gebhart/patrepeval huggingface dataset:
Bit-split string-matching engines for intrusion detection and prevention (2006)

Network Intrusion Detection and Prevention Systems have emerged as one of the most effective ways of providing security to those connected to the network and at the heart of almost every modern intrusion detection system is a string-matching algorithm. String matching is one of the most critical elements because it allows for the system to make decisions based not just on the headers, but the actual content flowing through the network. Unfortunately, checking every byte of every packet to see if it matches one of a set of thousands of strings becomes a computationally intensive task as network speeds grow into the tens, and eventually hundreds, of gigabits/second. To keep up with these speeds, a specialized device is required, one that can maintain tight bounds on worst-case performance, that can be updated with new rules without interrupting operation, and one that is efficient enough that it could be included on-chip with existing network chips or even into wireless devices. We have developed an approach that relies on a special purpose architecture that executes novel string matching algorithms specially optimized for implementation in our design. We show how the problem can be solved by converting the large database of strings into many tiny state machines, each of which searches for a portion of the rules and a portion of the bits of each rule. Through the careful codesign and optimization of our architecture with a new string-matching algorithm, we show that it is possible to build a system that is 10 times more efficient than the currently best known approaches.
Inhibiting and Remodeling Toxic Amyloid-Beta Oligomer Formation Using a Computationally Designed Drug Molecule That Targets Alzheimer’s Disease (2018)

Alzheimer's disease (AD) is rapidly reaching epidemic status among a burgeoning aging population. Much evidence suggests the toxicity of this amyloid disease is most influenced by the formation of soluble oligomeric forms of amyloid β-protein, particularly the 42-residue alloform (Aβ42). Developing potential therapeutics in a directed, streamlined approach to treating this disease is necessary. Here we utilize the joint pharmacophore space (JPS) model to design a new molecule [AC0107] incorporating structural characteristics of known Aβ inhibitors, blood-brain barrier permeability, and limited toxicity. To test the molecule's efficacy experimentally, we employed ion mobility mass spectrometry (IM-MS) to discover [AC0107] inhibits the formation of the toxic Aβ42 dodecamer at both high (1:10) and equimolar concentrations of inhibitor. Atomic force microscopy (AFM) experiments reveal that [AC0107] prevents further aggregation of Aβ42, destabilizes preformed fibrils, and reverses Aβ42 aggregation. This trend continues for long-term interaction times of 2 days until only small aggregates remain with virtually no fibrils or higher order oligomers surviving. Pairing JPS with IM-MS and AFM presents a powerful and effective first step for AD drug development. Graphical Abstract.
Effect of Silicon Activity on Liquid‐Phase Sintering of Nitrogen Ceramics (1985)

Volatilization resulting from the thermal decomposition of Si 3 N 4 causes the large weight loss and desintering phenomenon observed during pressureless sintering of Si 3 N 4 ‐5% MgO and sialon (z =2)‐5% MgO. The addition of a few weight percent of Si to the powder suppresses this volatilazation and helps to achieve fully dense Si 3 N 4 components.
Estimating Gaze Direction of Vehicle Drivers Using a Smartphone Camera (2014)

Many automated driver monitoring technologies have been proposed to enhance vehicle and road safety. Most existing solutions involve the use of specialized embedded hardware, primarily in high-end automobiles. This paper explores driver assistance methods that can be implemented on mobile devices such as a consumer smartphone, thus offering a level of safety enhancement that is more widely accessible. Specifically, the paper focuses on estimating driver gaze direction as an indicator of driver attention. Input video frames from a smartphone camera facing the driver are first processed through a coarse head pose direction. Next, the locations and scales of face parts, namely mouth, eyes, and nose, define a feature descriptor that is supplied to an SVM gaze classifier which outputs one of 8 common driver gaze directions. A key novel aspect is an in-situ approach for gathering training data that improves generalization performance across drivers, vehicles, smartphones, and capture geometry. Experimental results show that a high accuracy of gaze direction estimation is achieved for four scenarios with different drivers, vehicles, smartphones and camera locations.
Automatic task-specific model reduction for humanoid robots (2013)

Simple inverted pendulum models and their variants are often used to control humanoid robots in order to simplify the control design process. These simple models have significantly fewer degrees of freedom than the full robot model. The design and choice of these simple models are based on the designer's intuition, and the reduced state mapping and the control input mapping are manually chosen. This paper presents an automatic model reduction procedure for humanoid robots, which is task-specific. It also presents an optimization framework that uses the auto-generated task-specific reduced models to control humanoid robots. Successful simulation results of balancing, fast arm swing, and hip rock and roll motion tasks are demonstrated.
Exploring the scientific basis of surgery: transmyocardial revascularization. (1999)

Transmyocardial revascularization (TMR) is a new surgical procedure aimed at increasing blood flow to the ischemic myocardium. It has been used for treatment of patients with end-stage coronary artery disease who are not candidates for conventional measures such as medication, percutaneous transluminal coronary angioplasty, and coronary artery bypass grafting. TMR involves creating transmural channels in the myocardium using lasers, in areas shown to be ischemic during preoperative testing. This procedure has shown promising results in clinical trials, but the mechanism of its efficacy remains largely unknown. TMR was originally developed as a means of supplying blood to the ventricular myocardium, directly through channels made in the wall of the ventricle. This was in an attempt to recreate the situation that exists in the reptilian heart, in which the myocardium is perfused directly from the ventricular chamber through a rich network of sinusoids that bathe the myocardial cells. However, the existence of a significant sinusoidal network in the human heart is doubtful. Whether the myocardium can be perfused directly via the TMR channels is controversial; it is becoming clear that other mechanisms such as angiogenesis are also at work. This review will use TMR as an example to illustrate how surgical practice and thinking can be based on theories that have little or no sound experimental evidence to support them. The importance of elucidating the valid scientific basis of surgical procedures in this modern era of evidence-based medicine will be emphasized.
Genetic association and linkage analysis of the apolipoprotein CII locus and familial Alzheimer's disease (1992)

We previously reported a genetic association between the 3.5 kb (F) Taq I restriction fragment length polymorphism allele of the apolipoprotein CII gene on chromosome 19 and familial Alzheimer's disease. Here, we report an additional analysis of this association performed on an expanded and better defined data set of 23 families with familial Alzheimer's disease. The F allele frequency in affected family members in the expanded set was 0.62 +/- 0.06 (mean +/- standard error, n = 51 subjects), which differed significantly from a frequency of 0.39 +/- 0.02 (n = 226) for unrelated control subjects (Z = 3.75, p less than 0.0002). These results are consistent with our previous findings and suggest an association between the F allele of apolipoprotein CII and familial Alzheimer's disease. When the apolipoprotein CII locus was tested for linkage to familial Alzheimer's disease, LOD scores summed for the complete group of families were negative and close linkage was excluded. Close linkage was also excluded for early-onset families (mean onset age less than or equal to 60 years), but small positive LOD scores were obtained for late-onset kindreds.
Waveguide Optical Isolators for Integrated Optics (2011)

Waveguide optical isolators are investigated for an application to integrated optics. A nonreciprocal loss shift isolator has the advantage of high compatibility with optical active devices. The interferometric waveguide optical isolator that uses nonreciprocal phase shift brought about by the first-order magneto-optic effect is applicable to a variety of waveguide platforms. In a silicon-on-insulator (SOI) waveguide, the low refractive index of buried oxide layer enhances the magneto-optic phase shift, which contributes to reduce the device size of isolator. We developed the surface activated direct bonding technique to integrate a magneto-optic garnet crystal onto dissimilar crystals. The performance of SOI waveguide optical isolator was demonstrated with an optical isolation of 21 dB at a wavelength of 1559 nm.
High power single-frequency narrow-linewidth erbium-doped fiber laser (2004)

In this paper, we report the demonstration of a 200-mW stable single-frequency narrow-linewidth DBR erbium doped fibre laser.
Electrode position and the multi‐focal visual‐evoked potential: Role in objective visual field assessment (1998)

With this technique, the multi-focal VEP can be used to objectively assess the visual field.
Sheared Interpolation and Gradient Estimation for Real-Time Volume Rendering (1994)

In this paper we present a technique for the interactive control and display of static and dynamic 3D datasets. We describe novel ways of tri-linear interpolation and gradient estimation for a real-time volume rendering system, using coherency between rays. We show simu lation results that compare the proposed methods to tra ditional algorithms and present them in the cantezt of Cube-B, a special-purpose architecture capable afrender ing 5123 16-bit per vozel datasets at over 20 frames per second.
Failure to isolate human T cell lymphotropic virus type I and to detect variant-specific genomic sequences by polymerase chain reaction in Melanesians with indeterminate Western immunoblot (1992)

The controversy over the endemicity of human T cell lymphotropic virus type I (HTLV-I) in Melanesia has been settled recently by the isolation of genetically distinct, highly divergent sequence variants of HTLV-I from unrelated inhabitants of Papua New Guinea and the Solomon Islands. Still at issue, however, is the significance of the high frequency of indeterminate HTLV-I Western blots (defined as reactivity to only gag-encoded proteins) among Melanesians. To investigate whether this indeterminate seroreactivity reflects specific reactivity to the Melanesian HTLV-I variants, 27 seroindeterminate Melanesians from Papua New Guinea and the Solomon Islands were studied for evidence of HTLV-I infection. Although antibodies against Melanesian variant-specific env gene products and variant-specific env gene sequences were detected by Western blot analysis and polymerase chain reaction, respectively, in all 11 HTLV-I Western blot-positive Melanesians, none of the 27 seroindeterminate Melanesians had such variant-specific antibodies or HTLV-I proviral sequences. In addition, attempts to isolate HTLV-I from seroindeterminate individuals were unsuccessful. These data indicate that HTLV-I infection is not the cause of the indeterminate Western blot reactivity seen in Melanesia.
Attenuated hepatitis A virus: genetic determinants of adaptation to growth in MRC-5 cells (1994)

A live candidate hepatitis A virus vaccine, developed from the HM-175 strain and adapted to growth in primary African green monkey kidney (AGMK) cells, was adapted to growth in MRC-5 cells. The nucleotide sequence of the MRC-5 cell-adapted virus was determined and compared with the known sequence of the AGMK cell-adapted virus. Thirteen unique mutations, which occurred during passage in MRC-5 cells, were identified. Four of the unique mutations were located in a cluster in the 5' noncoding region (NC), and three of the remaining nine mutations encoded amino acid changes. Infectious chimeric cDNAs were constructed from infectious cDNA clones of the AGMK cell-adapted and wild-type HM-175 viruses and PCR-amplified cDNA segments of the MRC-5 cell-adapted virus. The viruses encoded by these plasmids were recovered after transfection of cultured cells with in vitro transcripts, and their growth phenotypes in fetal rhesus kidney 4 (FRhK-4) and MRC-5 cells were determined. The important growth-enhancing mutations could be divided into three sets. Two of these were located in the 5' NC region, and the third was located in the 2C nonstructural gene. The mutations in the 5' NC region that developed during passage in MRC-5 cells were indispensable for efficient growth in MRC-5 cells, but a combination of the two groups in the 5' NC region and one in the 2C gene were required to increase growth dramatically in MRC-5 cells.
Fast Light Modulator Based On Stressed Liquid Crystals (2004)

We introduce stressed liquid crystals as new ultra fast light modulating materials that provide large shift of phase retardation in a submillisecond time frame. Performance of these materials in a number of applications, including those that work in the IR region, is discussed.
StEERING: A software-defined networking for inline service chaining (2013)

Network operators are faced with the challenge of deploying and managing middleboxes (also called inline services) such as firewalls within their broadband access, datacenter or enterprise networks. Due to the lack of available protocols to route traffic through middleboxes, operators still rely on error-prone and complex low-level configurations to coerce traffic through the desired set of middleboxes. Built upon the recent software-defined networking (SDN) architecture and OpenFlow protocol, this paper proposes StEERING, short for SDN inlinE sERvices and forwardlNG. It is a scalable framework for dynamically routing traffic through any sequence of middleboxes. With simple centralized configuration, StEERING can explicitly steer different types of flows through the desired set of middleboxes, scaling at the level of per-subscriber and per-application policies. With its capability to support flexible routing, we further propose an algorithm to select the best locations for placing services, such that the performance is optimized. Overall, StEERING allows network operators to monetize their middlebox deployment in new ways by allowing subscribers flexibly to select available network services.
Nonlinear antenna technology (2002)

Nonlinear antennas combine advances in nonlinear dynamics, active antenna design, and analog microelectronics to generate beam steering and beam forming across an array of nonlinear oscillators. Nonlinear antennas exploit two phenomena typically shunned in traditional designs: nonlinear unit cells and interelement coupling. The design stems from nonlinear coupled differential equation analysis that by virtue of the dynamic control is far less complex than the linear counterparts by eliminating the need for phase shifters and beam forming computers. These advantages arise from incorporating nonlinear dynamics rather than limiting the system to linear quasisteady state operation. A theoretical framework describing beam shaping and beam forming by exploiting the phase, amplitude, and coupling dynamics of nonlinear oscillator arrays is presented. Experimental demonstration of nonlinear beam steering is realized using analog microelectronics.
The Dickkopf1‐cytoskeleton‐associated protein 4 axis creates a novel signalling pathway and may represent a molecular target for cancer therapy (2017)

This article is part of a themed section on WNT Signalling: Mechanisms and Therapeutic Opportunities. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v174.24/issuetoc.
Characterization of Polarization-Maintaining Fiber Using High-Sensitivity Optical-Frequency-Domain Reflectometry (2006)

Optical-frequency-domain reflectometry is used to measure the group-index difference and the refractive-index difference (i.e., beat length) between the fast and slow modes in polarization-maintaining optical fiber. The Rayleigh scatter normally present in the fiber is measured in reflection. This measurement, in turn, enables a distributed measurement of the fiber's birefringence that is rapid and completely nondestructive
Hyperglycosylated hcg, a potential alternative to hcg in Down syndrome screening (1998)

Hyperglycosylated hCG (H-hCG) is a minor variant of hCG with abnormal oligosaccharide side chains. It is the principal gonadotropin detected in the serum and urine of patients with gestational choriocarcinoma. A monoclonal antibody was produced against this antigen and an immunoassay developed. Levels of hCG and H-hCG were determined in 142 urine samples from normal pregnancies from 10 to 21 weeks of gestation. Levels were normalized to urine creatinine concentration, and were each plotted against gestational age. Bi-weekly median values were calculated, the best-fitting regression lines were determined, and multiples of the normal median (MoM) were computed. 10 Down syndrome pregnancy samples were tested from 11 to 21 weeks of gestation. The median hCG and H-hCG levels in the Down syndrome cases were 1.9 MoM and 5.7 MoM of unaffected cases, respectively. Four of 10 hCG measurements and 9 of 10 H-hCG determinations exceeded the 95th centile of unaffected cases. H-hCG identified 90 per cent of Down syndrome cases with a 5 per cent false-positive rate. This is more than twice the number of cases detected by an hCG assay. H-hCG may be an effective replacement for hCG in antenatal Down syndrome screening. This is a preliminary report consisting of only 152 samples. Further studies are needed now to verify the Down syndrome screening utility of this potentially valuable new marker.
Cross‐Reactive Antibodies Prevent the Lethal Effects of<i>Staphylococcus aureus</i>Superantigens (1999)

The exotoxins produced by Staphylococcus aureus, staphylococcal enterotoxins (SE) A-E and toxic shock syndrome toxin (TSST)-1, which are associated with serious diseases, including food poisoning and toxic shock syndrome, are termed superantigens (SAgs). To examine whether common antigenic epitopes were present and whether vaccination with 1 bacterial SAg could protect against challenge with a different SE or TSST-1, mice were vaccinated with SEA, SEB, SEC1, or TSST-1 individually or in combination. Mice injected with a single toxin developed high antibody titers against other SAgs. Marked improvement in survival was observed when immunized mice were challenged with a heterologous toxin. Mice vaccinated with a mixture of toxins were fully protected against 1 or multiple toxin challenges, indicating no interference effects of multivalent vaccinations. More importantly, higher titers were found against each SAg with the multivalent vaccination than with injection with a single SAg. Thus, immunizations with 1 SAg can induce cross-protective antibodies to heterologous SAgs, and multicomponent vaccination can enhance antibody responses against each bacterial SAg.
Applications of Nanocrystalline Zeolites to CWA Decontamination (2009)

Nanocrystalline zeolites (crystal sizes of less than 100 nm) are porous aluminosilicate nanomaterials with increased surface areas relative to conventional micron-sized zeolites. Nanocrystalline zeolites are potentially useful for CWA decontamination applications because of their enhanced absorptive and catalytic properties. This chapter describes FTIR and solid state NMR studies of the thermal reactivity of two CWA simulants, 2-CEES (2 chloroethyl sulfide) and DMMP (dimethylmethylphosphonate) on nanocrystalline zeolites, such as NaZSM-5 (silicalite, purely siliceous form of ZSM-5) and NaY, with crystal sizes of approximately 25 nm.
Hypoxia-inducible Factor-1 Mediates Transcriptional Activation of the Heme Oxygenase-1 Gene in Response to Hypoxia (1997)

Exposure of rats to hypoxia (7% O2) markedly increased the level of heme oxygenase-1 (HO-1) mRNA in several tissues. Accumulation of HO-1 transcripts was also observed after exposure of rat aortic vascular smooth muscle (VSM) cells to 1% O2, and this induction was dependent on gene transcription. Activation of the mouse HO-1 gene by all agents thus far tested is mediated by two 5'-enhancer sequences, SX2 and AB1, but neither fragment was responsive to hypoxia in VSM cells. Hypoxia-dependent induction of the chloramphenicol acetyltransferase (CAT) reporter gene was mediated by a 163-bp fragment located approximately 9.5 kilobases upstream of the transcription start site. This fragment contains two potential binding sites for hypoxia-inducible factor 1 (HIF-1). A role for HIF-1 in HO-1 gene regulation was established by the following observations: 1) HIF-1 specifically bound to an oligonucleotide spanning these sequences, 2) mutation of these sequences abolished HIF-1 binding and hypoxia-dependent gene activation in VSM cells, 3) hypoxia increased HIF-1alpha and HIF-1beta protein levels in VSM cells, and 4) hypoxia-dependent HO-1 mRNA accumulation was not observed in mutant hepatoma cells lacking HIF-1 DNA-binding activity. Taken together, these data demonstrate that hypoxia induces HO-1 expression in animal tissues and cell cultures and implicate HIF-1 in this response.
<i>TERT</i>Promoter Mutations and Their Association with<i>BRAF</i>V600E Mutation and Aggressive Clinicopathological Characteristics of Thyroid Cancer (2014)

In this large cohort, we found TERT promoter mutations to be common, particularly in FTC and BRAF mutation-positive PTC, and associated with aggressive clinicopathological characteristics.
Optimization of Imperative Programs in a Relational Database (2017)

For decades, RDBMSs have supported declarative SQL as well as imperative functions and procedures as ways for users to express data processing tasks. While the evaluation of declarative SQL has received a lot of attention resulting in highly sophisticated techniques, the evaluation of imperative programs has remained naive and highly inefficient. Imperative programs offer several benefits over SQL and hence are often preferred and widely used. But unfortunately, their abysmal performance discourages, and even prohibits their use in many situations. We address this important problem that has hitherto received little attention. We present Froid, an extensible framework for optimizing imperative programs in relational databases. Froid's novel approach automatically transforms entire User Defined Functions (UDFs) into relational algebraic expressions, and embeds them into the calling SQL query. This form is now amenable to cost-based optimization and results in efficient, set-oriented, parallel plans as opposed to inefficient, iterative, serial execution of UDFs. Froid's approach additionally brings the benefits of many compiler optimizations to UDFs with no additional implementation effort. We describe the design of Froid and present our experimental evaluation that demonstrates performance improvements of up to multiple orders of magnitude on real workloads.