gebhart/patrepeval huggingface dataset:
Controlled-Channel Attacks: Deterministic Side Channels for Untrusted Operating Systems (2015)

The presence of large numbers of security vulnerabilities in popular feature-rich commodity operating systems has inspired a long line of work on excluding these operating systems from the trusted computing base of applications, while retaining many of their benefits. Legacy applications continue to run on the untrusted operating system, while a small hyper visor or trusted hardware prevents the operating system from accessing the applications' memory. In this paper, we introduce controlled-channel attacks, a new type of side-channel attack that allows an untrusted operating system to extract large amounts of sensitive information from protected applications on systems like Overshadow, Ink Tag or Haven. We implement the attacks on Haven and Ink Tag and demonstrate their power by extracting complete text documents and outlines of JPEG images from widely deployed application libraries. Given these attacks, it is unclear if Over shadow's vision of protecting unmodified legacy applications from legacy operating systems running on off-the-shelf hardware is still tenable.
Breath-by-breath detection of apneic events for OSA severity estimation using non-contact audio recordings (2015)

Obstructive sleep apnea (OSA) is a prevalent sleep disorder, characterized by recurrent episodes of upper airway obstructions during sleep. We hypothesize that breath-by-breath audio analysis of the respiratory cycle (i.e., inspiration and expiration phases) during sleep can reliably estimate the apnea hypopnea index (AHI), a measure of OSA severity. The AHI is calculated as the average number of apnea (A)/hypopnea (H) events per hour of sleep. Audio signals recordings of 186 adults referred to OSA diagnosis were acquired in-laboratory and at-home conditions during polysomnography and WatchPat study, respectively. A/H events were automatically segmented and classified using a binary random forest classifier. Total accuracy rate of 86.3% and an agreement of κ=42.98% were achieved in A/H event detection. Correlation of r=0.87 (r=0.74), diagnostic agreement of 76% (81.7%), and average absolute difference AHI error of 7.4 (7.8) (events/hour) were achieved in in-laboratory (at-home) conditions, respectively. Here we provide evidence that A/H events can be reliably detected at their exact time locations during sleep using non-contact audio approach. This study highlights the potential of this approach to reliably evaluate AHI in at home conditions.
Rapid characterization of the normal and disturbed vaginal microbiota by application of 16S rRNA gene terminal RFLP fingerprinting (2007)

Bacterial vaginosis (BV) is a prevalent infection in women of reproductive age associated with numerous sequelae, including preterm delivery, amniotic fluid infections and an increased risk of acquiring sexually transmitted diseases. The vaginal microbiota in BV patients is characterized by a shift from lactobacilli to a diverse spectrum of mostly anaerobic bacteria. In this study, terminal restriction fragment length polymorphism (T-RFLP) was used to characterize the vaginal bacterial communities from 50 women with BV and 20 healthy subjects. In the BV samples, 23 species or phylotypes from 17 genera could be identified, including Atopobium vaginae, Megasphaera sp., Lactobacillus iners, Gardnerella vaginalis and three recently described phylotypes from the order Clostridiales. The number of detected species or phylotypes was on average 6.3 per sample (range 2-14). In contrast, in normal samples, only Lactobacillus species could be identified. In conclusion, T-RFLP provides a rapid and reliable technique to investigate the diversity of the predominant vaginal microbiota and allows differentiation of the flora of BV and healthy women. As such, T-RFLP may be helpful both in the diagnosis of BV from vaginal fluids and in a better understanding of the bacterial succession involved in the aetiology of BV.
A Common Inhibitory Receptor for Major Histocompatibility Complex Class I Molecules on Human Lymphoid and Myelomonocytic Cells (1997)

Natural killer (NK) cell-mediated lysis is negatively regulated by killer cell inhibitory receptors specific for major histocompatibility complex (MHC) class I molecules. In this study, we characterize a novel inhibitory MHC class I receptor of the immunoglobulin-superfamily, expressed not only by subsets of NK and T cells, but also by B cells, monocytes, macrophages, and dendritic cells. This receptor, called Ig-like transcript (ILT)2, binds MHC class I molecules and delivers a negative signal that inhibits killing by NK and T cells, as well as Ca2+ mobilization in B cells and myelomonocytic cells triggered through the B cell antigen receptor and human histocompatibility leukocyte antigens (HLA)-DR, respectively. In addition, myelomonocytic cells express receptors homologous to ILT2, which are characterized by extensive polymorphism and might recognize distinct HLA class I molecules. These results suggest that diverse leukocyte lineages have adopted recognition of self-MHC class I molecules as a common strategy to control cellular activation during an immune response.
Polymer microdisk and microring lasers (1995)

Dye-doped polymer microlasers have been fabricated by photolithography and self-assembly. Microdisk lasers 5 to 30 microm in diameter were photolithographically patterned on thin planar polymer waveguides. We formed polymer microring lasers on thinned silica fibers by dipping the fibers in polymers and allowing the polymer droplets to cure.
An anti-HIV microbicide comes alive (2005)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Chirped switchable reflection grating in holographic polymer-dispersed liquid crystal for spectral flattening in free-space optical communication systems (2004)

We report the design and fabrication of a chirped switchable reflective grating (CSRG) recorded in a holographic polymer-dispersed liquid-crystal material. This CSRG is a spatial wavelength-selective flattener in a free-space dynamic gain equalizer for use in wavelength-division multiplexing (WDM) networks. Prelimenary experimental results show that this device permits the management of the spectral power of a WDM stream with an attenuation range of 6 dB. The polarization-dependent loss introduced by the CSRG is shown to be less than 0.1 dB.
Peptide-based, but not whole protein, vaccines elicit immunity to HER-2/neu, oncogenic self-protein (1996)

HER-2/neu, an overexpressed oncogenic protein, has been proposed as a human cancer vaccine target. HER-2/neu is a "self" protein, however, and methods of vaccine strategies that would be effective in immunizing patients to a "self" tumor Ag have not been established. Many of the tumor Ags defined in humans are nonmutated self proteins, e.g., MAGE, and overcoming tolerance may be key in the generation of effective anti-tumor immunity. One theory states that tolerance to self proteins is directed only to dominant epitopes of proteins and not to every portion of the protein. Accordingly, tolerance can be circumvented by immunization to peptide fragments, but not whole protein. The studies outlined here demonstrate rat neu-specific immunity could be elicited in rats by vaccination with immunogenic rat neu peptides, but not by immunization with the intact protein. A rat model was used since rat neu protein is 89% homologous to human HER-2/neu protein and has a similar tissue distribution and level of expression. Rats were immunized with groups of peptides derived from the amino acid sequence of the intracellular domain or extracellular domain of rat neu protein and both groups developed CD4+ T cell immunity and Ab immunity to rat neu peptides and protein. Animals immunized in a similar fashion with intact purified rat neu protein did not develop Ab or T cell immunity to rat neu. Furthermore, rats that developed neu-specific immunity showed no histopathologic evidence of autoimmunity directed against organs expressing basal levels of rat neu protein. These studies suggest an immunization strategy that might be effective in human cancer vaccines targeting self tumor Ag.
Fast and Scalable Pattern Matching for Network Intrusion Detection Systems (2006)

High-speed packet content inspection and filtering devices rely on a fast multipattern matching algorithm which is used to detect predefined keywords or signatures in the packets. Multipattern matching is known to require intensive memory accesses and is often a performance bottleneck. Hence, specialized hardware-accelerated algorithms are required for line-speed packet processing. We present hardware-implementable pattern matching algorithm for content filtering applications, which is scalable in terms of speed, the number of patterns and the pattern length. Our algorithm is based on a memory efficient multihashing data structure called Bloom filter. We use embedded on-chip memory blocks in field programmable gate array/very large scale integration chips to construct Bloom filters which can suppress a large fraction of memory accesses and speed up string matching. Based on this concept, we first present a simple algorithm which can scan for several thousand short (up to 16 bytes) patterns at multigigabit per second speeds with a moderately small amount of embedded memory and a few mega bytes of external memory. Furthermore, we modify this algorithm to be able to handle arbitrarily large strings at the cost of a little more on-chip memory. We demonstrate the merit of our algorithm through theoretical analysis and simulations performed on Snort's string set
Uncommon Mutation, but Common Amplifications, of thePIK3CAGene in Thyroid Tumors (2005)

These data suggest that mutation of the PIK3CA gene is not common, but its amplification is relatively common and may be a novel mechanism in activating the PI3K/Akt pathway in some thyroid tumors.
EGF receptor variant III as a target antigen for tumor immunotherapy (2008)

The EGF receptor (EGFR) is the first tyrosine kinase receptor ever cloned and remains at the forefront of targeted therapies against cancer. Currently, there are four US FDA-approved drugs and several more in Phase III studies that target the EGFR. These drugs, while resulting in some dramatic remissions, have not resulted in strong nor consistent improvements in survival. EGFR variant III (EGFRvIII) is the most common variant of the EGFR and is present in many different cancer types but not in normal tissue. It results from the fusion of exon 1 to exon 8 of the EGFR gene, which results in a novel glycine at the junction. This mutant receptor is constitutively active in these tumors and can lead directly to cancer phenotypes due to its oncogenic properties. EGFRvIII is an attractive target antigen for cancer immunotherapy because it is not expressed in normal tissue and because cells producing EGFRvIII have an enhanced capacity for dysregulated growth, survival, invasion and angiogenesis. In this review, we will discuss preclinical and clinical data from studies using EGFRvIII as the target antigen for immunotherapy, with a focus on the potential for greatly improved survival for patients diagnosed with glioblastoma multiforme.
Rat preprocarboxypeptidase A: cDNA sequence and preliminary characterization of the gene. (1982)

Rat carboxypeptidase A cDNA clones have been isolated from a cDNA library prepared from pancreatic mRNA. An almost complete mRNA sequence has been deduced that predicts a polypeptide having 78% amino acid sequence homology with bovine carboxypeptidase A. The amino acid sequence of the activation and signal peptides of the carboxypeptidase A precursor were inferred from the nucleotide sequence. The cDNA was used as a probe to identify DNA fragments containing carboxypeptidase A sequences in a bacteriophage lambda library of rat genomic DNA. Heteroduplexes revealed that the DNA coding sequence occupies 5.5 kilobases and is interrupted by nine intervening sequences. The nucleotide sequence of the 5' end of the gene and the adjacent flanking region provides information on the site of initiation of transcription and the putative control regions. There is no evident relationship between the localization of intervening sequences in the gene and functional/structural domains of the protein.
Interleukin-6 and the acute phase response (1990)

ACTH Acutephas specific receptors on different target cells leading to a Corsol proteins systemic reaction characterized by fever, leukocytosis, increase in erythrocyte sedimentation rate, increases in Leucocytosis secretion of ACTH and glucocorticoids, activation of Complement activat
Design and analysis of a magnetically actuated and compliant capsule endoscopic robot (2011)

In this paper, we propose a compliant and tetherless magnetic capsule endoscopic robot. The proposed capsule robot has two key features. First, it has one extra degree of freedom axial contraction capability to perform additional tasks such as a drug releasing, a drug injection, or a biopsy. Also, design features of the magnetically deformed capsule robot are introduced. Its characteristic deformation curve, which was measured using an indentation setup, presents not only the deformation behavior of the magnetic capsule robot but also considerations in the capsule design process. Next, by implementing a magnetically actuated rolling locomotion scheme, the capsule can be controlled externally using a permanent magnet. The proposed magnetic capsule robot is anchored on a tissue wall by the magnetic attraction and rotated by a magnetic torque. This behavior allows a stable locomotion of the magnetic capsule robot and its orientation is controllable during locomotion. To verify the feasibility of proposed locomotion method and the compliant capsule's shape deformation, the magnetic capsule robot was actuated in a synthetic stomach model. The experimental results show that locomotion behavior of the capsule is stable and a successful tracking performance of the proposed magnetic actuation method; average distance gap between the capsule and the external magnet was only 20% of the capsule's body length. Such a soft and tetherless capsule robot can potentially enable minimally invasive diagnostic and treatment applications for stomach diseases.
Image-guided neurosurgery : integration of medical image data with real-time view of the surgical field (1997)

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 1997.
Enhanced attenuation of meningeal inflammation and brain edema by concomitant administration of anti-CD18 monoclonal antibodies and dexamethasone in experimental Haemophilus meningitis. (1991)

Antiinflammatory therapy has been shown to reduce the adverse pathophysiological consequences that occur in bacterial meningitis and to improve outcome from disease. In the present study, modulation of two principal steps of the meningeal inflammatory cascade was accomplished by concomitant administration of dexamethasone to diminish overproduction of cytokines in response to a bacterial stimulus and of a monoclonal antibody directed against adhesion-promoting receptors on leukocytes to inhibit recruitment of white blood cells into the subarachnoid space. Dexamethasone and antibody therapy produced a marked attenuation of all indices of meningeal inflammation and reduction of brain water accumulation after H. influenzae-induced meningitis in rabbits compared with results of each agent given alone and of untreated animals. In addition, the enhanced host's meningeal inflammatory reaction that follows antibiotic-induced bacterial lysis was profoundly ameliorated when dual therapy was administered without affecting clearance rates of bacteria from cerebrospinal fluid and vascular compartments. The combination of both therapeutic approaches may offer a promising mode of treatment to improve further the outcome from bacterial meningitis.
Enhancement of lithographic patterns by using serif features (1991)

Serifs were designed for the thin-oxide level pattern of a CMOS SRAM cell with submicrometer design rules, using two-dimensional aerial image simulations for optimization. Results of experiments using I-line lithography showed good agreement with the simulations, and significant pattern shape improvement was observed when serifs were used. The proximity effects in the electron-beam mask-making process were found to reduce the full effectiveness of this technique due to the resulting deviations in serif sizes on the reticle. Further enhancement of pattern fidelity may be possible if this issue is resolved.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
RNA-binding proteins (2006)

The C. elegans genome encodes many RNA-binding proteins (RBPs) with diverse functions in development, indicative of extensive layers of post-transcriptional control of RNA metabolism. A number of C. elegans RBPs have been identified by forward or reverse genetics. They tend to display tissue-specific mutant phenotypes, which underscore their functional importance. In addition, several RBPs that bind regulatory sequences in the 3'untranslated regions of mRNAs have been identified molecularly. Most C. elegans RBPs are conserved throughout evolution, suggesting that their study in C. elegans may uncover new conserved biological functions. In this review, we primarily discuss RBPs that are associated with well-characterized mutant phenotypes in the germ line, the early embryo, or in somatic tissues. We also discuss the identification of RNA targets of RBPs, which is an important first step to understand how an RBP controls C. elegans development. It is likely that most RBPs regulate multiple RNA targets. Once multiple RNA targets are identified, specific features that distinguish target from non-target RNAs and the type(s) of RNA metabolism that each RBP controls can be determined. Furthermore, one can determine whether the RBP regulates all targets by the same mechanism or different targets by distinct mechanisms. Such studies will provide insights into how RBPs exert coordinate control of their RNA targets, thereby affecting development in a concerted fashion.
Developmental regulation of zebrafish MyoD in wild-type, no tail and spadetail embryos (1996)

We describe the isolation of the zebrafish MyoD gene and its expression in wild-type embryos and in two mutants with altered somite development, no tail (ntl) and spadetail (spt). In the wild-type embryo, MyoD expression first occurs in an early phase, extending from mid-gastrula to just prior to somite formation, in which cells directly adjacent to the axial mesoderm express the gene. In subsequent phases, during the anterior-to-posterior wave of somite formation and maturation, expression occurs within particular regions of each somite. In spt embryos, which lack normal paraxial mesoderm due to incorrect cell migration, early MyoD expression is not observed and transcripts are instead first detected in small groups of trunk cells that will develop into aberrant myotomal-like structures. In ntl embryos, which lack notochords and tails, the early phase of MyoD expression is also absent. However, the later phase of expression within the developing somites appears to occur at the normal time in the ntl mutants, indicating that the presomitogenesis and somitogenesis phases of MyoD expression can be uncoupled. In addition, we demonstrate that the entire paraxial mesoderm of wild-type embryos has the potential to express MyoD when Sonic hedgehog is expressed ubiquitously in the embryo, and that this potential is lost in some of the cells of the paraxial mesoderm lineage in no tail and spadetail embryos. We also show that MyoD expression precedes myogenin expression and follows or is coincident with expression of snaill in some regions that express this gene.
Enhanced Transdermal Delivery of Acyclovir Sodium via Elastic Liposomes (2008)

The elastic liposomes bearing acyclovir sodium were prepared for its enhanced transdermal delivery by conventional rotary evaporation method and characterized for various parameters such as vesicle shape and surface morphology, size and size distribution, entrapment efficiency, elasticity, polydispersity index, turbidity and in vitro release pattern. Permeability studies of acyclovir sodium incorporated in elastic liposomes were performed across artificial membranes and rat skin. Skin permeation potential of the developed formulation was assessed using confocal laser scanning microscopy, that revealed an enhanced permeation of the formulation to the deeper layers of the skin (up to 160 microm) following channel like pathways. Skin permeation profile of elastic liposomal formulation bearing acyclovir sodium was observed and the investigations revealed an enhanced transdermal flux (6.21 +/- 1.8 microg/cm(2)/hr) and decreased lag time (0.6 hr) for acyclovir sodium. The obtained flux was nearly 2.0 and 6.3 times higher than conventional liposomal formulation bearing acyclovir sodium and plain drug solution, respectively (p < 0.01). The elastic liposomal formulation for transdermal delivery of acyclovir sodium provides better transdermal flux, higher entrapment efficiency, ability as a self-penetration enhancer and effectiveness for transdermal delivery as compared with conventional liposomes. In vivo studies showed that on transdermal application of elastic liposomes, the concentration of acyclovir sodium in plasma was found to be 105 +/- 9.4 ng/ml after 24 hr which is about 4.2 times compared with conventional liposomes. Thus it is concluded that the elastic liposomes may be promising vehicles for the transdermal delivery of acyclovir sodium.
Cerebrospinal fluid HIV infection and pleocytosis: Relation to systemic infection and antiretroviral treatment (2005)

CSF HIV infection is common across the spectrum of infection and is directly related to CSF pleocytosis, though whether the latter is a response to or a contributing cause of CSF infection remains uncertain. Slowing in the rate of CSF response to ART compared to plasma as CD4 counts decline indicates a changing character of CSF infection with systemic immunological progression. Longer-term responses indicate that CSF infection generally responds well to ART, even in the face of systemic virological failure due to drug resistance. We present simple models to explain the differing relationships of CSF to plasma HIV in these settings.
Micro Machining of Injection Mold Inserts for Fluidic Channel of Polymeric Biochips (2007)

Recently, the polymeric micro-fluidic biochip, often called LOC (lab-on-a-chip), has been focused as a cheap, rapid and simplified method to replace the existing biochemical laboratory works. It becomes possible to form miniaturized lab functionalities on a chip with the development of MEMS technologies. The micro-fluidic chips contain many micro-channels for the flow of sample and reagents, mixing, and detection tasks. Typical substrate materials for the chip are glass and polymers. Typical techniques for micro-fluidic chip fabrication are utilizing various micro pattern forming methods, such as wet-etching, micro-contact printing, and hot-embossing, micro injection molding, LIGA, and micro powder blasting processes, etc. In this study, to establish the basis of the micro pattern fabrication and mass production of polymeric micro-fluidic chips using injection molding process, micro machining method was applied to form micro-channels on the LOC molds. In the research, a series of machining experiments using micro end-mills were performed to determine optimum machining conditions to improve surface roughness and shape accuracy of designed simplified micro-channels. Obtained conditions were used to machine required mold inserts for micro-channels using micro end-mills. Test injection processes using machined molds and COC polymer were performed, and then the results were investigated.