gebhart/patrepeval huggingface dataset:
Algorithms using Java for Spreadsheet Dependent Cell Recomputation (2002)

Abstract : Java implementations of algorithms used by spreadsheets to antomatically recompute the set of cells dependent on a changed cell are described using a mathematical model for spreadsheets based on graph theory. Theses solutions comprise part of a Java API that allows a client application to read, modify, and maintain spreadsheet data without using the spreadsheet application program that produced it. Features of the Java language that successfully improve the running time performance of the algorithms are also described.
Comprehensive and Efficient Protection of Kernel Control Data (2011)

Protecting kernel control data (e.g., function pointers and return addresses) has been a serious issue plaguing rootkit defenders. In particular, rootkit authors only need to compromise one piece of control data to launch their attacks, while defenders need to protect thousands of such values widely scattered across kernel memory space. Worse, some of this data (e.g., return addresses) is volatile and can be dynamically generated at run time. Existing solutions, however, offer either incomplete protection or excessive performance overhead. To overcome these limitations, we present indexed hooks, a scheme that greatly facilitates kernel control-flow enforcement by thoroughly transforming and restricting kernel control data to take only legal jump targets (allowed by the kernel's control-flow graph). By doing so, we can severely limit the attackers' possibility of exploiting them as an infection vector to launch rootkit attacks. To validate our approach, we have developed a compiler-based prototype that implements this technique in the FreeBSD 8.0 kernel, transforming 49 025 control transfer instructions (~7.25% of the code base) to use indexed hooks instead of direct pointers. Our evaluation results indicate that our approach is generic, effective, and can be implemented on commodity hardware with a low performance overhead (<;5% based on benchmarks).
Engineering brown fat into skeletal muscle using ultrasound‐targeted microbubble destruction gene delivery in obese Zucker rats: Proof of concept design (2017)

Ultrasound-targeted microbubble destruction (UTMD) is a novel means of tissue-specific gene delivery. This approach systemically infuses transgenes precoupled to gas-filled lipid microbubbles that are burst within the microvasculature of target tissues via an ultrasound signal resulting in release of DNA and transfection of neighboring cells within the tissue. Previous work has shown that adenovirus containing cDNA of UCP-1, injected into the epididymal fat pads in mice, induced localized fat depletion, improving glucose tolerance, and decreasing food intake in obese diabetic mice. Our group recently demonstrated that gene therapy by UTMD achieved beta cell regeneration in streptozotocin (STZ)-treated mice and baboons. We hypothesized that gene therapy with BMP7/PRDM16/PPARGC1A in skeletal muscle (SKM) of obese Zucker diabetic fatty (fa/fa) rats using UTMD technology would produce a brown adipose tissue (BAT) phenotype with UCP-1 overexpression. This study was designed as a proof of concept (POC) project. Obese Zucker rats were administered plasmid cDNA contructs encoding a gene cocktail with BMP7/PRDM16/PPARGC1A incorporated within microbubbles and intravenously delivered into their left thigh. Controls received UTMD with plasmids driving a DsRed reporter gene. An ultrasound transducer was directed to the thigh to disrupt the microbubbles within the microcirculation. Blood samples were drawn at baseline, and after treatment to measure glucose, insulin, and free fatty acids levels. SKM was harvested for immunohistochemistry (IHC). Our IHC results showed a reliable pattern of effective UTMD-based gene delivery in enhancing SKM overexpression of the UCP-1 gene. This clearly indicates that our plasmid DNA construct encoding the gene combination of PRDM16, PPARGC1A, and BMP7 reprogrammed adult SKM tissue into brown adipose cells in vivo. Our pilot established POC showing that the administration of the gene cocktail to SKM in this rat model of genetic obesity using UTMD gene therapy, engineered a BAT phenotype with UCP-1 over-expression. © 2017 IUBMB Life, 69(9):745-755, 2017.
Study on transfection of adeno associated virus 2-ND4 gene into mitochondria (2014)

Background Leber hereditary optic neuropathy (LHON) is mitochondrial DNA (mtDNA) disease and mainly leads to optical nerve degeneration.Its primary mechanism is synthesis disorder of DN4 protein due to variation of mtDNA 11778 locus.So to construct a vector with exogenous normal ND4 and transfect into mitochondria is a key of gene therapy for LHON.Objective This study was to investigate the in vitro transfection of adeno-associated virus (AAV)-ND4 gene into mitochondria.Methods Human renal epithelial cell lines transfected adenovirus E1A (293 cells) were regularly cultured and divided into two groups.Framework plasmids of recombinant AAV-ND4 or simple AAV2 were added to the cell medium respectively.The expression of ND4 in cells were located 12,24,36 and 48 hours after transfected by Y03 dual fluorescent quantum dots staining.The positive response for ND4 showed the green fluorescence.Results Cultured 293 cells grew well with 80％ confluence.Abundant green fluorescence particles were seen in cytoplasm in the AAV-ND4 transfected group,but only red fluorescence from mitochondrial protein was seen in the simple AAV transfected group under the fluorescence microscope.Conclusions Exogenous ND4 protein can been successfully transfected into mitochondria using the ND4 gene constructed AAV.This result provides experimental evidence for the further study on gene therapy of LHON.

Key words: 
Optic atrophy, hereditary, Leber/therapy;  Genetic therapeutic;  DNA, mitochondrial/genetics; Transfection;  Adeno-associated virus;  Retinal ganglion cell;  Cell line;  Y03 double fluorescent quantum dot
A Small, Dilute-Cytoplasm, High-Affinity, Novel Bacterium Isolated by Extinction Culture and Having Kinetic Constants Compatible with Growth at Ambient Concentrations of Dissolved Nutrients in Seawater (1998)

Dilutions of raw seawater produced a bacterial isolate capable of extended growth in unamended seawater. Its 2.9-Mb genome size and 40-fg dry mass were similar to values for many naturally occurring aquatic organotrophs, but water and DNA comprised a large portion of this small chemoheterotroph, as compared to Escherichia coli. The isolate used only a few aromatic hydrocarbons and acetate, and glucose and amino acid incorporation were entirely absent, although many membrane and cytoplasmic proteins were inducible; it was named Cycloclasticus oligotrophus. A general rate equation that incorporates saturation phenomena into specific affinity theory is derived. It is used to relate the kinetic constants for substrate uptake by the isolate to its cellular proteins. The affinity constant KA for toluene was low at 1.3 microg/liter under optimal conditions, similar to those measured in seawater, and the low value was ascribed to an unknown slow step such as limitation by a cytoplasmic enzyme; KA increased with increasing specific affinities. Specific affinities, a degreess, were protocol sensitive, but under optimal conditions were 47.4 liters/mg of cells/h, the highest reported in the literature and a value sufficient for growth in seawater at concentrations sometimes found. Few rRNA operons, few cytoplasmic proteins, a small genome size, and a small cell size, coupled with a high a degreess and a low solids content and the ability to grow without intentionally added substrate, are consistent with the isolation of a marine bacterium with properties typical of the bulk of those present.
Non-proteolytic activation of cellular protransglutaminase (placenta macrophage factor XIII) (1990)

Plasma Factor XIII is a zymogen (plasma protransglutaminase) with the tetrametric structure A2B2, whereas the cellular protransglutaminase, i.e. Factor XIII in the platelet and monocyte/macrophage, consists exclusively of A subunits (A2). It is generally accepted that at Ca2+ concentrations comparable with that in plasma the proteolytic removal of an N-terminal activation peptide is the prerequisite for the Ca2(+)-induced formation of a catalytically active configuration of subunit A. In this study it was demonstrated that at high concentrations NaCl or KCl induced a non-proteolytic activation of cellular (placental macrophage) but not plasma protransglutaminase. The activation depended on time and salt concentration, and Ca2+, in the range 0-20 mM, greatly enhanced the activation process. At 1.25 M-NaCl maximal activation occurred within 60 min in the presence of 2 mM-CaCl2, and even at physiological NaCl concentration a slow progressive activation could be observed in the presence of Ca2+. The specific activity of salt-activated Factor XIII was 1.5-2.0-fold higher than that obtained after thrombin activation. The non-proteolytic activation of cellular protransglutaminase was abolished by the addition of subunit B of plasma Factor XIII in stoichiometric amount, which suggests that (one of) the physiological function(s) of the B subunit in plasma Factor XIII is to prevent the slow spontaneous activation of A subunit that would occur in a plasmatic environment.
Interreality for the management and training of psychological stress: study protocol for a randomized controlled trial (2013)

http://clinicaltrials.gov/ct2/show/NCT01683617.
《十九——二十世纪哲学与政治生活中之穆斯林观念》导言部分 (1984)

《十九——二十世纪哲学与政治生活中之穆斯林观念》一书系苏联哲学博士M．斯捷潘扬茨的专著。这本书经苏联科学院哲学研究所审定，1982年苏联什学出版社出版。在书中，作者试图揭示最近两个世纪以来穆斯林民族在争取民族解放的斗争中和取得政治独立后思想发展的普遍观律。
Heparan Sulfate Proteoglycan Modulates Keratinocyte Growth Factor Signaling through Interaction with both Ligand and Receptor (1999)

Keratinocyte growth factor (KGF) is an unusual fibroblast growth factor (FGF) family member in that its activity is largely restricted to epithelial cells, and added heparin/heparan sulfate inhibits its activity in most cell types. The effects of heparan sulfate proteoglycan (HSPG) on binding and signaling by acidic FGF (aFGF) and KGF via the KGFR were studied using surface-bound and soluble receptor isoforms expressed in wild type and mutant Chinese hamster ovary (CHO) cells lacking HSPG. Low concentrations of added heparin (1 microgram/mL) enhanced the affinity of ligand binding to surface-bound KGFR in CHO mutants, as well as ligand-stimulated MAP kinase activation and c-fos induction, but had little effect on binding or signaling in wild type CHO cells. Higher heparin concentrations inhibited KGF, but not aFGF, binding and signaling. In addition to the known interaction between HSPG and KGF, we found that the KGFR also bound heparin. The biphasic effect of heparin on KGF, but not aFGF, binding and signaling suggests that occupancy of the HSPG binding site on the KGFR may specifically inhibit KGF signaling. In contrast to events on the cell surface, added heparin was not required for high-affinity soluble KGF-KGFR interaction. These results suggest that high-affinity ligand binding is an intrinsic property of the receptor, and that the difference between the HSPG-dependent ligand binding to receptor on cell surfaces and the HSPG-independent binding to soluble receptor may be due to other molecule(s) present on cell surfaces.
The first mutation identified in the thrombomodulin gene in a 45-year- old man presenting with thromboembolic disease (1995)

Thrombomodulin (TM) is the anticoagulant endothelial cell membrane-bound protein cofactor in the thrombin-mediated activation of protein C (PC). It has been clearly demonstrated that the anticoagulant and profibrinolytic functions of the PC system are important for the prevention of a thromboembolic disease. Patients with PC, protein S, or PC "'cofactor"' deficiency and/or dysfunction develop thromboembolic diseases. However, the molecular abnormality in at least 20% to 30% of thrombophilic patients cannot be identified by hitherto recognized defects. A putative pathologic lesion in the TM gene could be one of several candidates for these prothrombotic mutations. A directed search strategy for deletions, insertions, or point mutations in the TM gene has not been performed. Therefore, in the present study, we have analyzed the entire TM gene, including the promoter region, by polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP) in normal healthy volunteers and in patients presenting with a thromboembolic disease. We have identified a patient with a thromboembolic disease and a TM point mutation. In a 45-year-old Hispanic man with a documented pulmonary embolism, PCR-SSCP showed an aberrant band pattern and subsequent DNA sequence analysis showed a heterozygous substitution for G1456 to T. This substitution predicts an Asp468 to a Tyr change in the amino acid sequence that is located between the transmembrane domain and the sixth epidermal growth factor-like domain. The Asp468 to Tyr change would probably lead to significant structural changes not allowing the expression of the TM protein or to a conformational change that is not functional.
Apolipoprotein E enhances uptake of soluble but not aggregated amyloid‐β protein into synaptic terminals (2003)

The cellular mechanism by which apolipoprotein E (apoE) affects the pathogenesis of Alzheimer's disease (AD) is not understood. We have examined the effect of apolipoprotein E on the internalization of exogenous amyloid-beta 1-40 (Abeta40) into a rat brain crude synaptosomal preparation. Abeta40 peptide in soluble (within 1 h of dilution in buffer) or aggregated (aged 4 days before dilution in buffer) form was pre-incubated with lipidated apoE then added to synaptosomes; intraterminal amyloid-beta labeling was quantified using flow cytometry following immunolabeling with the anti-Abeta (10G4) antibody. The number of Abeta-positive synaptosomes was increased ( approximately 50%) by treatment with a soluble Abeta/apoE mixture compared with treatment with soluble Abeta40 alone. However, when the Abeta was aggregated, less sodium dodecyl sulfate (SDS)-stable Abeta/apoE complex was formed and the addition of apoE decreased the number of Abeta-positive terminals. The addition of the lipoprotein-receptor related protein (LRP) antagonist receptor-associated protein (RAP) inhibited the apoE-induced increase in synaptosomal Abeta, and controls treated with trypsin and heparinase confirm intraterminal localization of the majority of the soluble Abeta. The apoE-mediated increase in Abeta labeling was confirmed in intact cells by immunocytochemistry of dorsal root ganglion (DRG) neurons. These results suggest that complex formation with apoE enhances internalization of soluble Abeta uptake into terminals.
Attention, reliability, and validity of perceptual asymmetries in the fused dichotic words test (2005)

The present experiment investigated the claim that the fused dichotic words test (FDWT) is affected minimally by attentional factors. A total of 40 right-handed undergraduate students were randomly assigned to either a free recall or exogenous cueing condition. In the free recall condition, participants circled on a response sheet the word corresponding to the percept they heard for each trial. In the exogenous cueing condition, a lateralised tone cue was presented with a stimulus onset asynchrony (SOA) of either 150 or 450 ms. Participants responded by circling the word presented to the ear where the tone sounded. Results of the free recall condition showed the expected large right ear advantage (REA). In the exogenous cueing condition, the significant SOA by ear of presentation interaction predicted by an attentional explanation of perceptual asymmetries was obtained. Specifically, the REA obtained at the 150 ms SOA was reduced at the 450 ms SOA for both correct responses and intrusions. These findings suggest that, contrary to claims conveyed in the literature, the FDWT is subject to the influences of attention. This supports the claim that the large and reliable laterality effects obtained with the fused dichotic words test are due in part to a consistent attentional bias.
Editor's Note (1974)

In the Fall 1973 issue of Chinese Studies in Philosophy we presented translations of some selected writings of Professor T'ang Chün-i, whose Confucianistic-Humanistic philosophy is well known in Asia and beginning to be appreciated in this country. In this sequel to that issue we present Professor T'ang's expositions of his thoughts on the reconstruction of the humanistic spirit, on the development of the Chinese humanistic spirit, as well as on the relation between cultural consciousness and moral reason. In these writings Professor T'ang argues that a universal religion can be founded on the moral conscience of man and that specifically it can be founded on the moral nature or mind of man as understood by Confucianism. He also presents his critique of some Western and Buddhistic philosophical doctrines or views in a framework of distinctions between the proper humanistic thought on the one hand and the super-, non-, and subhumanistic thoughts on the other.
In Situ Laser-Furnace TOF Mass Spectrometry of C<sub>36</sub>and the Large-Scale Production by Arc-Discharge (2000)

A greatly improved synthesis of C36, obtained as its hydrides C36H4 and C36H6 and oxyhydrides C36H4O and C36H6O, via a high- temperature laser vaporization (laser-furnace) method and the conventional DC arc-discharge method is reported. We have found that doping metal catalysts such as Ni/Co or Ni/Y into the laser target graphite rod or the DC arc-discharge electrode, respectively, significantly enhanced the production of C36 species; the methods have been known for efficient production methods of single-wall carbon nanotubes (SWNTs). The results suggest that the catalytic formation of C36 species and SWNTs is closely related with each other in their early stage of formation. Furthermore, a molecular C36H6 gives C18H3 (m/z = 219) as a magic fragment upon desorption/ionization. By using a high-performance liquid chromatography (HPLC), C36H6 was purified (99%) in milligram quantity for the first time. The purified C36H6 exists as a cluster-assembled material such as oligomers or clusters in the solid state, not as a molecular crystal such as C60.
Expression for the estimation of time-averaged acoustic energy density using the two-microphone method (L) (2003)

Acoustic energy density has been shown to exhibit lower spatial variance in reactive sound fields compared to the acoustic potential energy estimate offered by microphones, making it a very useful measure of the acoustic energy within an enclosure. Previously, frequency domain time-averaged energy density estimates have come about by estimating the pressure average and particle velocity between two closely spaced microphones using either analog or digital electronics. A frequency domain expression can be obtained by adding the weighted sum of the auto-spectral densities of both the pressure and particle velocity magnitude. The purpose of this letter is to derive an expression for the time-averaged acoustic energy density in the frequency domain using the auto- and cross-spectral densities between the two closely spaced microphones. The resulting expression is validated numerically.
Vitamin D <sub>3</sub> cryosensitization increases prostate cancer susceptibility to cryoablation via mitochondrial‐mediated apoptosis and necrosis (2011)

The present study suggests that the use of VD(3) as a cryosensitizer increases cryoablation efficacy through the increased activity of apoptosis as well as through necrosis. The data show that through VD(3) treatment the overall level of AI CaP cell tolerance to freezing is reduced to a level similar to that of AS CaP. VD(3) pre-treatment in conjunction with cryoablation may increase treatment efficacy and reduce disease recurrence for CaP patients.
A More Sensitive Method for the Quantitation of Genomic DNA by Alu Amplification (2002)

Current procedures for human DNA quantitation reach their limit at 150 pg DNA, which is above the limit of the PCR profiling range using Profiler-Plus (Applied Biosystems, CA). This study tested the potential for the use of primate specific Alu sequences in forensic science for the sensitive detection and quantitaion of DNA. A fluorescently labelled primer pair was designed enabling high efficiency amplification of the core Alu sequence within primate DNA. Quantitation was performed by measurement of fluorescence intensity and comparison to a series of standard template DNA amounts via the construction of a standard curve. The new Alu-based quantitation protocol developed has shown its feasibility in more sensitively quantitating (100-2.5 pg) unknown amounts of human DNA for forensic use. The method is compatible with the use and throughput of current forensic procedures.
Vapor Pressure of Water in Mixtures with Hydrophilic Ionic Liquids – A Contribution to the Design of Processes for Drying of Gases by Absorption in Ionic Liquids (2010)

Abstract The low water vapor pressures of mixtures of water with the ionic liquids (ILs), [EMIM][EtSO 4 ] and [BEIM][EtSO 4 ], indicate that a process of gas dehydration by absorption in ILs might be an alternative to the classical absorption process with triethylene glycol (TEG). The activity coefficient for an infinite dilution of water in the IL ( x IL → 1), which should be low for efficient dehydration, is only about 0.2 for [EMIM][EtSO 4 ] compared to 0.6 for triethylene glycol. In contrast to TEG, losses by evaporation are excluded with ILs as solvents, because they have a negligible vapor pressure. The number of separation stages needed for the absorption in the IL and for the subsequent regeneration of the water‐loaded IL is small, about six and eight, respectively. IL regeneration can be achieved by distillation of water out of the IL (e.g., at 120 °C) and stripping with ambient air, which is not possible in the case of TEG (chemical attack by O 2 ).
Optimizing the location of assembly tasks in a manipulator's workspace (1990)

Abstract Off‐line programming of robotic workcells has become an invaluable tool for the workcell designer, however, current robot programming systems lack the capability to automatically determine the locations for performing assembly operations within the manipulator's workspace. A gradient function of manipulability in Cartesian space was developed based on an explicit determination of the manipulability function and the gradient of the manipulability function in joint space. A modified method of the steepest descent optimization procedure was then used as the basis for an algorithm that automatically locates an assembly task away from singularities within a manipulator's workspace. This algorithm can readily be extended to any nonredundant manipulator.
Deep Questions without Deep Understanding (2015)

Igor Labutov, Sumit Basu, Lucy Vanderwende. Proceedings of the 53rd Annual Meeting of the Association for Computational Linguistics and the 7th International Joint Conference on Natural Language Processing (Volume 1: Long Papers). 2015.