechanisms between the thymus and harmopoiesis.
Immune cell expression of TGFβ1 in cancer with lymphoid stroma: dendritic cell and regulatory T cell contact (2018)

Although cancer tissue generally shows limited immune responses, some cancers abound with lymphocytes, which generally show favorable prognosis. These cancers, despite their rarity, are important in analyzing immune responses in cancer tissue. Transforming growth factor β1 (TFGβ1) is a multifunctional cytokine, generally having an immunosuppressive function. The present study analyzes the in situ TGFβ1 expression in 23 cases of lymphocyte-rich gastric carcinomas (Ly-rich GCs) using immunohistochemistry and in situ hybridization. Immunohistochemistry revealed that latency-associated peptide (LAP) of TGFβ1 was localized in mainly immune cells in all cases, which was more abundant than in control GCs. Expression of LAP by cancer cells was only focal. In situ hybridization also confirmed abundant TGFβ1 mRNA expression in the lymphoid stroma. Double immunofluorescent microscopy identified LAP<sup>+</sup> cells as macrophages, dendritic cells, and part of T cells. Close cell-to-cell contact was observed between LAP<sup>+</sup> dendritic-shaped cells and FoxP3<sup>+</sup> regulatory T cells (T<sub>reg</sub> cells). Mature dendritic cells in Ly-rich GCs expressed LAP more frequently than those in the secondary lymphoid organs. Our data revealed abundant expression of TGFβ1 in immune cells with contact to T<sub>reg</sub> cells in lymphoid stroma, which is consistent with the notion that TGFβ1 is one of the immunosuppressive factors in cancer stroma.
Enteropathogenic and Enterohemorrhagic<i>Escherichia coli</i>Infections: Translocation, Translocation, Translocation (2005)

Escherichia coli is the most abundant facultative anaerobic gram-negative bacterium of the intestinal microflora, naturally colonizing the mucous layer of the colon. A conserved core genomic structure is common to both commensal and pathogenic strains, providing the microorganisms with mechanisms
PTEN Positively Regulates UVB-Induced DNA Damage Repair (2011)

Nonmelanoma skin cancer is the most common cancer in the United States, where DNA-damaging ultraviolet B (UVB) radiation from the sun remains the major environmental risk factor. However, the critical genetic targets of UVB radiation are undefined. Here we show that attenuating PTEN in epidermal keratinocytes is a predisposing factor for UVB-induced skin carcinogenesis in mice. In skin papilloma and squamous cell carcinoma (SCC), levels of PTEN were reduced compared with skin lacking these lesions. Likewise, there was a reduction in PTEN levels in human premalignant actinic keratosis and malignant SCCs, supporting a key role for PTEN in human skin cancer formation and progression. PTEN downregulation impaired the capacity of global genomic nucleotide excision repair (GG-NER), a critical mechanism for removing UVB-induced mutagenic DNA lesions. In contrast to the response to ionizing radiation, PTEN downregulation prolonged UVB-induced growth arrest and increased the activation of the Chk1 DNA damage pathway in an AKT-independent manner, likely due to reduced DNA repair. PTEN loss also suppressed expression of the key GG-NER protein xeroderma pigmentosum C (XPC) through the AKT/p38 signaling axis. Reconstitution of XPC levels in PTEN-inhibited cells restored GG-NER capacity. Taken together, our findings define PTEN as an essential genomic gatekeeper in the skin through its ability to positively regulate XPC-dependent GG-NER following DNA damage.
Effect of photocoagulation on the barrier function of the pigment epithelium. II. A study by electron microscopy. (1977)

The healing of retinal photocoagulation burns and their permeability to colloidal carbon and horseradish peroxidase was studied by electron microscopy. Recent burns showed disruption of intercellular junctions in the pigment epithelium. By 2 days there was infiltration of the burn by proliferating pigment epithelial cells, and by 7 days the burn was composed of a mass of interconnected cells of pigment epithelial and Müller cell origin. Fresh photocoagulation burns result in complete disruption of the blood-ocular barrier, permitting particles as large as colloidal carbon to pass between disrupted pigment epithelial cells. Healed photocoagulation burns remain permeable to smaller tracers such as horseradish peroxidase.
Comparative Study on a New One-Stage Clotting Assay for Heparin and Its Low Molecular Weight Derivatives (1989)

The effects of a normal and a low molecular weight (LMW) heparin fraction were compared by four coagulation methods. Plasma samples of patients were investigated who were treated with normal heparin or with a LMW heparin. The study was undertaken to analyze the interrelationship between the coagulation methods: Heptest, activated partial thromboplastin time, thrombin clotting time, and S 2222 chromogenic anti-factor Xa test. The results showed a high correlation between Heptest and S 2222 anti-factor Xa method for unfractionated and LMW heparin (r = 0.91 and 0.90). Comparing the coagulation times in seconds of Heptest and aPTT, the correlations were r = 0.56 (normal heparin) and 0.15 (LMW heparin). The correlation between the coagulation times of Heptest and thrombin clotting time were r = 0.65 and 0.25, respectively. The correlations between the coagulation methods were higher, when coagulation times rather than transformed values to units per liter of the Heptest and of the S 2222 anti-factor Xa method were employed. Furthermore, the data demonstrate a high sensitivity of the Heptest to conventional and LMW heparin, whereas activated partial thromboplastin time and thrombin clotting time are less sensitive to either heparin. For laboratory control of LMW heparin, Heptest and S 2222 chromogenic method are reliable tests. Therapeutic ranges will have to be established.
Poly(acrylic acid‐<i>co</i>‐vinylsulfonic acid): Synthesis, characterization, and properties as polychelatogen (2003)

Abstract The synthesis of the water‐soluble poly(acrylic acid‐ co ‐vinylsulfonic acid) at different feed monomer ratios, while maintaining constant the total number of mol, was carried out by radical polymerization. The copolymers were characterized by FTIR and 1 H‐NMR spectroscopies. The copolymer composition was determined by its sulfur content and by potentiometric titration. The metal ion binding properties for Ni(II) and Cu(II) in the aqueous phase were studied using the liquid‐phase polymer‐based retention (LPR) technique for two values of ionic strength. For comparison, the retention properties of both homopolymers were included. The complexing ability of the polymer was determined by the relative amount of carboxylic acid groups. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 88: 1698–1704, 2003
Microscale resin-bonded permanent magnets for magnetic micro-electro-mechanical systems applications (2003)

A micromachining technique has been developed for the fabrication of microscale resin-bonded permanent magnets. Magnetic paste has been prepared from Sr-ferrite powder and an epoxy resin, filled into lithographically defined molds, and formed into resin-bonded magnets after room temperature curing. Coercivity of 356 kA/m (4480 Oe), retentivity of 33 mT (330 G), and energy density of 2.7 kJ/m3 have been achieved in 65-μm-thick disk arrays with lateral dimensions ranging from 50 to 200 μm. Based on the developed magnet, a magnetic MEMS actuator has been designed, fabricated, and characterized. Actuation current up to ±60 mA operated the actuator up to 70 μm in attractive and repulsive motion. This work can be used for producing thick-film type permanent magnets, which can be scaled from a few tens of micrometers to millimeters on various substrates.
Systematic Reverse Genetic Screening of T-DNA Tagged Genes in Rice for Functional Genomic Analyses: MADS-box Genes as a Test Case (2003)

We have generated 47 DNA pools and 235 subpools from 21,049 T-DNA insertion lines of rice. DNA pools of 500-1,000 lines were adequate for screening a T-DNA insertion within a 2-kb region. To examine the efficacy of the DNA pools, we selected MADS-box genes, which play an important role in controlling various aspects of plant development. A total of 34 MIKC-type MADS-box genes have now been identified from rice sequence databases. Our PCR screening for T-DNA insertions within 12 MADS-box genes resulted in the identification of five insertions in four different genes. These DNA pools will be valuable when isolating T-DNA insertional mutants in various rice genes. The DNA pool screening service and the mutant seeds are available upon request to genean@postech.ac.kr.
A Web Collaboration Architecture (2006)

Computer supported collaborative work (CSCW) has typically been bound within organizations. Groupware applications are designed with organizational structures in mind, in a top-down approach that predicts communication and collaboration interactions between people. With Internet adoption in society, CSCW overflows organizational borders towards Internet supported collaborative work (ISCW), where the organization of work becomes decentralized, centered on individual interests and pretty dynamic. This paper proposes a Web collaboration architecture for the new Web environment. The article reviews common groupware problems and reflects recent organizational changes. It presents Web 2.0 features and technical state-of-the-art. Then, it describes the architecture proposed, to finish with conclusions and future research lines
Alterations in membrane type-1 matrix metalloproteinase abundance after the induction of thoracic aortic aneurysm in a murine model (2010)

Thoracic aortic aneurysms (TAAs) develop as a result of dysregulated extracellular matrix remodeling mediated by several matrix metalloproteinases (MMPs). Membrane type-1 MMP (MT1-MMP) is the prototypical member of a unique family of membrane-bound MMPs, possessing multiple substrates and functions. The present study tested the hypothesis that MT1-MMP expression, abundance, and activity would be elevated during TAA development and that this protease is produced primarily by mesenchymal cells within the thoracic aorta. Descending thoracic aortas were harvested from C57BL/6J mice at multiple time points (2, 4, 8, and 16 wk, n = 15 each) post-TAA induction (0.5M CaCl(2), 15 min) and compared with reference controls (n = 15). The expression and abundance of MT1-MMP, MMP-2, and tissue inhibitor of metalloproteinase (TIMP)-2 were assessed by quantitative PCR and immunoblot analysis. MT1-MMP activity was determined by fluorescent peptide assay. MT1-MMP was localized within the aortic wall by immunohistochemistry. MT1-MMP abundance and localization in live animals (8 wk post-TAA induction vs. control) was determined by micro-ultrasound imaging with an MT1-MMP-targeted microbubble contrast agent. Aortic diameter was increased 172 +/- 7% at 16 wk post-TAA induction (P < 0.05). MT1-MMP and MMP-2 mRNA levels were elevated at 2 wk post-TAA induction (P < 0.05). MT1-MMP protein abundance increased progressively to a maximum of 178 +/- 26% at 16 wk post-TAA induction, whereas MMP-2 and TIMP-2 peaked at 2 wk post-TAA induction (526 +/- 93% and 376 +/- 48%, respectively, P < 0.05). MT1-MMP colocalized with fibroblasts, and MT1-MMP-targeted contrast binding was elevated in 8-wk TAA-induced mice versus control mice (217 +/- 53% vs. 81 +/- 8%, P < 0.05). In conclusion, these novel results suggest that MT1-MMP plays a dynamic multifunctional role in TAA development and, therefore, may provide a significant target for therapeutic strategies.
Structured Generative Models of Natural Source Code (2014)

We study the problem of building generative models of natural source code (NSC); that is, source code written by humans and meant to be understood by humans. Our primary contribution is to describe new generative models that are tailored to NSC. The models are based on probabilistic context free grammars (PCFGs) and neuro-probabilistic language models (Mnih & Teh, 2012), which are extended to incorporate additional source code-specific structure. These models can be efficiently trained on a corpus of source code and outperform a variety of less structured baselines in terms of predictive log likelihoods on held-out data.
Aluminum nitride based thin film bulk acoustic resonator using germanium sacrificial layer etching (2004)

We report the development of aluminum nitride (AlN) thin film bulk acoustic resonator (FBAR). This resonator has an air gap beneath the resonator to obtain high Q factor and low spurious response. Germanium (Ge) was used as a sacrificial layer for the air gap. This technique gives very simple process and high CMOS compatibility. The FBAR was evaluated about the effect of the air gap and the electrode size. The FBAR achieved a resonant frequency of 2 GHz, a Q factor of 780 and an effective electro-mechanical coupling constant (k/sub eff//sup 2/) of 5.36%.
Low molar excess of 4-oxo-2-nonenal and 4-hydroxy-2-nonenal promote oligomerization of alpha-synuclein through different pathways (2017)

Aggregated alpha-synuclein is the main component of Lewy bodies, intraneuronal inclusions found in brains with Parkinson's disease and dementia with Lewy bodies. A body of evidence implicates oxidative stress in the pathogenesis of these diseases. For example, a large excess (30:1, aldehyde:protein) of the lipid peroxidation end products 4-oxo-2-nonenal (ONE) or 4-hydroxy-2-nonenal (HNE) can induce alpha-synuclein oligomer formation. The objective of the study was to investigate the effect of these reactive aldehydes on alpha-synuclein at a lower molar excess (3:1) at both physiological (7.4) and acidic (5.4) pH. As observed by size-exclusion chromatography, ONE rapidly induced the formation of alpha-synuclein oligomers at both pH values, but the effect was less pronounced under the acidic condition. In contrast, only a small proportion of alpha-synuclein oligomers were formed with low excess HNE-treatment at physiological pH and no oligomers at all under the acidic condition. With prolonged incubation times (up to 96h), more alpha-synuclein was oligomerized at physiological pH for both ONE and HNE. As determined by Western blot, ONE-oligomers were more SDS-stable and to a higher-degree cross-linked as compared to the HNE-induced oligomers. However, as shown by their greater sensitivity to proteinase K treatment, ONE-oligomers, exhibited a less compact structure than HNE-oligomers. As indicated by mass spectrometry, ONE modified most Lys residues, whereas HNE primarily modified the His50 residue and fewer Lys residues, albeit to a higher degree than ONE. Taken together, our data show that the aldehydes ONE and HNE can modify alpha-synuclein and induce oligomerization, even at low molar excess, but to a higher degree at physiological pH and seemingly through different pathways.
Finding the Most Efficient Way to Remove Residual Copper from Steel Scrap (2019)

Abstract The supply of end-of-life steel scrap is growing, but residual copper reduces its value. Once copper attaches during hammer shredding, no commercial process beyond hand-picking exists to extract it, yet high-value flat products require less than 0.1 wt pct copper to avoid metallurgical problems. Various techniques for copper separation have been explored in laboratory trials, but as yet no attempt has been made to provide an integrated assessment of all options. Therefore, for the first time, a framework is proposed to define the full range of separation routes and evaluate their potential to remove copper, while estimating their energy and material input requirements. The thermodynamic, kinetic, and technological constraints of the various techniques are analyzed to show that copper could be removed to below 0.1 wt pct with relatively low energy and material consumption. Higher-density shredding allows for greater physical separation, but requires proper incentivization. Vacuum distillation could be viable with a reactor that minimizes radiation heat losses. High-temperature solid scrap pre-treatments would be less energy intensive than melt treatments, but their efficacy with typical shredded scrap is yet unconfirmed. The framework developed here can be applied to other impurity-base metal systems to coordinate process innovation as the scrap supply expands.
Don’t Give Me the Details, Just the Summary! Topic-Aware Convolutional Neural Networks for Extreme Summarization (2018)

We introduce extreme summarization, a new single-document summarization task which does not favor extractive strategies and calls for an abstractive modeling approach. The idea is to create a short, one-sentence news summary answering the question "What is the article about?". We collect a real-world, large scale dataset for this task by harvesting online articles from the British Broadcasting Corporation (BBC). We propose a novel abstractive model which is conditioned on the article's topics and based entirely on convolutional neural networks. We demonstrate experimentally that this architecture captures longrange dependencies in a document and recognizes pertinent content, outperforming an oracle extractive system and state-of-the-art abstractive approaches when evaluated automatically and by humans. 1