gebhart/patrepeval huggingface dataset:
Nazca: Detecting Malware Distribution in Large-Scale Networks (2014)

Malware remains one of the most significant security threats on the Internet.Antivirus solutions and blacklists, the main weapons of defense against these attacks, have only been (partially) successful.One reason is that cyber-criminals take active steps to bypass defenses, for example, by distributing constantly changing (obfuscated) variants of their malware programs, and by quickly churning through domains and IP addresses that are used for distributing exploit code and botnet commands.We analyze one of the core tasks that malware authors have to achieve to be successful: They must distribute and install malware programs onto as many victim machines as possible.A main vector to accomplish this is through drive-by download attacks where victims are lured onto web pages that launch exploits against the users' web browsers and their components.Once an exploit is successful, the injected shellcode automatically downloads and launches the malware program.While a significant amount of previous work has focused on detecting the drive-by exploit step and the subsequent network traffic produced by malware programs, little attention has been paid to the intermediate step where the malware binary is downloaded.In this paper, we study how clients in real-world networks download and install malware, and present Nazca, a system that detects infections in large scale networks.Nazca does not operate on individual connections, nor looks at properties of the downloaded programs or the reputation of the servers hosting them.Instead, it looks at the telltale signs of the malicious network infrastructures that orchestrate these malware installation that become apparent when looking at the collective traffic produced and becomes apparent when looking at the collective traffic produced by many users in a large network.Being content agnostic, Nazca does not suffer from coverage gaps in reputation databases (blacklists), and is not susceptible to code obfuscation.We have run Nazca on seven days of traffic from a large Internet Service Provider, where it has detected previously-unseen malware with very low false positive rates.
Host Plant Resistance Genes for Fusarium Head Blight: Mapping and Manipulation with Molecular Markers (2001)

Fusarium head blight (FHB), caused by Fusarium graminearum Schwabe [teleomorph Gibberella zeae (Schwein.)], or scab, causes severe reductions in yield and quality of wheat ( Triticum aestivum L.) and barley ( Hordeum vulgare L.). Evaluation of FHB resistance is laborious and subject to environmental influence; therefore, molecular markers for FHB resistance genes will greatly enhance selection for FHB resistance. This review seeks to summarize information on molecular markers associated with quantitative trait loci (QTL) for resistance to FHB in wheat and barley and the use of those markers for marker assisted selection. Our goal is to summarize the current state of knowledge on the genetics of FHB resistance, the map locations of QTL for FHB resistance, and the future directions and potential applications of this research. In wheat, five types of resistance have been described, and Type II resistance (expressed in Chinese wheat cultivar Sumai 3) is the easiest type to assess. Several research groups are developing molecular markers associated with genes for FHB resistance from Sumai 3, a widely used source of Type II resistance in wheat breeding programs worldwide. In four different populations, each having Sumai 3 or a derivative as one parent, one to four QTL have been identified that explain up to 63% of the variation in resistance. QTL were identified on chromosomes 3BS and 6BL in three or more populations. Recently, in barley, restriction fragment length polymorphism (RFLP) markers associated with genes for FHB resistance, deoxynivalenol (DON) accumulation, and kernel discoloration were identified on all seven chromosomes. Three regions, located on chromosomes 2, 3, and 5 were identified in several mapping populations. Comparing the QTL locations between wheat and barley shows that the barley chromosome 3 QTL is located in a syntenous region in wheat. The following areas of research on molecular markers associated with FHB resistance should be emphasized: (i) identifying and mapping better resistance sources in wheat and barley; (ii) validating QTL in additional populations; and (iii) developing markers that can be easily used in breeding programs and across populations.
A Role for the Granzyme B Inhibitor Serine Protease Inhibitor 6 in CD8+ Memory Cell Homeostasis (2004)

Generation and maintenance of protective immunological memory is the goal of vaccination programs. It has recently become clear that CD8+ memory T cells are derived directly from CTLs. The mechanisms underlying this transformation and the subsequent survival of memory cells are not completely understood. However, some effector molecules required by CTLs to eliminate infected cells have also been shown to control the number of Ag-specific cells. We report that memory cells express high levels of serine protease inhibitor (Spi) 6, an inhibitor of the effector molecule granzyme B, and that Spi6 can protect T cells from granzyme B-mediated apoptosis. In mouse models, both elevated expression of Spi6 and the complete absence of granzyme B in CD8+ T cells led to an increase in memory cells after infection with lymphocytic choriomeningitis virus. This was not the result of increased levels of antilymphocytic choriomeningitis virus CD8+ T cells during the expansion or contraction phases, but rather transgenic Spi6 directly influenced the survival of CD8+ memory T cells. We propose that expression of protective molecules, like Spi6, serves to shield metabolically active CD8+ memory T cells from their own effector molecules.
Multiplexed cell analysis on CellCards for drug discovery (2004)

The desire to obtain more biologically relevant data is expanding the use of cell-based assays in drug discovery. These assays are performed and analyzed in ever more sophisticated ways (e.g. high content screening) that allow the collection of multiparametric information about cells affected by the screened compounds. The driver for these developments is the desire to increase data quality and density and reduce the use of valuable reagents and time. Here we describe an approach that adds a new dimension to the data quality/quantity mix by simultaneously analyzing several cell types in the same microplate well. The system is based on the use of encoded carriers (CellCards) that permit the reading and analysis of cellular responses, and at the same time allow decoding and the attribution of these responses to the appropriate cell line. CellCards are rectangular particles with an expandable color barcode and a transparent section upon which cells can be grown and imaged for cellular readout. Before performing the assay, each cell line is grown on a different class of CellCards. CellCards, with attached cells, are mixed and dispensed into a microtiter plate where the assay is performed. Next the plates are imaged, decoded and the cells associated with each CellCard class are analyzed. Multiplexing cell lines allows assay controls and data normalization within each well, reducing well-to-well variability. It also allows the simultaneous interrogation of multiple targets and thus concurrent potency and selectivity screening. This may significantly reduce the time required to take a compound from primary screening into the clinic.
A disposable and multifunctional capsule for easy operation of microfluidic elastomer systems (2011)

The global lab-on-chip and microfluidic markets for cell-based assays have been predicted to grow considerably, as novel microfluidic systems enable cell biologists to perform in vitro experiments at an unprecedented level of experimental control. Nevertheless, microfluidic assays must, in order to compete with conventional assays, be made available at easily affordable costs, and in addition be made simple to operate for users having no previous experience with microfluidics. We have to this end developed a multifunctional microfluidic capsule that can be mass-produced at low cost in thermoplastic material. The capsule enables straightforward operation of elastomer inserts of optional design, here exemplified with insert designs for molecular gradient formation in microfluidic cell culture systems. The integrated macro–micro interface of the capsule ensures reliable connection of the elastomer fluidic structures to an external perfusion system. A separate compartment in the capsule filled with superabsorbent material is used for internal waste absorption. The capsule assembly process is made easy by integrated snap-fits, and samples within the closed capsule can be analyzed using both inverted and upright microscopes. Taken together, the capsule concept presented here could help accelerate the use of microfluidic-based biological assays in the life science sector.
Acceleration of the single electron transfer–degenerative chain transfer mediated living radical polymerization (SET–DTLRP) of vinyl chloride in water at 25 °C (2004)

Abstract The accelerated single electron transfer–degenerative chain transfer mediated living radical polymerization (SET–DTLRP) of vinyl chloride (VC) in H 2 O/tetrahydrofuran (THF) at 25 °C is reported. This process is catalyzed by sodium dithionite (Na 2 S 2 O 4 )‐sodium bicarbonate (NaHCO 3 ). Electron transfer cocatalysts (ETC) 1,1′‐dialkyl‐4,4′‐bipyridinum dihalides or alkyl viologens were also employed in this polymerization. The resulting poly(vinyl chloride) (PVC) has a number‐average molecular weight ( M n ) = 2,000–12,000, no detectable amounts of structural defects, and both active chloroiodomethyl and inactive chloromethyl chain ends. The molecular weight distribution of PVC obtained is M w / M n = 1.5. The surface active agents afford the final polymers as a powder and provide an acceleration of the rate of polymerization. The role of ETC is to accelerate the single electron transfer (SET) step, whereas THF enhances the degenerative chain transfer (DT) step. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 6364–6374, 2004
A Balloon-borne Measurement of High Latitude Atmospheric Neutrons Using a LiCAF Neutron Detector (2013)

PoGOLino is a scintillator-based neutron detector. Its main purpose is to provide data on the neutron flux in the upper stratosphere at high latitudes at thermal and nonthermal energies for the PoGOLite instrument. PoGOLite is a balloon borne hard X-ray polarimeter for which the main source of background stems from high energy neutrons. No measurements of the neutron environment for the planned flight latitude and altitude exist. Furthermore this neutron environment changes with altitude, latitude and solar activity, three variables that will vary throughout the PoGOLite flight. PoGOLino was developed to study the neutron environment and the influences from these three variables upon it. PoGOLino consists of two Europium doped Lithium Calcium Aluminium Fluoride (Eu:LiCAF) scintillators, each of which is sandwiched between 2 Bismuth Germanium Oxide (BGO) scintillating crystals, which serve to veto signals produced by gamma-rays and charged particles. This allows the neutron flux to be measured even in high radiation environments. Measurements of neutrons in two separate energy bands are achieved by placing one LiCAF detector inside a moderating polyethylene shield while the second detector remains unshielded. The PoGOLino instrument was launched on March 20th 2013 from the Esrange Space Center in Northern Sweden to an altitude of 30.9 km. A description of the detector design and read-out system is presented. A detailed set of simulations of the atmospheric neutron environment performed using both PLANETOCOSMICS and Geant4 will also be described. The comparison of the neutron flux measured during flight to predictions based on these simulations will be presented and the consequences for the PoGOLite background will be discussed.
Large moments in bcc FexCoyMnz ternary alloy thin films (2018)

The elemental magnetic moments and the average atomic moment of 10–20 nm thick single crystal bcc (bct) FexCoyMnz films deposited on MgO(001) have been determined as a function of a broad range of compositions. Thin film epitaxy stabilized the bcc structure for 80% of the available ternary compositional space compared to only a 23% stability region for the bulk. The films that display ferromagnetism represent 60% of the available compositional possibilities compared to 25% for the bulk. A maximum average atomic moment of 3.25 ± 0.3 μB/atom was observed for a bcc Fe9Co62Mn29 film (well above the limit of the Slater-Pauling binary alloy curve of 2.45 μB/atom). The FexCoyMnz ternary alloys that exhibit high moments can only be synthesized as ultrathin films since the bcc structure is not stable in the bulk for those compositions.
Portable advanced off-axis camera for quantitative phase microscopy (2014)

We propose and experimentally demonstrate a device in which common-path interferometry combined with off-axis holographic geometry is used to realize a digital holographic camera which can be attached to the camera port of a conventional transmission microscope for complex wavefront analysis. A thick transmission volume grating recorded holographically into thick photosensitive glass splits the beam containing the sample information in two beams. The untouched transmitted beam creates the sample arm of the interferometer. The Bragg diffracted order of the grating is spectrally and spatially filtered by diffraction to generate a clean reference beam. Double passing the diffracted order through the grating using a retroreflector device provides filtering in two dimensions. The spatial filtering done by the grating which works based on high angular selectivity of thick volume gratings, reduces the alignment spatial sensitivity which is an advantage over the conventional spatial filtering done by pinholes. Besides, using a second thick grating, we introduce a desired coherence plane tilt in the reference beam which is sufficient to create high-visibility interference over the entire field of view. The full-field off-axis interferograms are created from which the amplitude and phase can be reconstructed. The advantage of the proposed camera is the insensitivity to the alignment, thus can be the basis for a standalone camera mountable on a standard optical microscope.
Shrink (2017)

Streaming query deployments make up a vital part of cloud oriented applications. They vary widely in their data, logic, and statefulness, and are typically executed in multi-tenant distributed environments with varying uptime SLAs. In order to achieve these SLAs, one of a number of proposed resiliency strategies is employed to protect against failure. This paper has introduced the first, comprehensive, cloud friendly comparison between different resiliency techniques for streaming queries. In this paper, we introduce models which capture the costs associated with different resiliency strategies, and through a series of experiments which implement and validate these models, show that (1) there is no single resiliency strategy which efficiently handles most streaming scenarios; (2) the optimization space is too complex for a person to employ a "rules of thumb" approach; and (3) there exists a clear generalization of periodic checkpointing that is worth considering in many cases. Finally, the models presented in this paper can be adapted to fit a wide variety of resiliency strategies, and likely have important consequences for cloud services beyond those that are obviously streaming.
Characterization of a Family of Arabidopsis Genes Related to Xyloglucan Fucosyltransferase1 (2001)

To understand primary cell wall assembly in Arabidopsis, we have focused on identifying and characterizing enzymes involved in xyloglucan biosynthesis. Nine genes (AtFUT2-10) were identified that share between 47% and 62% amino acid similarity with the xyloglucan-specific fucosyltransferase AtFUT1. Reverse transcriptase-PCR analysis indicates that all these genes are expressed. Bioinformatic analysis predicts that these family members are fucosyltransferases, and we first hypothesized that some may also be involved in xyloglucan biosynthesis. AtFUT3, AtFUT4, and AtFUT5 were expressed in tobacco (Nicotiana tabacum L. cv BY2) suspension culture cells, and the resulting proteins did not transfer fucose (Fuc) from GDP-Fuc to tamarind xyloglucan. AtFUT3, AtFUT4, and AtFUT5 were overexpressed in Arabidopsis plants. Leaves of plants overexpressing AtFUT4 or AtFUT5 contained more Fuc than wild-type plants. Stems of plants overexpressing AtFUT4 or AtFUT5 contained more xylose, less arabinose, and less galactose than wild-type plants. We suggest that the AtFUT family is likely to include fucosyltransferases important for the synthesis of wall carbohydrates. A targeted analysis of isolated cell wall matrix components from plants altered in expression of these proteins will help determine their specificity and biological function.
Signal Processing Architectures for Low-Noise High-Resolution CMOS Image Sensors (2007)

In this paper, signal processing architectures for low-noise high-resolution CMOS image sensors are reviewed and discussed. For low-noise signal readout, a column amplifier plays an important role for reducing both the noises due to a wideband output buffer and a pixel source follower. With high amplifier gain, a double-stage noise canceling technique and an advanced signal processing using oversampling techniques effectively reduce the noise due to the pixel source follower. Architectures and topologies for on-chip A/D conversion including pixel parallel, column parallel and serial schemes are also discussed. On-chip column parallel analog-to-digital (A/D) conversion is particularly important for low-noise and high-speed signal readout.
Relative Ability of Orally Administered<i>Lactobacillus murinus</i>To Predominate and Persist in the Porcine Gastrointestinal Tract (2004)

Five porcine-derived Lactobacillus or Pediococcus isolates administered to pigs (n = 4), either singly or as a combination at approximately 10(10) CFU per day varied with respect to intestinal survival and persistence. Two Lactobacillus murinus strains survived best and were excreted at approximately 10(7) to 10(8) CFU/g of feces. In contrast, Pediococcus pentosaceus DPC6006 had the lowest fecal count at approximately 10(5) CFU/g and was excreted at a significantly lower level than both L. murinus strains. Fecal L. murinus DPC6003 counts were also significantly higher than both Lactobacillus salivarius DPC6005 and Lactobacillus pentosus DPC6004 ( approximately 10(6) CFU/g). The L. murinus strains persisted for at least 9 days postadministration in both the feces and the cecum. Animals fed a combination of all five strains excreted approximately 10(7) CFU of the administered strains/g, with L. murinus predominating, as determined by randomly amplified polymorphic DNA PCR. Postadministration, variation was observed between animals fed the strain combination, but in general, L. murinus DPC6002 and DPC6003 and L. pentosus DPC6004 predominated in the feces and the cecum while P. pentosaceus DPC6006 was detected only in the cecum. Fifteen days after the start of culture administration, mean fecal Enterobacteriaceae counts were significantly lower in some of the treatment groups. In addition, when mean preadministration counts were compared with those obtained after 21 days of culture administration, Enterobacteriaceae counts were reduced by approximately 87 to 98% in pigs fed L. salivarius DPC6005, P. pentosaceus DPC6006, L. pentosus DPC6004, and the culture mix. In conclusion, the porcine intestinal isolates have potential as probiotic feed additives for pigs, with differences in strain performance highlighting the advantages of using culture combinations.
Fluorous Metal−Organic Frameworks for High-Density Gas Adsorption (2007)

A fluorous metal−organic framework, FMOF-1, is obtained by reaction of Ag(I) with 3,5-bis(trifluoromethyl)-1,2,4-triazolate, giving rise to a neutral, hydrogen-free, extended 3D nanotubular porous framework consisting of tetranuclear clusters [Ag4Tz6] connected by three-coordinate Ag(I) centers. The fluoro-lined channels and cavities of the framework show hysteretic adsorption of H2 with a volumetric capacity of 41 kg/m3 at 77 K and 64 bar. The framework also exhibits very high adsorptions for O2 and N2 with volumetric uptake of ∼550 and 400 kg/m3 at 77 K even at very low pressures (<10-2 bar).
Specific Vesicular Acetylcholine Transporter Promoters Lie within the First Intron of the Rat Choline Acetyltransferase Gene (1995)

The sequence encoding the vesicular acetylcholine transporter (VAChT) has recently been localized within the first intron of the choline acetyltransferase (ChAT) gene in various species. In rat, we previously identified a class of VAChT mRNAs that may originate from the same promoter region as two ChAT mRNAs. Here, we demonstrate by a detailed analysis of the 5'-noncoding region of the VAChT gene, that two specific VAChT promoters lie within the first intron of the ChAT gene. Two VAChT mRNAs are generated from these promoters. These results demonstrate that the promoter regions of these two genes are intermingled, which highlight the unique organization of the ChAT/VAChT gene locus.
<title>Pixel bit-depth increase by bit replication</title> (1998)

In many applications, such as inverse dithering, it is necessary to increase the pixel bit-depth of images by expanding q-bit integer values to m-bit integer values (m greater than q). This paper describes a simple and efficient method that uses bit replication, instead of conventional multiplication, to achieve this expansion. First, we show that the optimal number of repetitions is given by ceiling (m/q) and that the method is equivalent to multiplication by the ideal gain when m/q is an integer. We then demonstrate that, in the case where m/q is not an integer, truncating the fraction bits to the right of the decimal point will lead to zero average error. The paper also includes two suggestions for implementing the bit-replication process, both of which have a vast complexity advantage over a multiplier. Two examples are given at the end to illustrate the bit- replication process in action.
The LAP1 MYB transcription factor orchestrates anthocyanidin biosynthesis and glycosylation in <i>Medicago</i> (2009)

MYB transcription factors help to control anthocyanin biosynthesis in plants, and ectopic expression of the Arabidopsis Production of Anthocyanin Pigment 1 (PAP1) transcription factor activates the anthocyanin pathway in tobacco, suggesting the general utility of such factors for metabolic engineering of anthocyanins and anthocyanin-derived compounds such as proanthocyanidins (condensed tannins). However, PAP1 does not activate anthocyanin biosynthesis in the model legume Medicago truncatula or in alfalfa (Medicago sativa). A related Legume Anthocyanin Production 1 (LAP1) gene was identified from the genome of M. truncatula. When constitutively expressed in transgenic alfalfa, M. truncatula or white clover, LAP1 induced massive accumulation of anthocyanin pigments comprising multiple glycosidic conjugates of cyanidin. Oligomeric/polymeric compounds with some diagnostic characteristics of proanthocyanidins also accumulated in LAP1-expressing plants, but these compounds were not composed of (epi)catechin units. Over 260 and 70 genes were up-regulated in leaves of alfalfa or M. truncatula, respectively, in response to constitutive expression of LAP1, many of which are involved in anthocyanin biosynthesis. In particular, the glucosyltransferase UGT78G1, previously identified as showing preference for isoflavonoid substrates in vitro, was strongly up-regulated by LAP1, and appears to function as an anthocyanin glycosyltransferase in vivo. Over-expression of UGT78G1 in transgenic alfalfa resulted in increased anthocyanin accumulation when plants were exposed to abiotic stress.