gebhart/patrepeval huggingface dataset:
Honeycomb (2004)

This paper describes a system for automated generation of attack signatures for network intrusion detection systems. Our system applies pattern-matching techniques and protocol conformance checks on multiple levels in the protocol hierarchy to network traffic captured a honeypot system. We present results of running the system on an unprotected cable modem connection for 24 hours. The system successfully created precise traffic signatures that otherwise would have required the skills and time of a security officer to inspect the traffic manually.
TDMA Protocol Requirements for Wireless Sensor Networks (2008)

TDMA is probably the best choice for an energy efficient multiple access protocol for wireless sensor networks. As such there exist many approaches of increased complexity, using different algorithms and combining information from other layers or multiple access techniques. There are many surveys detailing the protocols and their advantages and disadvantages, but we feel that they don't give a general image of TDMA techniques, which would be useful in choosing the protocol for a network deployment, or even for someone trying to develop a new MAC protocol. We analyze the different algorithms used in TDMA protocols and we present a list of characteristics that a robust TDMA protocol requires. We also give a brief survey of several protocols.
Using field size factors to characterize the in-air fluence of a proton machine with a range shifter (2017)

The excellent agreement between the model's prediction and measurements proved the efficiency and accuracy of the proposed method of using FSFs to characterize the proton fluence and configure the TPS for a PBS system with fixed RS.
On the computation of the bivariate normal integral (1990)

We propose a simple and efficient way to calculate bivariate normal probabilities. The algorithm is based on a formula for the partial derivative of the bivariate probability with respect to the correlation coefficient.
Phase measurement and adjustment of digital signals using random sampling technique (2006)

This paper introduces a technique to measure and adjust the relative phase of on-chip high speed digital signals using a random sampling technique of inferential statistics. The proposed technique as applied to timing uncertainty mitigation in the signaling of a digital system is presented as an example; the relative phase information is used to minimize the timing skew. The proposed circuit captures the state of the signals under measurement simultaneously at random instants of time and gathers a large sample data to estimate the relative phase between the signals. By carefully premeditating the sample size, the accuracy and confidence of the result can be set to a level as high as desired. Accurately sensed value of relative phase enables the correction circuit to reduce the maximum correction error, less than half the maximum delay resolution unit available for adjustment. A pure standard cell based circuit design approach is used that reduces the overall design time and circuit complexity. The test results of the proposed circuit manifest a very close correlation to the simulated and theoretically expected results. The random sampling unit (RSU) circuit proposed for phase measurement in this paper occupies 3350 (mum) <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2 </sup> area in 130nm technology, which is an order of magnitude smaller than what is required for its analog equivalent in the same technology
Synthesis of thiadiazolo-s-triazines for their antiviral activity based on QSAR studies (2003)

2-Amino-5-aralkyl-1,3,4-thiadiazole 1 on treatment with benzaldehyde yields 5-aralkyl-2-benzylideno-imino-1,3,4-thiadiazole 2 which on reaction with ammonium thiocyanate cyclises to give 2-phenyl-7-aralkyl-1,3,4-thiadiazolo-[3,2-a]-s-triazine-5-[6H,7H]-thione 3. Reaction of 3 with p-toluene sulphonyl chloride in anhydrous chloroform gives 2-phenyl-3-(p-toluenesulphonyl)-7-aralkyl-1,3,4-thiadiazolo-[3,2-a]-s-triazine-5-[6H,7H]-thiones 4g-1. Benzoyl chloride also reacts with 3 in anhydrous pyridine giving 2-phenyl-3-(benzoyl)-7-aralkyl-1,3,4-thiadiazolo-[3,2-a]-s-triazine-5-[6H,7H]-thiones 4a-f in quantitative yields. The antiviral activities of 4 based on QSAR studies have been reported using physicochemical method.
Radiation pattern control by subreflector shaping (2003)

Several design examples of shaped dual offset reflector antennas for shaped beam applications have been presented. In these designs, radiation control was obtained by simultaneously shaping both reflectors or shaping only the main reflector while the subreflector is an offset portion of a conventional conical surface (ellipsoid or hyperboloid). In both cases, crosspolarization is reduced by adjusting the relative position of the offset reflectors. We follow an alternative way by exploring the possibilities of using the dual offset configuration with a shaped subreflector and a parabolic main reflector, in order to obtain shaped beams or an increased efficiency of the focused beams. The shaping technique is briefly outlined and results confirming the performance improvement due to the subreflector shaping are shown. Significant results for elliptical beam coverage are also presented.
Cloning of a gene from Pseudomonas sp. strain PG2982 conferring increased glyphosate resistance (1990)

A plasmid carrying a 2.4-kilobase-pair fragment of DNA from Pseudomonas sp. strain PG2982 has been isolated which was able to increase the glyphosate resistance of Escherichia coli cells. The increase in resistance was dependent on the presence of a plasmid-encoded protein with a molecular weight of approximately 33,000, the product of a translational fusion between a gene on the vector, pACYC184, and the insert DNA. An overlapping region of the PG2982 chromosome carrying the entire gene (designated igrA) was cloned, and a plasmid (pPG18) carrying the gene was also able to increase glyphosate resistance in E. coli. A protein with a molecular weight of approximately 40,000 was encoded by the PG2982 DNA contained in pPG18. This plasmid was not able to complement a mutation in the gene for 5-enolpyruvylshikimate-3-phosphate synthase (aroA) in E. coli, and modification of glyphosate by E. coli cells containing the plasmid could not be demonstrated. The nucleotide sequence of the PG2982 DNA contained an open reading frame able to encode a protein with a calculated molecular weight of 39,396.
Synthesis, characterization, and electrogenerated chemiluminescence of phenyl-substituted, phenyl-annulated, and spirofluorenyl-bridged oligothiophenes (2001)

To overcome the insolubility of higher oligothiophenes and simultaneously to enhance their processability with respect to an application in molecularly doped organic light-emitting devices (OLEDs) we synthesized phenyl-substituted, phenyl-annulated, and spirofluorenyl-bridged oligothiophenes 1–5. Significantly improved solubilities in polar solvents of up to three orders of magnitude were found and their optical and electrochemical properties were investigated in solution. Reflecting small conformational changes and the almost complete electronic separation of the substituents, phenyl substitution and the introduction of a spiro core by bridging the central bithienyl unit only slightly affected optical and redox properties in comparison to the unmodified oligothiophenes (6–8). In contrast, the presence of an isothianaphthene (benzo[c]thiophene) unit in the oligomeric chain led to a distinct approximation of the frontier orbitals and consequently to a red-shift of both absorption and fluorescence. Finally, we demonstrated the applicability of some oligomers as dopants for OLEDs by electrogenerated chemiluminescence (ECL).
Wisconsin's County Forest Program (1932)

Abstract In Wisconsin, tax delinquent lands revert to the county instead of the state as is the case in Michigan. This complicates the problem of attaching a destiny to these lands. With the new county forests being established, the total will exceed 400,000 acres in 1932. How Wisconsin is trying to solve this problem by county surveys and state aid, and what has been accomplished to date, is told by the author.
Resolution of Toll‐like receptor 4‐mediated acute lung injury is linked to eicosanoids and suppressor of cytokine signaling 3 (2011)

The purpose of this study was to investigate roles for Toll-like receptor 4 (TLR4) in host responses to sterile tissue injury. Hydrochloric acid was instilled into the left mainstem bronchus of TLR4-defective (both C3H/HeJ and congenic C.C3-Tlr4(Lps-d)/J) and control mice to initiate mild, self-limited acute lung injury (ALI). Outcome measures included respiratory mechanics, barrier integrity, leukocyte accumulation, and levels of select soluble mediators. TLR4-defective mice were more resistant to ALI, with significantly decreased perturbations in lung elastance and resistance, resulting in faster resolution of these parameters [resolution interval (R(i)); ∼6 vs. 12 h]. Vascular permeability changes and oxidative stress were also decreased in injured HeJ mice. These TLR4-defective mice paradoxically displayed increased lung neutrophils [(HeJ) 24×10(3) vs. (control) 13×10(3) cells/bronchoalveolar lavage]. Proresolving mechanisms for TLR4-defective animals included decreased eicosanoid biosynthesis, including cysteinyl leukotrienes (80% mean decrease) that mediated CysLT1 receptor-dependent vascular permeability changes; and induction of lung suppressor of cytokine signaling 3 (SOCS3) expression that decreased TLR4-driven oxidative stress. Together, these findings indicate pivotal roles for TLR4 in promoting sterile ALI and suggest downstream provocative roles for cysteinyl leukotrienes and protective roles for SOCS3 in the intensity and duration of host responses to ALI.
A software system generator for data structures (1994)

Although data structures are a fundamental part of most applications, using and writing data structures is time-consuming, difficult, and error-prone. Programmers often select inappropriate data structures for their applications because they do not know which data structure to use, they do not know how to implement a particular data structure, or they do not have an existing implementation of the data structure to use.
This dissertation describes a model and a technology for overcoming these problems. Our approach is based on non-traditional parameterized types (NPTs). NPTs are an extension to traditional parameterized types (TPTs), which are already familiar to most programmers. Our NPTs are based on the GenVoca domain modeling concepts, vertical parameterization, a consistent high-level interface, and a transformational compiler.
Our research has led to the construction of a software system generator for data structures called Predator. Predator is able to transform data structure declarations and data structure-independent functions into efficient code. Predator also allows programmers to adjust a data structure's implementation by simply changing its declaration and recompiling.
This dissertation discusses our model (and how it differs from standard models), our Predator compiler, and the results of our validation efforts.
Design and evaluation of the gemtc framework for GPU-enabled many-task computing (2014)

We present the design and first performance and usability evaluation of GeMTC, a novel execution model and runtime system that enables accelerators to be programmed with many concurrent and independent tasks of potentially short or variable duration. With GeMTC, a broad class of such "many-task" applications can leverage the increasing number of accelerated and hybrid high-end computing systems. GeMTC overcomes the obstacles to using GPUs in a many-task manner by scheduling and launching independent tasks on hardware designed for SIMD-style vector processing. We demonstrate the use of a high-level MTC programming model (the Swift parallel dataflow language) to run tasks on many accelerators and thus provide a high-productivity programming model for the growing number of supercomputers that are accelerator-enabled. While still in an experimental stage, GeMTC can already support tasks of fine (subsecond) granularity and execute concurrent heterogeneous tasks on 86,000 independent GPU warps spanning 2.7M GPU threads on the Blue Waters supercomputer.
Polyketide synthase genes and the natural products potential of<i>Dictyostelium discoideum</i> (2007)

A total of 45 Type I iterative PKS genes were found, 5 of which are probably pseudogenes. Catalytic domains that are homologous with known PKS sequences as well as possible novel domains were identified. The genes often occurred in clusters of 2-5 genes, where members of the cluster had very similar sequences. The D.discoideum PKS genes formed a clade distinct from fungal and bacterial genes. All nine genes examined by RT-PCR were expressed, although at different developmental stages. The promoters of PKS genes were much more divergent than the structural genes, although we have identified motifs that are unique to some PKS gene promoters.
Monolithic Multi‐Color Tunable Inorganic Light‐Emitting Diodes (2021)

Abstract Inorganic light‐emitting diodes (LEDs) possess exceptional advantages for achieving wide wavelength emission ranges. However, certain material limitations should be overcome to alleviate the green gap between InGaN and AlInGaP‐based LEDs. In this study, monolithic red, green, and bluish‐green emissions are achieved by exploiting the blueshift phenomenon, caused by the band‐filling and piezoelectric screening effects. Different‐sized LEDs are designed to control the injection current density on the same wafer. The smaller the size of the LED, the shorter the emission wavelength, resulting in multi‐color emission (from red to bluish‐green). As a result, red, green, and white emissions are individually and simultaneously obtained using dichromatic LED systems, comprising three red and one green LED cell. In addition, a wide range of visible light colors are achieved by adjusting the size of the LEDs and the applies injection current.
Interference suppression via orthogonal projections: a performance analysis (1993)

Several recent studies indicate the promise of subspace separation principles when applied to adaptive jammer suppression in phased array antennas. This paper theoretically analyzes the performance of a subspace separation technique based on orthogonal projections (OP) for adaptively suppressing interference in phased arrays; the theoretical performance predictions are validated using computer simulations. This analysis holds for the case when it is possible to differentiate between the vector spaces spanned by jammers and additive noise. The performance parameters used are (a) the average residual interference (jammer plus noise) power at the output of the adapted array as a function of the number of jammer snapshots used for calculating the weight vector, and (b) the similarity of the adapted array pattern to the design pattern away from the jammer locations. The performance of the OP-based subspace separation technique is compared with the sample matrix inversion (SMI) algorithm. It is shown that the weight vector calculated using OP converges more quickly to the optimal solution (infinite number of interference snapshots) than the SMI weight vector. Further, in contrast to the SMI adapted pattern, which exhibits large sidelobe levels away from the jammer locations, the OP adapted pattern closely follows the design pattern both in the mainbeam and in the sidelobe region away from the jammer locations.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Identification and characterization of cDNA clones encoding two homologous proteins that are part of the asialoglycoprotein receptor. (1987)

The asialoglycoprotein receptor (ASGP-R) from rat liver contains the following three distinct protein species when it is analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis: RHL1 (42 kilodaltons), RHL2 (49 kilodaltons), and RHL3 (54 kilodaltons). In this paper we describe the isolation of cDNA clones encoding RHL1 and RHL2 from a cDNA library constructed from rat liver mRNA. A comparison of the predicted coding sequence for RHL2 with that for RHL1 showed that these sequences are highly homologous. The library also contained numerous cDNA clones for both RHL1 and RHL2 that were derived from unspliced precursor mRNAs. Differential splicing at the 5' end of the RHL1 transcript was inferred from the finding that two different types of RHL1 cDNA were identified, each having a different 5' terminus.
Combined anterior cruciate reconstruction and Oxford unicompartmental knee arthroplasty (2006)

The options for treatment of the young active patient with isolated symptomatic osteoarthritis of the medial compartment and pre-existing deficiency of the anterior cruciate ligament are limited. The potential longevity of the implant and levels of activity of the patient may preclude total knee replacement, and tibial osteotomy and unicompartmental knee arthroplasty are unreliable because of the ligamentous instability. Unicompartmental knee arthroplasties tend to fail because of wear or tibial loosening resulting from eccentric loading. Therefore, we combined reconstruction of the anterior cruciate ligament with unicompartmental arthroplasty of the knee in 15 patients (ACLR group), and matched them with 15 patients who had undergone Oxford unicompartmental knee arthroplasty with an intact anterior cruciate ligament (ACLI group). The clinical and radiological data at a minimum of 2.5 years were compared for both groups. The groups were well matched for age, gender and length of follow-up and had no significant differences in their pre-operative scores. At the last follow-up, the mean outcome scores for both the ACLR and ACLI groups were high (Oxford knee scores of 46 (37 to 48) and 43 (38 to 46), respectively, objective Knee Society scores of 99 (95 to 100) and 94 (82 to 100), and functional Knee Society scores of 96 and 96 (both 85 to 100). One patient in the ACLR group needed revision to a total knee replacement because of infection. No patient in either group had radiological evidence of component loosening. The radiological study showed no difference in the pattern of tibial loading between the groups. The short-term clinical results of combined anterior cruciate ligament reconstruction and unicompartmental knee arthroplasty are excellent. The previous shortcomings of unicompartmental knee arthroplasty in the presence of deficiency of the anterior cruciate ligament appear to have been addressed with the combined procedure. This operation seems to be a viable treatment option for young active patients with symptomatic arthritis of the medial compartment, in whom the anterior cruciate ligament has been ruptured.
Antitumor Activity of a Dual Cytokine/Single-chain Antibody Fusion Protein for Simultaneous Delivery of GM-CSF and IL-2 to Ep-CAM Expressing Tumor Cells (2006)

Cytokine targeting to tumor-associated antigens via antibody cytokine fusion proteins has demonstrated potent antitumor activity in numerous animal models and has led to the clinical development of 2 antibody-interleukin-2 (IL-2) fusion proteins. We previously reported on the construction and in vitro properties of a "dual" cytokine fusion protein for simultaneous targeted delivery of human granulocyte macrophage-colony stimulating factor (GM-CSF) and IL-2 to human tumors. The fusion protein is based on a heterodimerized core structure formed by human CH1 and Ckappa domains (heterominibody) with C-terminally fused human cytokines and N-terminally fused single-chain antibody fragments specific for the tumor-associated surface antigen epithelial cell adhesion molecule (Ep-CAM). For testing the antitumor activity in syngeneic mouse xenograft models, we developed "dual cytokine heterominibodies" with murine cytokines (mDCH). mDCH fusion proteins and, as controls, "single cytokine heterominibodies" (SCH) carrying either murine GM-CSF (mGM-CSF) or murine IL-2 (mIL-2) were constructed, of which all retained the specific activities of cytokines and binding to the Ep-CAM antigen on human Ep-CAM transfected mouse colon carcinoma CT26-KSA cells. Over a 5-day treatment course, DCH fusion proteins induced significant inhibition of established pulmonary CT26-KSA metastases in immune-competent Balb/c mice at low daily doses of 1 mug of fusion protein per mouse. However, with the tested dosing schemes, antitumor activity of mDCH was largely independent of cytokine targeting to tumors as demonstrated by a control protein with mutated Ep-CAM binding sites. Single cytokine fusion proteins mSCH-GM-CSF and mSCH-IL-2 showed similar antitumor activity as the dual cytokine fusion protein mDCH, indicating that GM-CSF and IL-2 in one molecule did not significantly synergize in tumor rejection under our experimental conditions. Our results seem to contradict the notion that IL-2 and GM-CSF can synergize in antitumor activity and that with conventional dose regimens, their specific targeting to tumors, as tested here with 2 antibodies of different affinities, enhances their antitumor activity.
Spatially resolved endpoint detector for plasma etcher (2002)

In this paper we present a novel spatially resolved sensor to detect the endpoint and monitor spatial uniformity for a plasma etching process. A scanning spatially-resolved optical emission spectroscopy (SROES) system was built and installed in Berkeley's Microfabrication Laboratory. This sensor system consists of a stepper motor, controller, and a monochrometer, which provides an in-situ real-time monitoring of the etching endpoint spatially. In this paper, we show the promise of this spatially-resolved endpoint detector, and explain our hardware design and the future experiment plan.
A synthetic peptide administered with IL-12 elicits immunity to Listeria monocytogenes (1997)

IL-12 is a pivotal cytokine signal for the development of Th1-type cellular responses that are required for control of intracellular pathogens. We previously demonstrated that coinjection of IL-12 with heat-killed Listeria monocytogenes, which was not immunogenic when injected alone, elicited intense Ag-specific T cell responses that conferred protection against subsequent challenge with Listeria. Herein we describe the remarkable finding that a nonimmunogenic synthetic peptide corresponding to a dominant MHC class II (H-2k)-restricted listerial determinant, when coinjected i.p. with murine IL-12, elicited potent Ag-specific immune responses that conferred protective immunity against Listeria.
Basis of neurovirulence in Sindbis virus encephalomyelitis of mice. (1988)

Neuroadapted Sindbis virus (NSV) was selected by serial passage of wild-type Sindbis virus (SV) in mouse brain. After intracerebral inoculation of weanling mice, NSV causes a severe encephalomyelitis with hindlimb paralysis and high mortality; SV causes nonfatal mild disease. In order to determine the biologic basis of neurovirulence in vivo, these viral infections have been compared by using infectivity assays, light and electron microscopy, in situ hybridization, immunohistochemistry, and double-labeling for neural cell markers and viral RNA. More infectious virus is present in the central nervous system during NSV than during SV infection. After intracerebral inoculation, both viruses enter the central nervous system via the ependyma and spread to gray matter areas, including the ventral horns of the spinal cord. Their cellular targets are not different, and neuronal infection is prominent. NSV infects more neurons, and causes more severe injury than SV. In NSV infection, there is marked swelling of lumbar and thoracic neurons and their processes in the ventral horns. Relatively mild changes are detected in SV infection only by electron microscopy. Neuroadaptation likely occurs by increasing the efficiency of viral replication in neurons, rather than by a fundamental change in the cellular tropism or the topography of the infection in the central nervous system.