gebhart/patrepeval huggingface dataset:
Distributed aggregation for data-parallel computing (2009)

Data-intensive applications are increasingly designed to execute on large computing clusters. Grouped aggregation is a core primitive of many distributed programming models, and it is often the most efficient available mechanism for computations such as matrix multiplication and graph traversal. Such algorithms typically require non-standard aggregations that are more sophisticated than traditional built-in database functions such as Sum and Max. As a result, the ease of programming user-defined aggregations, and the efficiency of their implementation, is of great current interest.
The human cytomegalovirus UL78 gene is highly conserved among clinical isolates, but is dispensable for replication in fibroblasts and a renal artery organ-culture system (2005)

The human cytomegalovirus (HCMV) UL78 ORF is considered to encode a seven-transmembrane receptor. However, neither the gene nor the UL78 protein has been characterized so far. The objective of this study was to investigate the UL78 gene and to clarify whether it is essential for replication. UL78 transcription was activated early after infection, was inhibited by cycloheximide but not by phosphonoacetic acid, and resulted in a 1.7 kb mRNA. Later in the replication cycle, a second mRNA of 4 kb evolved, comprising the UL77 and UL78 ORFs. The 5' end of the UL78 mRNA initiated 48 bp upstream of the translation start and the polyadenylated tail started 268 bp downstream of the UL78 translation stop codon within the UL79 ORF. By using bacterial artificial chromosome technology, a recombinant HCMV lacking most of the UL78 coding region was constructed. Successful reconstitution of the UL78-deficient virus proved that the gene was not essential for virus replication in fibroblasts. The deletion also did not reduce virus replication in ex vivo-cultured sections of human renal arteries. Analysis of viral proteins at different stages of the replication cycle confirmed these results. Among clinical HCMV isolates, the predicted UL78 protein was highly conserved. However, an accumulation of different single mutations could be found in the N-terminal region and at the very end of the C terminus. Due to the absence of an in vivo HCMV model, the role of UL78 in the pathogenesis of HCMV infection in humans remains unclear.
Possible Retrogenesis Observed with Fiber Tracking: An Anteroposterior Pattern of White Matter Disintegrity in Normal Aging and Alzheimer's Disease (2011)

Retrogenesis refers to the phenomenon by which degenerative processes in aging reverse the sequence of acquisition in development. Although there has been some evidence for brain retrogenesis in abnormal aging, e.g., Alzheimer's disease (AD), it has not been explicitly addressed in the normal aging. Using diffusion tensor imaging and tractography, we explored the effects of normal and abnormal aging on the integrity of white matter (WM) in fifty participants, including 18 AD patients, 17 normal elderly, and 15 normal young adults. Compared with young adults, the traditional voxel-based analysis, and the quantitative fiber tracking methods revealed lower fractional anisotrophy (FA) for both normal elderly and AD patients, indicating WM disintegrity in the anterior part of the brain with developmentally late-myelinating fiber bundles. Furthermore, AD patients showed lower FA in the posterior part of the brain with relatively early-myelinating fiber bundles. Additional analysis on axial diffusion and radial diffusion measures suggest that demyelination may be the main mechanism underlying the observed microstructural impairments. Consistent with a proposal of retrogenesis, our results demonstrate an anteroposterior pattern of white matter disintegrity in both normal aging and AD, with the pattern being more salient in the latter than in the former.
Regulation of Epidermal Growth Factor Receptor Signaling and Erlotinib Sensitivity in Head and Neck Cancer Cells by miR-7 (2012)

Elevated expression and activity of the epidermal growth factor receptor (EGFR)/protein kinase B (Akt) signaling pathway is associated with development, progression and treatment resistance of head and neck cancer (HNC). Several studies have demonstrated that microRNA-7 (miR-7) regulates EGFR expression and Akt activity in a range of cancer cell types via its specific interaction with the EGFR mRNA 3'-untranslated region (3'-UTR). In the present study, we found that miR-7 regulated EGFR expression and Akt activity in HNC cell lines, and that this was associated with reduced growth in vitro and in vivo of cells (HN5) that were sensitive to the EGFR tyrosine kinase inhibitor (TKI) erlotinib (Tarceva). miR-7 acted synergistically with erlotinib to inhibit growth of erlotinib-resistant FaDu cells, an effect associated with increased inhibition of Akt activity. Microarray analysis of HN5 and FaDu cell lines transfected with miR-7 identified a common set of downregulated miR-7 target genes, providing insight into the tumor suppressor function of miR-7. Furthermore, we identified several target miR-7 mRNAs with a putative role in the sensitization of FaDu cells to erlotinib. Together, these data support the coordinate regulation of Akt signaling by miR-7 in HNC cells and suggest the therapeutic potential of miR-7 alone or in combination with EGFR TKIs in this disease.
Isolated osteoclasts resorb the organic and inorganic components of bone. (1986)

Osteoclasts are the principal resorptive cells of bone, yet their capacity to degrade collagen, the major organic component of bone matrix, remains unexplored. Accordingly, we have studied the bone resorptive activity of highly enriched populations of isolated chicken osteoclasts, using as substrate devitalized rat bone which had been labeled in vivo with L-[5-3H]proline or 45Ca, and bone-like matrix produced and mineralized in vitro by osteoblast-like rat osteosarcoma cells. When co-cultured with a radiolabeled substrate, osteoclast-mediated mineral mobilization reached a maximal rate within 2 h, whereas organic matrix degradation appeared more slowly, reaching maximal rate by 12-24 h. Thereafter, the rates of organic and inorganic matrix resorption were essentially linear and parallel for at least 6 d when excess substrate was available. Osteoclast-mediated degradation of bone collagen was confirmed by amino acid analysis. 39% of the solubilized tritium was recovered as trans-4-hydroxyproline, 47% as proline. 10,000 osteoclasts solubilized 70% of the total radioactivity and 65% of the [3H]-trans-4-hydroxyproline from 100 micrograms of 25-50 micron bone fragments within 5 d. Virtually all released tritium-labeled protein was of low molecular weight, 99% with Mr less than or equal to 10,000, and 65% with Mr less than or equal to 1,000. Moreover, when the 14% of resorbed [3H]proline-labeled peptides with Mr greater than or equal to 2,000 were examined for the presence of TCA and TCB, the characteristic initial products of mammalian collagenase activity, none was detected by SDS PAGE. In addition, osteoclast-conditioned medium had no collagenolytic activity, and exogenous TCA and TCB fragments were not degraded by osteoclasts. On the other hand, osteoclast lysates have collagenolytic enzyme activity in acidic but not in neutral buffer, with maximum activity at pH 4.0. These data indicate that osteoclasts have the capacity to resorb the organic phase of bone by a process localized to the osteoclast and its attachment site. This process appears to be independent of secretion of neutral collagenase and probably reflects acid protease activity.
Two-Year Toxicity and Carcinogenicity Study of Methyleugenol in F344/N Rats and B6C3F1Mice (2000)

Methyleugenol (MEG) was tested for toxicity/carcinogenicity in a 2-yr carcinogenesis bioassay because of its widespread use in a variety of foods, beverages, and cosmetics as well as its structural resemblance to the known carcinogen safrole. F344/N rats and B6C3F(1) mice (50 animals/sex/dose group) were given MEG suspended in 0.5% methylcellulose by gavage at doses of 37, 75, or 150 mg/kg/day for 2 yr. Control groups (60 rats/sex and 50 mice/sex) received only the vehicle. A stop-exposure group of 60 rats/sex received 300 mg/kg/day by gavage for 53 weeks followed by the vehicle only for the remaining 52 weeks of the study. A special study group (10 animals/sex/species/dose group) were used for toxicokinetic studies. All male rats given 150 and 300 mg/kg/day died before the end of the study; survival of female rats given 150 mg/kg/day and all treated female mice was decreased. Mean body weights of treated male and female rats and mice were decreased when compared to control. Area under the curve results indicated that greater than dose proportional increases in plasma MEG occurred for male 150 and 300 mg/kg/day group rats (6 and 12 month) and male 150 mg/kg/day mice (12 month). Target organs included the liver, glandular stomach, forestomach (female rats) and kidney, mammary gland, and subcutaneous tissue (male rats). Liver neoplasms occurred in all dose groups of rats and mice and included hepatoadenoma, hepatocarcinoma, hepatocholangioma (rats only), hepatocholangiocarcinoma, and hepatoblastoma (mice only). Nonneoplastic liver lesions included eosinophilic and mixed cell foci (rats only), hypertrophy, oval cell hyperplasia, cystic degeneration (rats only), and bile duct hyperplasia. Mice also exhibited necrosis, hematopoietic cell proliferation, and hemosiderin pigmentation. Glandular stomach lesions in rats and mice included benign and malignant neuroendocrine tumors, neuroendocrine cell hyperplasia, and atrophy and in mice included glandular ectasia/chronic active inflammation. In female rats, the forestomach showed a positive trend in the incidences of squamous cell papilloma or carcinoma (combined). Male rats also exhibited kidney (renal tubule hyperplasia, nephropathy, and adenomacarcinoma), mammary gland (fibroadenoma), and subcutaneous tissue (fibroma, fibrosarcoma) lesions. Male rats also exhibited malignant mesotheliomas and splenic fibrosis. These data demonstrate that MEG is a multisite, multispecies carcinogen.
CD8– dendritic cells preferentially cross‐present Saccharomyces cerevisiae antigens (2008)

Mouse splenic dendritic cell (DC) subsets possess distinct antigen-presentation abilities. CD8(+) DC are specialized in cross-presentation of antigens to CD8(+) T cells, whereas CD8(-) DC are more efficient in antigen presentation to CD4(+) T cells. In this study, we examined the capacity of CD8(+) and CD8(-) DC subsets to present fungal antigens in MHC class I and II molecules to CD8(+) and CD4(+) T cells, respectively. We used ovalbumin-expressing Saccharomyces cerevisiae (yeast-OVA) as a fungal model system. Both CD8(+) and CD8(-) DC subsets phagocytosed yeast in equal amounts and uptake was mediated via dectin-1. In addition, both DC subsets induced similar OVA-specific CD4(+) T cell proliferation after incubation with yeast-OVA. However, the induction of OVA-specific CD8(+) T cell activation was largely restricted to the CD8(-) DC subset. Furthermore, only CD8(-) DC produced cytokines such as IL-10 and TNF-alpha and increased IL-23p19 and IL-23p40 mRNA levels in response to yeast. Our results strongly suggest that DC subsets have different functions in the elicitation of adaptive immune responses in vivo.
Green and biodegradable electronics (2012)

We live in a world where the lifetime of electronics is becoming shorter, now approaching an average of several months. This poses a growing ecological problem. This brief review will present some of the initial steps taken to address the issue of electronic waste with biodegradable organic electronic materials. Many organic materials have been shown to be biodegradable, safe, and nontoxic, including compounds of natural origin. Additionally, the unique features of such organic materials suggest they will be useful in biofunctional electronics; demonstrating functions that would be inaccessible for traditional inorganic compounds. Such materials may lead to fully biodegradable and even biocompatible/biometabolizable electronics for many low-cost applications. This review highlights recent progress in these classes of material, covering substrates and insulators, semiconductors, and finally conductors.
A performance comparison of the temporally-ordered routing algorithm and ideal link-state routing (2002)

We present a relative performance comparison of the temporally-ordered routing algorithm (TORA) with an ideal link state (ILS) routing algorithm. The performance metrics evaluated include bandwidth efficiency for both control and data, as well as end-to-end message packet delay and throughput. The routing algorithms are compared in the context of a dynamic, multihop, wireless network employing broadcast transmissions. The network parameters varied include network size, average rate of topological changes and average network connectivity. While the average network connectivity was found not to be a significant factor, the relative performance of TORA and ILS was found to be critically dependent on the network size, and the average rate of topological changes. The results further indicate that for a given available bandwidth-as either the size of network increases or the rate of network topological change increases, the performance of TORA eventually exceeds that of ILS.
Transcranial Doppler Ultrasound: Technique and Application (2013)

Transcranial Doppler (TCD) ultrasound provides rapid, noninvasive, real-time measures of cerebrovascular function. TCD can be used to measure flow velocity in the basal arteries of the brain to assess relative changes in flow, diagnose focal vascular stenosis, or to detect embolic signals within these arteries. TCD can also be used to assess the physiologic health of a particular vascular territory by measuring blood flow responses to changes in blood pressure (cerebral autoregulation), changes in end-tidal CO2 (cerebral vasoreactivity), or cognitive and motor activation (neurovascular coupling or functional hyperemia). TCD has established utility in the clinical diagnosis of a number of cerebrovascular disorders such as acute ischemic stroke, vasospasm, subarachnoid hemorrhage, sickle cell disease, as well as other conditions such as brain death. Clinical indication and research applications for this mode of imaging continue to expand. In this review, the authors summarize the basic principles and clinical utility of TCD and provide an overview of a few TCD research applications.
Nitrite in Human Saliva. Its Possible Relationship to Nitrosamine Formation23 (1974)

Nitrite was consistently found in human saliva at levels of usually 6-10 ppm. The nitrite level did not seem to be strongly influenced by the composition of a meal, and in some individuals a narrow range of nitrite concentration was maintained for a long time. In agreement with earlier work, parotid ductal saliva was found to be free of nitrite, and a major route of nitrite formation was via microbial reduction of nitrate naturally present in saliva. Exploration of various parameters related to the reduction of nitrate to nitrite did not demonstrate a clear correlation between measurements on individuals and their level of salivary nitrite. The microorganisms responsible for nitrite formation were identified and quantified, and the relationships between nitrate consumption and nitrite formation explored. These complex relationships suggested that the tree nitrite in saliva represents the “spillover” of that formed in microbial cells.
<title>Applications of resonance ionization spectroscopy for semiconductor, environmental and biomedical analysis, and for DNA sequencing</title> (1991)

Resonance Ionization Spectroscopy (RIS), an analytical technique with extremely high element specificity and sensitivity, is becoming recognized as an emerging field with wide applications. The sensitivity and selectivity of the RIS process is especially valuable for ultra-trace element analysis in semiconductor, geological, biological, and environmental samples, where the complexity of the matrix is frequently a serious source of interference. Using either Sputter-Initiated RIS (SIRIS) or Laser Atomization RIS (LARIS), it is possible to localize with high spatial resolution ultra-trace concentrations of a selected element to the sub-parts per billion level. The authors describe the implementation of RIS to solve a number of analysis problems and illustrate its salient characteristic with data from a wide range of applications. Results presented will include (a) concentration plots of ultra- trace elements in semiconductors and biological matrices, (b) characterization of dopants as a function of depth in semiconductors, (c) spatial distribution of natural uranium in bone and bone marrow, and (d) localization of stable isotope-labeled DNA in the development of faster DNA sequencing methods. The practical capabilities of SIRIS/LARIS to determine trace elements as a function of depth and lateral position in semiconductors and biological matrices are discussed.
RNAML: A standard syntax for exchanging RNA information (2002)

Analyzing a single data set using multiple RNA informatics programs often requires a file format conversion between each pair of programs, significantly hampering productivity. To facilitate the interoperation of these programs, we propose a syntax to exchange basic RNA molecular information. This RNAML syntax allows for the storage and the exchange of information about RNA sequence and secondary and tertiary structures. The syntax permits the description of higher level information about the data including, but not restricted to, base pairs, base triples, and pseudoknots. A class-oriented approach allows us to represent data common to a given set of RNA molecules, such as a sequence alignment and a consensus secondary structure. Documentation about experiments and computations, as well as references to journals and external databases, are included in the syntax. The chief challenge in creating such a syntax was to determine the appropriate scope of usage and to ensure extensibility as new needs will arise. The syntax complies with the eXtensible Markup Language (XML) recommendations, a widely accepted standard for syntax specifications. In addition to the various generic packages that exist to read and interpret XML formats, an XML processor was developed and put in the open-source MC-Core library for nucleic acid and protein structure computer manipulation.
Application of Multidimensional (Heart-Cut) Gas Chromatography to the Analysis of Complex Mixtures of Organic Pollutants in Environmental Samples (2003)

This contribution presents some applications developed in our laboratory of multidimensional (heart-cut) gas chromatography (MDGC) applied to the analysis of complex mixtures of pollutants in environmental samples. Practical aspects of this technique as well as qualitative and quantitative examples are discussed. Determination of trace levels of pesticides, polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs) with MDGC-ECD/ECD and MDGC-ECD/MS in fish, mussels, or sewage sludge is presented.
Phase dispersion optical tomography applied to study sub-cellular motions (2001)

Summary form only given. We present a novel phase sensitive imaging technique - phase dispersion optical tomography (PDOT), which totally eliminates interferometer jitter noise - the major source of phase measurement error in interferometers. The technique is based on a modified low-coherence Michelson interferometer. The input light is a pair of overlapped beams of laser light at wavelength /spl lambda/ and wavelength 2/spl lambda/.
Heparin-induced thrombocytopenia: new evidence for the dynamic binding of purified anti-PF4–heparin antibodies to platelets and the resultant platelet activation (2000)

Immune heparin-induced thrombocytopenia (HIT) is associated with antibodies directed against a complex of platelet factor 4 (PF4) and heparin. We were able to affinity purify anti-PF4-heparin IgG (HIT IgG) from the plasma of 2 patients with HIT. Under conditions that were more physiological and sensitive than those in previous studies, we observed that this HIT IgG caused platelet aggregation on the addition of heparin. Platelets activated with HIT IgG increased their release and surface expression of PF4. We quantitated, for the first time, the binding of affinity-purified HIT iodine 125-IgG to platelets as they activated in a plasma milieu. Binding of the HIT IgG was dependent on heparin and required some degree of platelet activation. Blocking the platelet FcgammaRII with the monoclonal antibody IV.3 did not prevent HIT IgG binding to activated platelets. We concluded that anti-PF4-heparin IgG is the component in these HIT plasmas that induces platelet aggregation. The Fab region of HIT IgG binds to PF4-heparin on the surface of activated platelets. We propose that only then does the Fc portion of the bound IgG further activate the same or adjacent platelets through the Fc receptor. Our data support a dynamic model of platelet activation in which released PF4 enhances further antibody binding and more release.
Cytochrome P 450 Epoxygenase Promotes Human Cancer Metastasis (2007)

Cytochrome P450 (CYP) epoxygenases convert arachidonic acid to four regioisomeric epoxyeicosatrienoic acids (EET), which exert diverse biological activities in a variety of systems. We previously reported that the CYP2J2 epoxygenase is overexpressed in human cancer tissues and cancer cell lines and that EETs enhance tumor growth, increase carcinoma cell proliferation, and prevent apoptosis of cancer cells. Herein, we report that CYP epoxygenase overexpression or EET treatment promotes tumor metastasis independent of effects on tumor growth. In four different human cancer cell lines in vitro, overexpression of CYP2J2 or CYP102 F87V with an associated increase in EET production or addition of synthetic EETs significantly induced Transwell migration (4.5- to 5.5-fold), invasion of cells (3- to 3.5-fold), cell adhesion to fibronectin, and colony formation in soft agar. In contrast, the epoxygenase inhibitor 17-ODYA or infection with the antisense recombinant adeno-associated viral vector (rAAV)-CYP2J2 vector inhibited cell migration, invasion, and adhesion with an associated reduction in EET production. CYP overexpression also enhanced metastatic potential in vivo in that rAAV-CYP2J2-infected MDA-MB-231 human breast carcinoma cells showed 60% more lung metastases in athymic BALB/c mice and enhanced angiogenesis in and around primary tumors compared with control cells. Lung metastasis was abolished by infection with the antisense rAAV-CYP2J2 vector. CYP epoxygenase overexpression or EET treatment up-regulated the prometastatic matrix metalloproteinases and CD44 and down-regulated the antimetastatic genes CD82 and nm-23. Together, these data suggest that CYP epoxygenase inhibition may represent a novel approach to prevent metastasis of human cancers.