gebhart/patrepeval huggingface dataset:
Local matching of random restriction maps (2001)

Optical mapping is a new technique to generate restriction maps of DNA easily and quickly. DNA restriction maps can be aligned by comparing corresponding restriction fragment lengths. To relate, organize, and analyse these maps it is necessary to rapidly compare maps. The issue of the statistical significance of approximately matching maps then becomes central, as in BLAST with sequence scoring. In this paper, we study the approximation to the distribution of counts of matched regions of specified length when comparing two DNA restriction maps. Distributional results are given to enable us to compute p -values and hence to determine whether or not the two restriction maps are related. The key tool used is the Chen-Stein method of Poisson approximation. Certain open problems are described.
Automatic analysis of firewall and network intrusion detection system configurations (2004)

Given a network that deploys multiple firewalls and network intrusion detection systems (NIDSs), ensuring that these security components are correctly configured is a challenging problem. Although models have been developed to reason independently about the effectiveness of firewalls and NIDSs, there is no common framework to analyze their interaction. This paper presents an integrated, constraint-based approach for modeling and reasoning about these configurations. Our approach considers the dependencies among the two types of components, and can reason automatically about their combined behavior. We have developed a tool for the specification and verification of networks that include multiple firewalls and NIDSs, based on this approach. This tool can also be used to automatically generate NIDS configurations that are optimal relative to a given cost function.
Increased plasma levels of tissue factor pathway inhibitor-activated factor X complex in patients with disseminated intravascular coagulation (2000)

Plasma levels of tissue factor pathway inhibitor (TFPI)-activated factor Xa (FXa) complex were measured in patients with disseminated intravascular coagulation (DIC), pre-DIC, and DIC. Plasma levels of plasmin-plasmin inhibitor complex (PPIC), D-dimer, and soluble fibrin monomer (SFM) were significantly higher in patients with DIC than in those with pre-DIC or non-DIC; the levels of these hemostatic markers were significantly higher in patients with pre-DIC than in those with non-DIC. Plasma levels of thrombin-antithrombin complex (TAT) were significantly higher in patients with DIC or pre-DIC than in those with non-DIC. Plasma levels of tissue factor (TF), total TFPI, free TFPI, and TFPI-Xa complex were significantly higher in patients with DIC than in those with non-DIC. Plasma levels of TFPI-Xa complex were significantly increased in patients with pre-DIC as compared to those with non-DIC; however, plasma free TFPI levels were significantly decreased in patients with pre-DIC as compared to those with non-DIC. These findings suggest that free TFPI might be consumed in the pre-DIC state, thereby confirming the activation of the extrinsic pathway. Plasma levels of TFPI-Xa complex were significantly correlated with TF, free TFPI, and total TFPI. Increased plasma TFPI-Xa complex levels might be useful for the diagnosis of DIC or pre-DIC, particularly that occurring by activation of the extrinsic pathway of blood coagulation.
Alterations in the Phospholipid Composition of <i>Escherichia coli</i> B During Growth at Different Temperatures (1969)

The major phospholipid classes of Escherichia coli B, phosphatidyl ethanolamine, cardiolipin, and phosphatidyl glycerol, were quantitated at different stages of the growth cycle. The organisms were incubated at both 27 and 37 C. Significant differences were observed both in the amounts of total lipid phosphorus per gram (dry weight) of cells and in the relative percentages of the individual phospholipids. At 37 C the total amount of lipid phosphorus decreased significantly throughout the growth cycle. However, at 27 C total lipid phosphorus accumulated. The patterns of the three major phospholipid classes of Escherichia coli exhibited complex quantitative changes. In addition, some evidence based on glycerol to phosphate molar ratios indicated that phosphatidyl glycerolphosphate replaced phosphatidyl glycerol during the late growth stages of E. coli B when grown at 27 C. A comparative analysis of phospholipid and fatty acid patterns led to a hypothesis attempting to explain some reported variations in the lipid composition of E. coli under different conditions of growth.
OASIS/CREB3L1 Induces Expression of Genes Involved in Extracellular Matrix Production But Not Classical Endoplasmic Reticulum Stress Response Genes in Pancreatic β-Cells (2010)

Old astrocyte specifically induced substance (OASIS) has previously been shown to be a putative endoplasmic reticulum (ER) stress sensor in astrocytes with a mechanism of activation that is similar to ATF6. In this study we investigated the expression and activation of endogenous and overexpressed OASIS in pancreatic beta-cells. OASIS mRNA expression was detected in pancreatic beta-cell lines and rodent islets, and the expression level was up-regulated by ER stress-inducing compounds. Endogenous OASIS protein, however, is expressed at low levels in pancreatic beta-cell lines and rodent islets, possibly due to abundant levels of the micro-RNA miR-140 present in these cells. In contrast, expression of both full-length and cleaved (active) OASIS was readily detectable in the developing mouse pancreas (embryonic d 15.5). Microarray analysis after expression of an active nuclear-localized version of OASIS in an inducible INS-1 beta-cell line resulted in the up-regulation of many genes implicated in extracellular matrix production and protein transport but not classical ER stress response genes. Consistent with this, expression of active OASIS failed to induce glucose-regulated protein 78 kDa promoter activity in pancreatic beta-cells. These results suggest that the repertoire of genes induced by OASIS is cell type-dependent and that the OASIS protein may have a role in pancreas development.
Characterization of Gastrin-Induced Proangiogenic Effects <b> <i>In vivo</i> </b> in Orthotopic U373 Experimental Human Glioblastomas and <b> <i>In vitro</i> </b> in Human Umbilical Vein Endothelial Cells (2004)

The present study shows that gastrin has marked proangiogenic effects in vivo on experimental gliomas and in vitro on HUVECs. This effect depends in part on the level of E-selectin activation, but not on IL-8 expression/release by HUVECs.
TEXT system implementation (1985)

A portion of an Office of Naval Research (ONR) database was used to test the TEXT system. The portion used contains information about military vehicles and weapons. The ONR database was selected for TEXT in part because of its availability (it had been in use previously in a research project jointly with the Wharton School of the University of Pennsylvania) and in part because of its complex structure. Even using only a portion of the database provided a domain complex enough to allow for an interesting set of questions and answers.
Histopathological Image Analysis Using Image Processing Techniques: An Overview (2012)

To overcome this difficulty a computer assisted image analysis is needed for quantitative diagnosis of tissue. In this paper we reviews and summarize the applications of digital image processing techniques for histology image analysis mainly to cover segmentation and disease classification methods.
Development of BIM-based CPLM System for Civil Project Management (2011)

BIM technology, based on 3D model of civil engineering structures, creates and manages information of the structures throughout four stages: Planning, design, construction, and maintenance. BIM is now used around the globe for improvement of the construction productivity. However, in order to expect the efficient engineering work, collaboration system between participants in a construction project is necessary. Therefore, in this paper BIM based CPLM (Construction project lifecycle management) system was designed and developed by analyzing the requirements of participants of a construction project. CPLM system offers an environment which enables the sharing and management of information according to the each stage of construction. CPLM is expected to aid cooperative decision-making during the overall construction process through the process innovation and the efficient data management.
Review of recent full adders implemenetd in single electron technology; Invited Paper (2006)

This paper reviews several full adder designs in single electron technology (SET). Different SET designs of full adders were introduced recently. In addition to the structure and size reported for these full adders, this paper also provides a quantitative comparison in terms of delay and power dissipation. This allows for a better understanding of the advantages and disadvantages of each solution. In addition, an improved FA design based on capacitive threshold logic gates are presented.
Focal transformation, an imaging concept for signal restoration and noise removal (2006)

Abstract Interpolation of data beyond aliasing limits and removal of noise that occurs within the seismic bandwidth are still important problems in seismic processing. The focal transform is introduced as a promising tool in data interpolation and noise removal, allowing the incorporation of macroinformation about the involved wavefields. From a physical point of view, the principal action of the forward focal operator is removing the spatial phase of the signal content from the input data, and the inverse focal operator restores what the forward operator has removed. The strength of the method is that in the transformed domain, the focused signals at the focal area can be separated from the dispersed noise away from the focal area. Applications of particular interest in preprocessing are interpolation of missing offsets and reconstruction of signal beyond aliasing. The latter can be seen as the removal of aliasing noise.
Dual‐Functional PEI–Poly(γ‐Cholesterol‐<scp>l</scp>‐Glutamate) Copolymer for Drug/Gene Co‐delivery (2013)

Novel dual‐functional PEI‐poly(γ‐cholesterol‐ l ‐glutamate) (PEI‐PCHLG) copolymers are developed for the first time. A series of PEI‐PCHLG (PEI‐1, PEI‐2, PEI‐3, and PEI‐4) with various PEI percentages and molecular weights are successfully synthesized, among which the poor organic solvent solubility of PEI‐1 precludes its further application. The other three copolymers can spontaneously self‐assemble into micelles; the critical micelle concentration (CMC) values are 0.66, 1.3, and 0.95 μmol L −1 , respectively. PEI‐2 and PEI‐4, with lower CMC, are worth being further developed as promising drug carriers because of their resistance to dilution in circulation after systemic administration. However, PEI‐4 can form smaller‐sized micelles than PEI‐2 and has similar in vitro cytotoxicity to PEI. Thus, PEI‐4 is further investigated. PEI‐4 micelles can not only incorporate docetaxel (DTX) with high encapsulation efficiency (91.0%) and drug loading (4.3%), but also load pDNA efficiently at a ratio of 8:1 (w/w). DTX‐loaded PEI‐4 micelles (DTX‐PEI‐4) can also carry genes with the same gene‐binding capacity as PEI‐4 micelles. The above three micelles (DTX‐PEI‐4, pDNA‐PEI‐4, and pDNA/DTX‐PEI‐4) are sub‐micrometer‐sized and spherical. The results indicate that PEI‐4 containing 28.9% PEI, one of the PEI‐PCHLG copoly­mers, is a potential carrier for gene delivery, drug delivery, or even drug/gene co‐delivery. image
Antihyperglycemic Effects of Short Term Resveratrol Supplementation in Type 2 Diabetic Patients (2013)

The objective of this study was to examine the effectiveness of resveratrol in lowering blood glucose in the presence of standard antidiabetic treatment in patients with type 2 diabetes, in a randomized placebo-controlled double-blinded parallel clinical trial. A total of 66 subjects with type 2 diabetes were enrolled in this study and randomly assigned to intervention group which was supplemented with resveratrol at a dose 1 g/day for 45 days and control group which received placebo tablets. Body weight, blood pressure, fasting blood glucose, haemoglobin A1c, insulin, homeostatic assessments for insulin resistance, triglycerides, total cholesterol, low density lipoprotein, high density lipoprotein, and markers of liver and kidney damage were measured at baseline and after 45 days of resveratrol or placebo supplementation. Resveratrol treatment significantly decreased systolic blood pressure, fasting blood glucose, haemoglobin A1c, insulin, and insulin resistance, while HDL was significantly increased, when compared to their baseline levels. On the other hand, the placebo group had slightly increased fasting glucose and LDL when compared to their baseline levels. Liver and kidney function markers were unchanged in the intervention group. Overall, this study showed that resveratrol supplementation exerted strong antidiabetic effects in patients with type 2 diabetes.
Coiled-Tubing Pressure and Tension Limits (1991)

ABSTRACT The use of Coiled Tubing (CT) for servicing oil and gas wells is increasing rapidly. Larger CT sizes are being developed to meet new service requirements. The CT is being pushed closer to its performance limits for many of these services. To avoid CT failures in the field, it is important that these limits are well understood. There are three major types of CT limits: Life limits due to fatigue and corrosion [1].Pressure and tension limitsDiameter and ovality limits These limits are interrelated in some ways but can be analyzed separately. The corrosion effect on the CT must be considered for the first two limitations, but, the fatigue life of the CT does not significantly affect the pressure and tension limits. The diameter and ovality limits are determined based on present surface hardware such as the stripper bushings and BOP inserts. Real-time monitoring of the CT diameter is necessary to locate mechanical damage, such as dents and ballooning, which can not be predicted by computer modelling. This paper addresses the pressure and tension limits. It describes a mathematical model which is used to determine these limits. Test data used to validate the model is also presented. Selectipn of Limiting Criteria A criterion must be chosen as the limiting criteria for determining the pressure and tension limits. For this model, the initiation of yielding for a straight section CT with no residual internal stresses was chosen as the limiting criterion. This criterion is discussed further in the Incipient Yield Criteria section of this paper. The incipient yield criterion was chosen because it is well accepted in the industry; it is relatively simple to calculate; and it agrees well with test data. In fact, this criterion is not entirely accurate in representing CT. CT is plastically deformed when it is "bent" onto and off of the reel and over the gooseneck of the injector head [1]. This plastic deformation causes significant residual stresses which are not considered by this yield criterion. These residual stresses cause yielding to begin much earlier than this yield criterion would predict. This yielding due to the residual stresses acts to relieve the residual stresses; however, it is not this yielding that is being considered for determining the CT limits but the yielding that would occur if the CT did not have any residual stresses.
Extending the Cure: Policy Responses to the Growing Threat of Antibiotic Resistance (2007)

Foreword Executive Summary Introduction 1. Antibiotic resistance: The unfolding crisis 2. The epidemiology of antibiotic resistance: Policy levers 3. Patient and physician demand for antibiotics 4. The role of health care facilities 5. The role of the federal government 6. The role of health insurance 7. Supply-side strategies for tackling resistance 8. Next steps Acronyms and Abbreviations Biographies Consultation Participants
OpenSec: Policy-Based Security Using Software-Defined Networking (2016)

As the popularity of software-defined networks (SDN) and OpenFlow increases, policy-driven network management has received more attention. Manual configuration of multiple devices is being replaced by an automated approach where a software-based, network-aware controller handles the configuration of all network devices. Software applications running on top of the network controller provide an abstraction of the topology and facilitate the task of operating the network. We propose OpenSec, an OpenFlow-based security framework that allows a network security operator to create and implement security policies written in human-readable language. Using OpenSec, the user can describe a flow in terms of OpenFlow matching fields, define which security services must be applied to that flow (deep packet inspection, intrusion detection, spam detection, etc.) and specify security levels that define how OpenSec reacts if malicious traffic is detected. In this paper, we first provide a more detailed explanation of how OpenSec converts security policies into a series of OpenFlow messages needed to implement such a policy. Second, we describe how the framework automatically reacts to security alerts as specified by the policies. Third, we perform additional experiments on the GENI testbed to evaluate the scalability of the proposed framework using existing datasets of campus networks. Our results show that up to 95% of attacks in an existing data set can be detected and 99% of malicious source nodes can be blocked automatically. Furthermore, we show that our policy specification language is simpler while offering fast translation times compared to existing solutions.
Induction of hsp70-Mediated Th17 Autoimmunity Can Be Exploited as Immunotherapy for Metastatic Prostate Cancer (2007)

Abstract A close connectivity between autoimmune and tumor rejection responses is known to exist in the case of melanoma immunotherapy. However, relatively little is known about self-antigens on other types of normal cells, their relation to the development of autoimmune disease, and their possible coexistence as potential tumor rejection antigens on associated tumors. In the current study, we induced inflammatory killing of normal prostate tissue in situ using a fusogenic membrane glycoprotein along with the immune adjuvant hsp70. We show here that, in the prostate, hsp70 induces interleukin (IL)-6, which triggers a CD4- and CD8-dependent progressive autoimmune reactivity, associated with IL-17 expression. This autoimmune response was also able to induce the rejection of established prostate tumors, but not other histologic types of tumors, growing elsewhere in the animal. These data show that the intimate connectivity between autoimmune and tumor rejection responses extends beyond the classic melanoma paradigm and may be clinically valuable for the treatment of established metastatic disease of the prostate. [Cancer Res 2007;67(24):11970–9]
Metal–Organic Hybrid Interface States of A Ferromagnet/Organic Semiconductor Hybrid Junction as Basis For Engineering Spin Injection in Organic Spintronics (2011)

Abstract Electrons in organic semiconductors (OSC) possess remarkably long spin relaxation times. Hybrid spintronic devices that combine OSC with ferromagnetic (FM) substrates are therefore expected to provide a route to devices with improved and new functionalities. A crucial role is played by the FM‐OSC interface which governs the spin injection into the OSC. Using spin‐resolved photoelectron spectroscopy and ab initio calculations we study here such possible injection channels in metal phthalocyanines (MPc). We report the first direct observation of the successful engineering of different spin‐selective hybrid interface states at the Fermi level of a FM‐OSC hybrid junction only by changing the central metal atom of a MPc. Our results demonstrate that tailoring the chemical interaction at the FM‐OSC interface is a promising way to modify the spin injection channels and thus the spin injection capability.
SARS-CoV-2 Vaccination — An Ounce (Actually, Much Less) of Prevention (2020)

The Covid-19 epidemic continues to rage, especially in countries that have been unable or unwilling to institute strong public health measures. A return to normality has increasingly come to rely o...
The pod room - a group learning space (2009)

Extract: Bond University has recently completed construction of an engaging formal teaching space, known as the Pod Room, named as a result of its pod, or kidney-shaped, group work desks. The room has been designed to facilitate interactivity, teamwork, and sociability amongst students. Our concept of this pod space is based on an innovative design that has been successfully trialled at the University of Melbourne and the University of Queensland.
Fast and Accurate Finite Element Method for Deformation Animations (2009)

We present a matrix clustering method for speeding up finite element computations for non-rigid object animation. The method increases the efficiency of computing deformation dynamics through a compression scheme that decomposes the large force-displacement matrix into clusters of smaller matrices in order to facilitate the run-time computations of linear finite element based deformations. The deformation results are compared with the results produced by using modal analysis method and the standard linear finite element algorithm. We demonstrate that the proposed method is stable with comparative computational speed to modal analysis method. A hierarchical skeleton-based system is also implemented to add constraints to material nodes. Thus, real-time deformations can be directed by motion captured data sets or key-framed animations.
Hypoxia-inducible factor inhibitors: a survey of recent patented compounds (2004 – 2010) (2011)

Hypoxia-inducible factor (HIF) is a heterodimeric transcription factor consisting of α and β subunits that regulates the expression of angiogenic factors, including VEGF, which are involved in angiogenesis, invasion/metastasis, glucose uptake and cell survival during cancer development.This review summarizes the information about patented HIF inhibitors over the last 7 years (2004 - 2010). The reader will gain an outline of the structure and biological activity of recently developed HIF inhibitors.Inhibition of HIF is an attractive therapeutic target for tumor angiogenesis and, until now, various HIF inhibitors have been discovered and evaluated. It is expected that development of more potent and selective HIF inhibitors will provide an effective treatment of cancer and other HIF-related diseases, including inflammation and cardiovascular disorder. As VEGF plays an important role in angiogenesis during tumor growth and ischemic diseases, the inhibition of VEGF-induced HIF is an attractive approach for the suppression of hypoxia-mediated pathological angiogenesis. HIF inhibitors may not only have cytostatic antitumor effects with fewer side effects, but also synergetic effects combined with radiotherapy.