gebhart/patrepeval huggingface dataset:
Generating dynamic program analysis tools (2002)

Sophisticated instrumentation based systems exist for building dynamic analysis tools but to use these systems a developer must write the instrumentation and analysis code by hand. The paper describes how analysis tools can be generated automatically by specifying analysis algorithms using attribute grammars based on the static and dynamic structure of the program being analysed. Using methods similar to those used to generate compilers, this approach enables implicit storage allocation for analysis data, automatic sequencing of analysis steps and transparently supports a variety of data sources and independence from the underlying implementation technology. Furthermore, analysis algorithms can be described in a modular way, enabling reuse. To demonstrate the approach, the paper describes the Wyong system that generates dynamic analysis tools from specifications. An example analysis module specification is described and its reuse is illustrated. Wyong is based on the Eli compiler generation system and the ATOM program instrumentation system. To avoid having to build extremely large trees describing the dynamic structure of a program, Wyong automatically generates instrumentation code for ATOM. Combined with other modules generated by Eli, the ATOM instrumented binary evaluates the specified analysis attribute computations as it executes. Thus the benefits of a specification based method are combined with the efficiency of an instrumentation based implementation.
Benspænd for fremmedsprog (2015)

Temanummerets kronik
Comparing the MicroRNA Spectrum between Serum and Plasma (2012)

MicroRNAs (miRNAs) are small, non-coding RNAs that regulate various biological processes, primarily through interaction with messenger RNAs. The levels of specific, circulating miRNAs in blood have been shown to associate with various pathological conditions including cancers. These miRNAs have great potential as biomarkers for various pathophysiological conditions. In this study we focused on different sample types' effects on the spectrum of circulating miRNA in blood. Using serum and corresponding plasma samples from the same individuals, we observed higher miRNA concentrations in serum samples compared to the corresponding plasma samples. The difference between serum and plasma miRNA concentration showed some associations with miRNA from platelets, which may indicate that the coagulation process may affect the spectrum of extracellular miRNA in blood. Several miRNAs also showed platform dependent variations in measurements. Our results suggest that there are a number of factors that might affect the measurement of circulating miRNA concentration. Caution must be taken when comparing miRNA data generated from different sample types or measurement platforms.
Development and Homeostasis of T Cell Memory in Rhesus Macaque (2002)

The rhesus macaque (RM) is a critical animal model for studies of viral pathogenesis and immunity, yet fundamental aspects of their cellular immune response remain poorly defined. One such deficiency is the lack of validated phenotypic signatures for their naive and memory T cell subsets, and the resultant unavailability of accurate information on their memory T cell development, homeostasis, and function. In this study, we report a phenotypic paradigm allowing definitive characterization of these subsets and their comprehensive functional analysis. Naive T cells are optimally delineated by their homogeneous CD95(low)CD28(high)beta(7) integrin(int) (CD4+) or CD95(low)CD28(int)CD11a(low) (CD8+) phenotypes. This subset 1) was present in blood and secondary lymph tissues, but not effector sites; 2) vastly predominated in the fetal/neonatal immune system, but rapidly diminished with postnatal age; 3) lacked IFN-gamma production capability, and specific responses to RM CMV; and 4) demonstrated low in vivo proliferative activity. CD4+ and CD8+ memory subsets were CD95(high), but otherwise phenotypically heterogeneous and included all IFN-gamma production, RM CMV-specific responses, effector site T cells, and demonstrated high in vivo proliferative activity ( approximately 10 times the naive subset). These analyses also revealed the RM "effector memory" subset within the overall memory population. This population, best defined by lack of CD28 expression, contained the majority of RM CMV-specific cells, was highly enriched in extralymphoid effector sites, and comprised an increasing proportion of total memory cells with age. The effector memory subset demonstrated similar in vivo proliferative activity and survival as CD28+ "central memory" T cells, consistent with independent homeostatic regulation.
Comparison of Five Agents in Protecting the Cochlea Against the Ototoxic Effects of Cisplatin in the Hamster (1997)

The purpose of this investigation was to study the ameliorating effects of four agents on cisplatin-induced ototoxicity. Hamsters were given a series of five cisplatin injections either alone or in combination with sodium thiosulfate (STS), diethyldihydrothiocarbamate (DDTC), and S-2(3-aminopropylamino) ethylphosphorothioic acid (WR-2721), or fosfomycin. Ototoxicity was assessed anatomically by quantifying the extent of cochlear damage with the scanning electron microscope and physiologically with measures of the auditory brain stem response. When administered alone, cisplatin induced widespread loss of outer hair cells (OHCs) along much of the cochlea in the hamster, especially in the basal and middle turns, with an average survival of only 56% of the OHC population. In contrast, inner hair cells resisted cisplatin ototoxicity in the hamster. Thus the ameliorative effects of the different test agents were assessed by counting the number of surviving OHCs in each treatment group and comparing with cisplatin-treated controls. STS provided the most effective protection against the ototoxic effects of cisplatin, yielding 91% survival of OHCs. DDTC also reduced the ototoxic effects of cisplatin, yielding 68% survival of OHCs. Cotreatment with WR-2721 and fosfomycin yielded 45% and 52% OHC survival, respectively, and thus did not provide any chemoprotection. The results closely paralleled those based on auditory brain stem response recordings in that the magnitude of threshold shift was proportional to the amount of OHC loss; also, the amount of threshold shift at each frequency was in good agreement with the pattern of hair cell loss along the cochlear spiral. Thus both histologic and physiologic results suggest that STS and DDTC hold promise for ameliorating the ototoxic effects of cisplatin chemotherapy.
Isolation and characterization of the chains of type V/type XI collagen present in bovine vitreous (1993)

Previous studies show that the collagen fibrils of the mammalian vitreous humor are assembled largely from type II collagen with smaller amounts of type IX collagen and either type V or type XI collagen. In this paper, we report the separation of two chains of type V/type XI collagen from type II collagen by heparin-Sepharose chromatography. These chains were characterized by sequencing of selected cyanogen bromide or tryptic peptides with subsequent comparison of these sequences with cDNA-derived amino acid sequences of the alpha 1(V), alpha 1(XI), alpha 2(V), and alpha 2(XI) chains. The results show that vitreous fibrils are assembled from molecules containing the alpha 1(XI) and alpha 2(V) chains. These results, together with recent results from other laboratories, indicate that type V and type XI collagens are not separate collagen types but are part of a larger collagen family in which chains of both type V and type XI collagens participate in the formation of a variety of native molecules.
Human Hepatocytes as a Tool for Studying Toxicity and Drug Metabolism (2003)

Drugs are usually biotransformed into new chemical species that may have either toxic or therapeutic effects. Drug metabolism studies are routinely performed in laboratory animals but, due to metabolic interspecies differences when compared to man, they are not accurate enough to anticipate the metabolic profile of a drug in humans. Human hepatocytes in primary culture provide the closest in vitro model to human liver and the only model that can produce a metabolic profile of a given drug that is very similar to that found in vivo. However their availability is limited due to the restricted access to suitable tissue samples. The scarcity of human liver has led to optimising the cryopreservation of adult hepatocytes for long-term storage and regular supply. Human hepatocytes in primary culture express typical hepatic functions and express drug metabolising enzymes. Moreover, qualitative and quantitative similarities between in vitro and in vivo metabolism of drugs were observed. Different strategies have been envisaged to prolong cell survival and delay the spontaneous decay of the differentiated phenotype during culture. Thus, hepatocytes represent the most appropriate model for the evaluation of integrated drug metabolism, toxicity/metabolism correlations, mechanisms of hepatotoxicity, and the interactions (inhibition and induction) of xenobiotics and drug-metabolising enzymes. However, in view of limitations of primary hepatocytes, efforts are made to develop alternative cellular models (i.e. metabolic competent CYP-engineered cells stably expressing individual CYPs and transient expression of CYPs by transduction of hepatoma cells with recombinant adenoviruses). In summary, several cellular tools are available to address key issues at the earliest stages of drug development for a better candidate selection and hepatotoxicity risk assessment.
Flight controller alertness and performance during spaceflight shiftwork operations. (1998)

Decreased alertness and performance associated with fatigue, sleep loss, and circadian disruption are issues faced by a diverse range of shiftwork operations personnel. During Space Transportation System (STS) operations, Mission Operations Directorate (MOD) personnel provide 24-hr. coverage of critical tasks. A joint NASA Johnson Space Center and NASA Ames Research Center project was undertaken to examine these issues in flight controllers during MOD shiftwork operations. An initial operational test of procedures and measures was conducted during the STS-53 mission in December 1992. The study measures included a Background Questionnaire, a subjective daily logbook completed on a 24-hour basis (to report sleep patterns, work periods, etc.), and an 8 minute performance and mood test battery administered at the beginning, middle, and end of each shift period. Seventeen flight controllers representing the 3 Orbit shifts participated. The initial results clearly support the need for further data collection during other STS missions to document baseline levels of alertness and performance during MOD shiftwork operations. Countermeasure strategies specific to the MOD environment are being developed to minimize the adverse effects of fatigue, sleep loss, and circadian disruption engendered by shiftwork operations. These issues are especially pertinent for the night shift operations and the acute phase advance required for the transition of day shift personnel into the night for shuttle launch. Implementation and evaluation of the countermeasure strategies to maximize alertness and performance is planned. As STS missions extend to further EDO (extended duration orbiters), and timelines and planning for 24-hour Space Station operations continue, alertness and performance issues related to sleep and circadian disruption will remain highly relevant in the MOD environment.
Argon: Performance Insulation for Shared Storage Servers (CMU-PDL-06-106 ) (2018)

Services that share a storage system should realize the same efficiency, within their share of time, as when they have the system to themselves. The Argon storage server explicitly manages its resources to bound the inefficiency arising from inter-service disk and cache interference in traditional systems. The goal is to provide each service with at least a configured fraction (e.g., 0.9) of the throughput it achieves when it has the storage server to itself, within its share of the server—a service allocated 1 nth of a server should get nearly 1 nth (or more) of the throughput it would get alone. Argon uses automaticallyconfigured prefetch/write-back sizes to insulate streaming efficiency from disk seeks introduced by competing workloads. It uses explicit disk time quanta to do the same for non-streaming workloads with internal locality. It partitions the cache among services, based on their observed access patterns, to insulate the hit rate each achieves from the access patterns of others. Experiments show that, combined, these mechanisms and Argon’s automatic configuration of each achieve the insulation goal.
Conjunctival Hyperemia and Corneal Infiltrates With Chemically Disinfected Soft Contact Lenses (1980)

For three cosmetic soft contact lens wearers who chemically disinfected their lenses, conjunctival hyperemia and anterior stromal infiltrates of the cornea developed. When the conjunctival hyperemia and corneal infiltrates resolved, two of the three patients were challenged with their chemically disinfected soft contact lenses, with reappearance of the conjunctival and corneal reactions. Bacterial cultures of the conjunctiva, lids, lens cases, lens solutions, and eye cosmetics were not helpful. Conjunctival cultures for adenovirus and chlamytdial titers were negative. Giemsa stain of conjunctival scrapings showed a few mononuclear cells, polymorphonuclear leukocytes, and rare eosinophils but no inclusion bodies. Occlusive patch tests and intradermal tests showed positive delayed hypersensitivity reactions to the chemical disinfectants in all three patients. Occlusive patch tests with thimerosal suggested that this preservative was responsible for the reactions. Delayed hypersensitivity to thimerosal may play a role in the development of the conjunctival hyperemia and corneal infiltrates described in these patients.
Biochemical Characterization of <i>Junonia coenia</i> Densovirus Nonstructural Protein NS-1 (2002)

Junonia coenia densovirus (JcDNV) is an autonomous parvovirus that infects the larvae of the common buckeye butterfly, Junonia coenia. Unlike vertebrate parvoviruses, the genes encoding the structural protein and nonstructural (NS) proteins of JcDNV are in opposite orientations; thus, each strand contains a sense and antisense open reading frame (ORF). The promoter at map position 93 controls expression of NS ORFs 2, 3, and 4, which encode three NS proteins, NS-1, NS-2, and NS-3. These proteins are likely to be involved in viral DNA replication, among other functions. In contrast to the nonstructural proteins of the vertebrate parvoviruses, the NS proteins of the Densovirinae have not been characterized. Here, we describe biochemical properties of the NS-1 protein of JcDNV. The NS-1 ORF was cloned in frame with the Escherichia coli malE gene, which encodes the bacterial maltose binding protein (MBP). Using electrophoretic mobility shift and DNase I protection assays, we identified the region of the JcDNV terminal sequence that is recognized specifically by the MBP-NS-1 fusion protein. The site consists of (GAC)4 and is located on the A-A' region of the terminal palindrome. In addition, the MBP-NS-1 fusion protein catalyzes the cleavage of single-stranded DNA (ssDNA) substrates derived from the JcDNV putative origin of replication, primarily at two sites in the motif 5'-G*TAT*TG-3'. One cleavage site is between the thymidine dinucleotide at positions 92 and 93 and the other site corresponds to thymidine at nucleotide 95; both sites are on the complementary strand of the sequence assigned GenBank accession number A12984. Cleavage of ssDNA is dependent on the presence of a divalent metal cofactor but does not require nucleoside triphosphate hydrolysis. Parvovirus NS proteins contain the phylogenically conserved Walker A- and B-site ATPase motifs. These sites in JcDNV NS-1 diverge from the consensus, yet despite these atypical motifs our analyses support that MBP-NS-1 has ATP-dependent helicase activity. These results indicate that JcDNV NS-1 possesses activities common to the superfamily of rolling-circle replication initiator proteins in general and the parvovirus replication proteins in particular, and they provide a basis for comparative analyses of the structure and function relationships among the parvovirus NS-1 equivalents.
Variability of polymerase chain reaction‐based detection of human papillomavirus DNA is associated with the composition of vaginal microbial flora (1994)

The results of repeated human papillomavirus (HPV) DNA testing were compared to changes in cervical pathology and the composition of vaginal microorganisms. A cohort of 19 women with HPV cervical infections in the absence of cervical intraepithelial neoplasia at enrollment was reexamined on average at 7.3-month intervals over a 2-year period. At each follow-up visit, cytological and colposcopic examinations were done and vaginal microorganisms were assessed quantitatively by Gram staining of secretions, and anaerobic and aerobic culture. HPV genotypes 6, 11, 16, and 18 were detected by polymerase chain reaction analysis using DNA isolated from exfoliated cervical cells. The detection of HPV DNA was significantly associated with carriage of Grade II flora (P < 0.001), isolation of Gardnerella vaginalis (P = 0.03), Ureaplasma urealyticum (P = 0.04), Candida albicans (P = 0.01), Bacteroides species (P = 0.01), and overgrowth by anaerobes (P = 0.004). Normal vaginal flora, characterised by the predominance of Lactobacillus species, was significantly associated (P < 0.001) with a negative HPV test. The detection of HPV DNA is associated with the composition of microorganisms present in the vagina at the time of testing.
Impementing and extending the Optimized Link State Routing Protocol (2004)

A MANET is a multi-hop ad-hoc wireless network\nwhere nodes can move arbitrary in the topology. The network has no\ngiven infrastructure and can be set up quickly in any environment.\nThe Optimized Link State Routing(OLSR) protocol is a route\nmanagement protocol for such mobile ad hoc networks.\n\nThis study presents the work of implementing the \nOLSR routing protocol. The implementation is done\nin a modular fashion, allowing for the use of external plugins.\nAlso,this study analyzes certain extensions to the protocol done in\nrelation to the implementation, including Internet connectivity,\nsecurity and auto-configuration. More technical implementation \ndesigns are also covered.
Self supervised learning improves dMMR/MSI detection from histology slides across multiple cancers (2021)

Microsatellite instability (MSI) is a tumor phenotype whose diagnosis largely impacts patient care in colorectal cancers (CRC), and is associated with response to immunotherapy in all solid tumors. Deep learning models detecting MSI tumors directly from H&amp;E stained slides have shown promise in improving diagnosis of MSI patients. Prior deep learning models for MSI detection have relied on neural networks pretrained on ImageNet dataset, which does not contain any medical image. In this study, we leverage recent advances in self-supervised learning by training neural networks on histology images from the TCGA dataset using MoCo V2. We show that these networks consistently outperform their counterparts pretrained using ImageNet and obtain state-of-the-art results for MSI detection with AUCs of 0.92 and 0.83 for CRC and gastric tumors, respectively. These models generalize well on an external CRC cohort (0.97 AUC on PAIP) and improve transfer from one organ to another. Finally we show that predictive image regions exhibit meaningful histological patterns, and that the use of MoCo features highlighted more relevant patterns according to an expert pathologist.
&lt;title&gt;Identification of blur parameters from motion-blurred images&lt;/title&gt; (1996)

A difficult problem in imaging systems is degradation of images caused by motion. This problem is common when the imaging system is in moving vehicles such as tanks or planes and even when the camera is held by human hands. For correct restoration of the degraded image we need to know the point spread function (PSF) of the blurring system. In this paper we propose a method to identify important parameters with which to characterize the PSF of the blur, given only the blurred image itself. A first step of this method has been suggested in a former paper where only the blur extent parameter was considered. The identification method here is based on the concept that image characteristics along the direction of motion are different than the characteristics in other directions. Depending on the PSF shape, the homogeneity and the smoothness of the blurred image in the motion direction are higher than in other directions. Furthermore, in the motion direction correlation exists between the pixels forming the blur of the original unblurred objects. The method proposed here identifies the direction and the extent of the PSF of the blur and evaluates its shape which depends on the type of motion during the exposure. Correct identification of the PSF parameters permits fast high resolution restoration of the blurred image.
Metal center dependent coordination modes of a tricarbene ligand (2012)

The reaction of the benzene derived trisimidazolium salt [1](PF(6))(3) with [PdCl(allyl)](2) gave complex [2](PF(6))(3) featuring three Pd(allyl) moieties sandwiched between two tricarbene ligands, whereas the reaction of [1](PF(6))(3) with [M(Cp*)(Cl)(2)](2) (M = Ir, Rh) resulted in the formation of dinuclear M(III) complexes [3]PF(6) (M = Ir) and [4]PF(6) (M = Rh) where each metal center is coordinated by an NHC donor and orthometallates the central phenyl ring. The remaining imidazolium group in [4]PF(6) can be metallated with [Rh(Cp*)(Cl)(2)](2) to give the trinuclear triply orthometallated complex [5].
Charateristics of decade-bandwidth, Balanced Antipodal Vivaldi Antenna (BAVA) phased arrays with time-delay beamformer systems (2013)

The first part of this paper presents measured performance of the Balanced Antipodal Vivaldi Antenna (BAVA) with U-shaped metallic channels. This new BAVA array is dual polarized with decade bandwidth and wide scan volume. Its depth is half-wavelength at the highest frequency of operation. It can be constructed as modular individual BAVA elements or as a subarray with integrated transmitter / receiver (T/R) modules. This is a unique feature that reduces manufacturing complexity and the cost of field repair. The second part of this paper overviews performance of the BAVA array scanned at wide scan angles using AFRL's Transformational Element Level Array (TELA) Time-Delay Units between 2 GHz to 8 GHz and using fixed delay lines between 2 GHz to 18 GHz. The authors offer guidelines for minimum aperture size to realize decade bandwidth beam scan performance without beam squinting at the lower end of the frequency band.
Histochemical and Immunocytochemical Approaches to the Study of Oxidative Stress (2000)

We review an array of newly developed in situ detection methods that can be used for the qualitative and semi-quantitative measurement of various indices related to oxidative stress. The importance of in situ methods over bulk analysis cannot be overstated when considering the structural and cellular complexity of tissue and the effects of diseases thereof. Indeed, in situ detection allows detection of specific cell types affected or specific localization such that a process affecting only a small fraction of the tissue or cells can be readily visualized. Consequently, a positive signal in situ indicates real levels that cannot be masked by unrelated or compensatory responses in adjacent cells, and corrections can be easily made for the modifications to long-lived proteins during physiological aging. In fact, the damage to extracellular matrix proteins of major vessels, provides a cumulative record of long-term oxidative insult. Yet the same properties that make vessels ideal markers for aging limits their sensitivity to detect disease-specific changes unless in situ techniques are used.