gebhart/patrepeval huggingface dataset:
Endotoxin tolerance: independent regulation of interleukin-1 and tumor necrosis factor expression (1991)

The injection of lethal or sublethal doses of bacterial lipopolysaccharide (LPS) into mice results in transient increases in both serum tumor necrosis factor (TNF) and interleukin-1 (IL-1). The peak in serum TNF was detected prior to maximal elevation in endogenous corticosterone and was no longer apparent 3 to 4 h post-LPS injection, a point at which corticosterone and IL-1 levels had significantly increased. The initial increase in serum IL-1 may, in part, be modulated by the preceding TNF peak, as pretreating animals with a monoclonal antibody against murine TNF resulted in a significant decrease in IL-1 levels 3 h post-LPS injection. A second injection of LPS at 20 h failed to result in a secondary TNF peak, suggesting an endotoxin-tolerant state. However, in contrast to TNF, significant increases in serum IL-1 were detected in the endotoxin-tolerant animals following a repeated LPS stimulus. This secondary increase in IL-1 occurred despite the elevation in serum corticosterone. While peritoneal macrophages from endotoxin-tolerant mice demonstrated only a modest 10 to 15% increase in TNF and IL-1 mRNA relative to the levels after the primary 1-h LPS stimulus, a secondary increase in IL-1 but not TNF mRNA in the spleen was apparent following a second LPS injection. The spleen, however, was not essential for the increase in serum IL-1, as endotoxin-tolerant splenectomized mice had comparable increases in IL-1 following a repeated LPS stimulus. These results demonstrate the differential regulation of IL-1 and TNF in vivo during endotoxin tolerance.
Study on Synchronization Using Bootstrap Signals for ATSC 3.0 Systems (2016)

ATSC 3.0 시스템에서는 각 프레임의 시작에 부트스트랩 (bootstrap) 신호가 먼저 전송된다. 본 논문에서는 부트스트랩 신호를 이용하여 ATSC 3.0 시스템의 초기 동기를 획득하는 방법을 제시한다. ATSC 3.0의 부트스트랩 신호는 시간 영역에서 반복되는 구조를 가지며 제안하는 방법은 이러한 구조를 이용하여 수신기에서 초기 동기를 획득한다. 또한, 전산 실험 결과는 제안하는 알고리즘이 매우 낮은 신호 대 잡음비 (signal-to-noise ratio)에서도 초기 동기를 획득할 수 있음을 보여준다. In ATSC 3.0 systems, a bootstrap signal is located at the start of each frame. In this paper, we propose an initial synchronization scheme for ATSC 3.0 systems using the bootstrap signal. The bootstrap signal of ATSC 3.0 has several repetition patterns in the time domain. By utilizing the repetition patterns within the bootstrap, the proposed scheme can obtain an initial synchronization at the receiver. Also, simulation results show that the proposed scheme can obtain an initial synchronization at very low signal-to-noise ratios.
High-level Petri net for incremental analysis of object-oriented system requirements (2001)

To complement the weakness of Petri nets in terms of naturalness, modularity, and reusability, high-level Petri nets with object concepts have been suggested. It is difficult to apply these nets to the requirements specification of object-oriented software systems because of insufficient support for the object-oriented concepts. A hierarchical object-oriented Petri net (HOONet) is developed to complement the weakness of the existing formalisms and formally define its syntax and semantics. A reachability analysis method is provided to check such behavioural properties as boundedness, liveness and persistence of the HOONet models. The HOONet provides incremental modelling and analysis of the requirements with the support of object-oriented concepts.
Signaling Pathway of GP88 (Progranulin) in Breast Cancer Cells: Upregulation and Phosphorylation of c-myc by GP88/Progranulin in Her2-Overexpressing Breast Cancer Cells (2015)

Her2 is a receptor tyrosine kinase overexpressed in 25% of breast tumors. We have shown that the 88 kDa autocrine growth and survival factor GP88 (progranulin) stimulated Her2 phosphorylation and proliferation and conferred Herceptin resistance in Her2-overexpressing cells. Herein, we report that GP88 stimulates c-myc phosphorylation and upregulates c-myc levels in Her2-overexpressing cells. c-myc phosphorylation and upregulation by GP88 were not observed in non-Her2-overexpressing breast cancer cells. c-myc activation was inhibited upon treatment with ERK, PI3 kinase, and c-src pathway inhibitors, U0126, LY294002, and PP2. GP88 also stimulated c-src phosphorylation, a known upstream regulator of c-myc. Thus, we describe here a signaling pathway for GP88 in Her2-overexpressing cells, with GP88 stimulating Src phosphorylation, followed by phosphorylation and upregulation of c-myc. These data would suggest that targeting GP88 could provide a novel treatment approach in breast cancer.
Catastrophe Risk Management: Using Alternative Risk Financing and Insurance Pooling Mechanisms (2001)

In providing support for disaster-prone areas such as the Caribbean, the development community has begun to progress from disaster reconstruction assistance to funding for investment in mitigation as an explicit tool for sustainable development. Now it must enter a new phase, applying risk transfer mechanisms to address the financial risk of exposure to catastrophic events that require funding beyond what can be controlled solely through mitigation and physical measures
ASP2408 and ASP2409, novel CTLA4-Ig variants with CD86-selective ligand binding activity and improved immunosuppressive potency, created by directed evolution (2016)

The CTLA4-Ig therapeutics abatacept and belatacept inhibit CD28-mediated T cell activation by binding CD80 (B7-1) and CD86 (B7-2) co-stimulatory ligands. Both compounds preferentially bind CD80, yet CD86 has been implicated as the dominant co-stimulatory ligand. Using directed evolution methods, novel CTLA4-Ig variants were created with selective CD86 binding affinity, a property that confers increased immunosuppressive potency and potentially improved efficacy and safety profiles. Relative to abatacept (wild-type CTLA4-Ig), ASP2408 and ASP2409 have 83-fold and 220-fold enhanced binding affinity to CD86 while retaining 1.5-fold and 5.6-fold enhanced binding affinity to CD80, respectively. Improvements in CD86 binding affinity correlates with increased immunosuppressive potencyin vitroandin vivo Our results highlight the power of directed evolution methods to obtain non-intuitive protein engineering solutions and represent the first examples of CD86-selective CTLA4-Ig compounds that have entered clinical trials.
A Tale of Coronary Artery Disease and Myocardial Infarction (2012)

The remarkable facts, that the paroxysm, or indeed the disease itself, is excited more especially upon walking up hill, and after a meal; that thus excited, it is accompanied with a sensation, which threatens instant death if the motion is persisted in; and, that on stopping, the distress immediately abates, or altogether subsides; have . . . formed a constituent part of the character of Angina Pectoris. 1 " R emarks on Angina Pectoris" by John Warren, M.D., appeared in 1812 as the first article in the first issue of The New England Journal of Medicine and Surgery. 1 Warren's description of angina pectoris (derived from the Latin angina, "infection of the throat"; from the Greek , "strangling"; and from the Latin pectus, "chest") is equally apt for physicians and medical students today. At the time, the pathogenesis was unknown, and treatment consisted of bloodletting, a tincture of opium, bed rest, or a combination thereof. In 1799, Caleb H. Parry speculated that Syncope Anginosa was related to coronary-artery ossification (i.e., calcification), occurring predominantly in men at about 50 years of age and rarely in women or children. Cardiovascular science emerged in the physiological era of the late 19th and early 20th centuries, first in Europe and subsequently in North America. To celebrate the 200th anniversary of the New England Journal of Medicine, our essay focuses on the themes of coronary artery disease and myocardial infarction to highlight the interplay between science and medicine, emphasizing how the remarkable advances in our understanding of the pathogenesis of heart disease have produced life-saving and life-extending therapies.
Crowd-based ontology engineering with the uComp Protégé plugin (2016)

Crowdsourcing techniques provide effective means for solving a variety of ontology engineering problems. Yet, they are mainly used as external support to ontology engineering, without being closely integrated into the work of ontology engineers. In this paper we investigate how to closely integrate crowdsourcing into ontology engineering practices. Firstly, we show that a set of basic crowdsourcing tasks are used recurrently to solve a range of ontology engineering problems. Secondly, we present the uComp Protégé plugin that facilitates the integration of such typical crowdsourcing tasks into ontology engineering from within the Protégé ontology editor. An evaluation of the plugin in a typical ontology engineering scenario where ontologies are built from automatically learned semantic structures, shows that its use reduces the working times for the ontology engineers 11 times, lowers the overall task costs by 40% to 83% depending on the crowdsourcing settings used and leads to data quality comparable with that of tasks performed by ontology engineers. Evaluations on a large anatomy ontology confirm that crowdsourcing is a scalable and effective method: good quality results (accuracy of 89% and 99%) are obtained while achieving cost reductions of 75% from the ontology engineer costs and providing comparable overall task duration.
Molecular Dynamics Study of the Morphology of Hydrated Perfluorosulfonic Acid Polymer Membranes (2016)

Many morphological models have been proposed to describe the water swelling behavior and proton transport mechanism of perfluorosulfonic acid (PFSA) polymer membranes through experimental and modeling studies. However, the ongoing structural debate has not been completely resolved yet. We here conducted a series of all-atom molecular dynamics simulations of hydrated PFSA membranes to evaluate changes in the membrane morphology at different water contents. We found a similar dependence of the morphology on the water content between PFSA membranes with equivalent weight (EW) of 844 and 1144 g/equiv. That is, the morphology of the aqueous domain changes with increasing water content from a channel-network structure to a tortuous layered structure, and once attaining the tortuous layered structure, the water layer just thickened gradually by further increasing water content. Furthermore, we found more heterogeneous water domains in the higher-EW PFSA membrane, demonstrating the stronger aggregation behavior of the aqueous domains in the high-EW membranes. The variation of the PFSA membrane morphology observed here is useful to understand the proton transport mechanism and design new materials suitable for polymer electrolyte fuel cells in the near future.
[Introduction and progress of molecular microbial ecology]. (2003)

Molecular microbial ecology is an interdisciplinary field of molecular biological techniques and microbial ecology, which deals with microbial population, diversity, function, and relationships between microorganisms and biotic and abotic environments in microbial ecosystem. All the progress in molecular microbial ecology, especially in microbial diversity, phylogeny and communities of some microoganisms, indicate the renovation in traditional microbial ecology by the introduction of molecular techniques and strategies. This article reviewed the ideation, development, key domains, main methods and the future hot fields in molecular microbial ecology.
Multiple substrates of the <i>Legionella pneumophila</i> Dot/Icm system identified by interbacterial protein transfer (2004)

Legionella pneumophila is an intracellular pathogen that multiplies in a specialized vacuole within host cells. Biogenesis of this vacuole requires the Dot/Icm type IV protein translocation system. By using a Cre/loxP-based protein translocation assay, we found that proteins translocated by the Dot/Icm complex across the host phagosomal membrane can also be transferred from one bacterial cell to another. The flexibility of this system allowed the identification of several families of proteins translocated by the Dot/Icm complex. When analyzed by immunofluorescence microscopy, a protein identified by this procedure, SidC, was shown to translocate across the phagosomal membranes to the cytoplasmic face of the L. pneumophila phagosome. The identification of large numbers of these substrates, and the fact that the absence of any one substrate rarely results in strong defects in intracellular growth, indicate that there is significant functional redundancy among the Dot/Icm translocation targets.
Active site specificity profiling of the matrix metalloproteinase family: Proteomic identification of 4300 cleavage sites by nine MMPs explored with structural and synthetic peptide cleavage analyses (2015)

Secreted and membrane tethered matrix metalloproteinases (MMPs) are key homeostatic proteases regulating the extracellular signaling and structural matrix environment of cells and tissues. For drug targeting of proteases, selectivity for individual molecules is highly desired and can be met by high yield active site specificity profiling. Using the high throughput Proteomic Identification of protease Cleavage Sites (PICS) method to simultaneously profile both the prime and non-prime sides of the cleavage sites of nine human MMPs, we identified more than 4300 cleavages from P6 to P6' in biologically diverse human peptide libraries. MMP specificity and kinetic efficiency were mainly guided by aliphatic and aromatic residues in P1' (with a ~32-93% preference for leucine depending on the MMP), and basic and small residues in P2' and P3', respectively. A wide differential preference for the hallmark P3 proline was found between MMPs ranging from 15 to 46%, yet when combined in the same peptide with the universally preferred P1' leucine, an unexpected negative cooperativity emerged. This was not observed in previous studies, probably due to the paucity of approaches that profile both the prime and non-prime sides together, and the masking of subsite cooperativity effects by global heat maps and iceLogos. These caveats make it critical to check for these biologically highly important effects by fixing all 20 amino acids one-by-one in the respective subsites and thorough assessing of the inferred specificity logo changes. Indeed an analysis of bona fide MEROPS physiological substrate cleavage data revealed that of the 37 natural substrates with either a P3-Pro or a P1'-Leu only 5 shared both features, confirming the PICS data. Upon probing with several new quenched-fluorescent peptides, rationally designed on our specificity data, the negative cooperativity was explained by reduced non-prime side flexibility constraining accommodation of the rigidifying P3 proline with leucine locked in S1'. Similar negative cooperativity between P3 proline and the novel preference for asparagine in P1 cements our conclusion that non-prime side flexibility greatly impacts MMP binding affinity and cleavage efficiency. Thus, unexpected sequence cooperativity consequences were revealed by PICS that uniquely encompasses both the non-prime and prime sides flanking the proteomic-pinpointed scissile bond.
Programmable SERS active substrates for chemical and biosensing applications using amorphous/crystalline hybrid silicon nanomaterial (2016)

We present the creation of a unique nanostructured amorphous/crystalline hybrid silicon material that exhibits surface enhanced Raman scattering (SERS) activity. This nanomaterial is an interconnected network of amorphous/crystalline nanospheroids which form a nanoweb structure; to our knowledge this material has not been previously observed nor has it been applied for use as a SERS sensing material. This material is formed using a femtosecond synthesis technique which facilitates a laser plume ion condensation formation mechanism. By fine-tuning the laser plume temperature and ion interaction mechanisms within the plume, we are able to precisely program the relative proportion of crystalline Si to amorphous Si content in the nanospheroids as well as the size distribution of individual nanospheroids and the size of Raman hotspot nanogaps. With the use of Rhodamine 6G (R6G) and Crystal Violet (CV) chemical dyes, we have been able to observe a maximum enhancement factor of 5.38 × 10(6) and 3.72 × 10(6) respectively, for the hybrid nanomaterial compared to a bulk Si wafer substrate. With the creation of a silicon-based nanomaterial capable of SERS detection of analytes, this work demonstrates a redefinition of the role of nanostructured Si from an inactive to SERS active role in nano-Raman sensing applications.
Neural Arithmetic Logic Units (2018)

Neural networks can learn to represent and manipulate numerical information, but they seldom generalize well outside of the range of numerical values encountered during training. To encourage more systematic numerical extrapolation, we propose an architecture that represents numerical quantities as linear activations which are manipulated using primitive arithmetic operators, controlled by learned gates. We call this module a neural arithmetic logic unit (NALU), by analogy to the arithmetic logic unit in traditional processors. Experiments show that NALU-enhanced neural networks can learn to track time, perform arithmetic over images of numbers, translate numerical language into real-valued scalars, execute computer code, and count objects in images. In contrast to conventional architectures, we obtain substantially better generalization both inside and outside of the range of numerical values encountered during training, often extrapolating orders of magnitude beyond trained numerical ranges.
Low-Rate DDoS Attacks Detection and Traceback by Using New Information Metrics (2011)

A low-rate distributed denial of service (DDoS) attack has significant ability of concealing its traffic because it is very much like normal traffic. It has the capacity to elude the current anomaly-based detection schemes. An information metric can quantify the differences of network traffic with various probability distributions. In this paper, we innovatively propose using two new information metrics such as the generalized entropy metric and the information distance metric to detect low-rate DDoS attacks by measuring the difference between legitimate traffic and attack traffic. The proposed generalized entropy metric can detect attacks several hops earlier (three hops earlier while the order α = 10 ) than the traditional Shannon metric. The proposed information distance metric outperforms (six hops earlier while the order α = 10) the popular Kullback-Leibler divergence approach as it can clearly enlarge the adjudication distance and then obtain the optimal detection sensitivity. The experimental results show that the proposed information metrics can effectively detect low-rate DDoS attacks and clearly reduce the false positive rate. Furthermore, the proposed IP traceback algorithm can find all attacks as well as attackers from their own local area networks (LANs) and discard attack traffic.
Rotation Invariant Classification of 3D Surface Texturesusing Photometric Stereo and Surface Magnitude Spectra (2000)

Many image-rotation invariant texture classification approaches have been presented. However, image rotation is not necessarily the same as surface rotation. This paper proposes a novel scheme that is surface-rotation invariant. It uses magnitude spectra of the partial derivatives of the surface obtained using photometric stereo. Unfortunately the partial derivative operator is directional. It is therefore not suited for direct use as a rotation invariant feature. We present a simple frequency domain method of removing the directional artefacts. Polarograms (polar functions of spectra) are extracted from resulting spectra. Classification is performed by comparing training and classification polarograms over a range of rotations (1° steps over the range 0° to 180°). Thus the system both classifies the test texture and estimates its orientation relative to the relevant training texture. A proof for the removal of directional artefacts from partial derivative spectra is provided. Results obtained using the classification scheme on synthetic and real textures are presented.
Dietary administration of inositol and/or inositol-6-phosphate prevents chemically-induced rat hepatocarcinogenesis. (2005)

Chemoprevention is considered a rational strategy for dietary approaches to prevention of cancer. Multiple lines of evidence suggest that many of our dietary principles are able to intervene in the multistage carcinogenesis process and phytic acid (inositol hexaphosphate, IP6), a phytochemical present in a variety of plant species, has been shown to prevent various cancers, including those of the mammary gland, colon and liver. However, the mechanism of chemoprevention by IP6 has not been fully elucidated. In the present study, we examined the effects of inositol and/or IP6 supplementation on rat hepatocarcinogenesis initiated by diethylnitrosamine (DEN) and promoted by partial hepatectomy (PH). Supplementation with either inositol or IP6, or their combination, starting one week prior to administration of DEN, resulted in a significant decrease in both the area and the number of placental glutathione S-transferase positive (GST-P+) foci, a preneoplastic marker for DEN-initiated hepatocarcinogenesis. The administration of inositol and/or IP6 in drinking water caused marked enhancement in the glutathione S-transferase (GST) activity. In addition, the production of thiobarbituric acid reactive substances and the catalase activity were significantly reduced in rats supplemented with inositol and /or IP6. Based on these findings, it is likely that the chemopreventive effects of inositol and/or IP6 on rat hepatocarcinogenesis initiated by DEN and promoted by PH are associated with induction of GST activity and suppression of lipid peroxidation.
Determination of radium isotope ratios and abundances in geological samples by thermal ionization mass spectrometry (1991)

We describe chemical separation and mass spectrometric procedures for the measurement of radium isotopes in geologic samples. These methods provide 226Ra/228Ra ratio measurements for 1 g or less of rock sample containing subpicogram amounts of radium with precision better than 1.5% (95% confidence level). Radium-226 concentrations were measured by isotope dilution for smaller sample sizes (100-500 mg) containing as little as 1-10 fg of total 226Ra with similar high precision.
Chain extenders for polyesters. IV. Properties of the polyesters chain-extended by 2,2′-bis(2-oxazoline) (1987)

Some properties of the polyesters treated with such an addition-type chain extender as 2,2′-bis(2-oxazoline) (BOZ) have been investigated. The molecular size distribution and the melting point of the resultant polyesters indicate that BOZ reacts to form linear chain-extended polymers without branching. As for their thermal stabilities, unreacted oxazoline remained in the polymer can act as a heat stabilizer by further reacting with carboxyl terminals of the polymers and by preventing decrease in the molecular weight even in the solid state. On the other hand, BOZ unit incorporated in the polyester chain was relatively thermally unstable compared with the ordinary polyester chain, especially under the polyester melt condition. The polyester treated with BOZ has a rather low carboxyl content, and considerable improvement in the hydrolytic stability has been observed. But unreacted oxazoline groups adversely affected the hydrolytic stability, although the effect was about eight times as small as that of carboxyl groups.