Miracle-dz/UniFAR-FTUs huggingface dataset:
Computing Types During Program Specialization

We have developed techniques for obtaining and using type information during program specialization (partial evaluation). Computed along with every residual expression and every specialized program is type information that bounds the possible values that the specialized program will compute at run time. The three keystones of this research are symbolic values that represent both a value and the code for creating the value, generalization of symbolic values, and the use of online fixed-point iterations for computing the type of values returned by specialized recursive functions. The specializer exploits type information to increase the efficiency of specialized functions. This research has two benefits, one anticipated and one unanticipated. The anticipated benefit is that programs that are to be specialized can now be written in a more natural style without losing accuracy during specialization. The unanticipated benefit is the creation of what we term concrete abstract interpretation. This is a method of performing abstract interpretation with concrete values where possible. The specializer abstracts values as needed, instead of requiring that all values be abstracted prior to abstract interpretation.
High glucose alters the secretome of mechanically stimulated osteocyte‐like cells affecting osteoclast precursor recruitment and differentiation

Diabetes mellitus (DM) induces bone deterioration, while mechanical stimulation promotes osteocyte‐driven bone formation. We aimed to evaluate the interaction of acute exposure (24 h) to high glucose (HG) with both the pro‐survival effect conferred to osteocytic MLO‐Y4 cells and osteoblastic MC3T3‐E1 cells by mechanical stimulation and the interaction of these cells with osteoclast precursor RAW264.7 cells. We found that 24 h of HG (25 mM) pre‐exposure prevented both cell survival and ERK and β‐catenin nuclear translocation upon mechanical stimulation by fluid flow (FF) (10 min) in both MLO‐Y4 and MC3T3‐E1 cells. However, migration of RAW 264.7 cells was inhibited by MLO‐Y4 cell‐conditioned medium (CM), but not by MC3T3‐E1 cell‐CM, with HG or FF. This inhibitory effect was associated with consistent changes in VEGF, RANTES, MIP‐1α, MIP‐1β MCP‐1, and GM‐CSF in MLO‐Y4 cell‐CM. RAW264.7 proliferation was inhibited by MLO‐Y4 CM under static or HG conditions, but it increased by FF‐CM with or without HG. In addition, both FF and HG abrogated the capacity of RAW 264.7 cells to differentiate into osteoclasts, but in a different manner. Thus, HG‐CM in static condition allowed formation of osteoclast‐like cells, which were unable to resorb hydroxyapatite. In contrast, FF‐CM prevented osteoclastogenesis even in HG condition. Moreover, HG did not affect basal RANKL or IL‐6 secretion or their inhibition induced by FF in MLO‐Y4 cells. In conclusion, this in vitro study demonstrates that HG exerts disparate effects on osteocyte mechanotransduction, and provides a novel mechanism by which DM disturbs skeletal metabolism through altered osteocyte‐osteoclast communication.
Immune Escape of Human Papillomavirus Type 16 in A Major Role for the Minor Capsid Protein

High-risk human papillomavirus (HPV) infection of the cervical epithelium is causally linked with the generation of cervical cancer. HPV does not activate Langerhans cells (LC), the APC at the site of infection, leading to immune evasion. The HPV protein responsible for inducing this immune escape has not been determined. We demonstrate that LC exposed to the minor capsid protein L2 in HPV16L1L2 virus-like particles do not phenotypically or functionally mature. However, HPV16L1 virus-like particles signiﬁcantly induce activation of LC. Our data suggest that the L2 protein plays a speciﬁc role in the induction of this immune escape of HPV16 through the manipulation of LC. This novel function is the ﬁrst immune modulating action attributed to the L2 protein and adds signiﬁcantly to our understanding of the mechanism of HPV immune escape. The Journal of Immunology, 2009, 183: 6151–6156.
Structural and Functional Determinants of γ-Secretase, an Intramembrane Protease Implicated in Alzheimer’s Disease

Alzheimer’s disease is the most common form of neurodegenerative diseases in humans, characterized by the progressive accumulation and aggregation of amyloid-β peptides (Aβ) in brain regions subserving memory and cognition. These 39-43 amino acids long peptides are generated by the sequential proteolytic cleavages of the amyloid-β precursor protein (APP) by β- and γ-secretases, with the latter being the founding member of a new class of intramembrane-cleaving proteases (I-CliPs) characterized by their intramembranous catalytic residues hydrolyzing the peptide bonds within the transmembrane regions of their respective substrates. These proteases include the S2P family of metalloproteases, the Rhomboid family of serine proteases, and two aspartyl proteases: the signal peptide peptidase (SPP) and γ-secretase. In sharp contrast to Rhomboid and SPP that function as a single component, γ-secretase is a multi-component protease with complex assembly, maturation and activation processes. Recently, two low-resolution three-dimensional structures of γ-secretase and three high-resolution structures of the GlpG rhomboid protease have been obtained almost simultaneously by different laboratories. Although these proteases are unrelated by sequence or evolution, they seem to share common functional and structural mechanisms explaining how they catalyze intramembrane proteolysis. Indeed, a water-containing chamber in the catalytic cores of both γ-secretase and GlpG rhomboid provides the hydrophilic environment required for proteolysis and a lateral gating mechanism controls substrate access to the active site. The studies that have identified and characterized the structural determinants critical for the assembly and activity of the γ-secretase complex are reviewed here.
Use of 16S Ribosomal DNA PCR and Denaturing Gradient Gel Electrophoresis for Analysis of the Microfloras of Healing and Nonhealing Chronic Venous Leg Ulcers

ABSTRACT The bacterial microfloras of 8 healing and 10 nonhealing chronic venous leg ulcers were compared by using a combination of cultural analysis and denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA gene products. Cultural analysis of the microflora revealed that the majority of both wound types carried the aerobes Staphylococcus and Pseudomonas spp. (89 and 80%, respectively). Sequencing of 16S ribosomal DNAs selected on the basis of DGGE profiling allowed the identification of strains not detected by cultural means. Of considerable interest was the finding that more than 40% of the sequences represented organisms not cultured from the wound from which they were amplified. DGGE profiles also revealed that all of the wounds possessed one apparently common band, identified by sequencing as Pseudomonas sp. The intensity of this PCR signal suggested that the bacterial load of nonhealing wounds was much higher for pseudomonads compared to healing wounds and that it may have been significantly underestimated by cultural analysis. Hence, the present study shows that DGGE could give valuable additional information about chronic wound microflora that is not apparent from cultural analysis alone.
1—THE EFFECT OF FIBRE AND PROCESSING VARIABLES ON YARN BULK AND RELATED PROPERTIES OF WOOL CARPETS

The various alternative parameters that may be manipulated by manufacturers to alter the bulk of wool carpet yarns and the consequent covering power of these yarns in carpets have been studied in processing trials carried out at WRONZ over a period of fifteen years. The main factors studied are differences in the bulk of the wools used, the processing route chosen and the yarn construction, and specialist bulking techniques. A prerequisite for this work was the development of reliable test methods for measuring the bulk of scoured wools, yarns, and carpets, and these methods are described along with definitions of the associated terminology. The work has produced not only a body of quantitative knowledge relating to this important aspect of wool-carpet manufacture but also a significant amount of additional information, which should be of value to those involved in the formulation of carpet-wool blends.
Aggression and personality: association with amino acids and monoamine metabolites

Synopsis Associations in 52 normal individuals were examined between plasma and cerebrospinal fluid (CSF) concentrations of tryptophan (Trp) and tyrosine, and concentrations of monoamine metabolites in the CSF, and scores on an aggression questionnaire, the Kinsey Institute Reaction List II, and the Eysenck Personality Questionnaire. There was a significantly positive correlation between CSF 5-hydroxyindoleacetic acid (5-HIAA) levels and extroverted aggression scores, and a significantly negative correlation between CSF 5-HIAA levels and introverted aggression scores. Males showed higher plasma Trp concentrations than females, and significantly positive correlations between plasma Trp concentrations and scores on extroverted aggression and the Eysenck E scale. Males, furthermore, showed a significantly negative correlation between CSF Trp levels and scores on the Eysenck P scale, and a significantly positive correlation between concentration of 3-methoxy-4-hydroxy-phenylglycol in CSF and scores on moral aggression. These results suggest that central serotonin influences aggression in normal individuals through effects on personality.
Liquid water absorption in uncoated Norway spruce (Picea abies) claddings as affected by origin and wood properties

Abstract Uncoated Norway spruce specimens from different spatial positions within stems from two origins with different growth conditions were exposed to liquid water over a prolonged time, and apparent diffusion coefficients and rates of void filling were calculated from sorption curves. Both apparent diffusion and rate of void filling were significantly affected by origin and by the difference between inner and outer boards. The differences between inner and outer boards were explained by heartwood proportion and density, but some effects of origin remained when these properties were accounted for. The apparent diffusion coefficient was reduced by increasing density, and increased by increasing heartwood proportion. Void filling rate was reduced by both increasing density and increasing heartwood proportion. Since the effect of heartwood proportion was more pronounced in the material from the highly productive area, it may have been confounded with properties of juvenile wood.
Mitochondrial diversity within modern human populations

With the recent increase in the available number of high-quality, full-length mitochondrial sequences, it is now possible to construct and analyze a comprehensive human mitochondrial consensus sequence. Using a data set of 827 carefully selected sequences, it is shown that modern humans contain extremely low levels of divergence from the mitochondrial consensus sequence, differing by a mere 21.6 nt sites on average. Fully 84.1% of the mitochondrial genome was found to be invariant and ‘private’ mutations accounted for 43.8% of the variable sites. Ninety eight percent of the variant sites had a primary nucleotide with an allele frequency of 0.90 or greater. Interestingly, the few truly ambiguous nucleotide sites could all be reliably assigned to either a purine or pyrimidine ancestral state. A comparison of this consensus sequence to several ancestral sequences derived from phylogenetic studies reveals a great deal of similarity, where, as expected, the most phylogenetically informative nucleotides in the ancestral studies tended to be the most variable nucleotides in the consensus. Allowing for this fact, the consensus approach provides variation data on the positions that do not contribute to phylogenetic reconstructions, and these data provide a baseline for measuring human mitochondrial variation in populations worldwide.
Redefining treatment failure for pediatric acute leukemia in the era of minimal residual disease testing

ABSTRACT Technologies for the detection of minimal residual disease (MRD) in leukemia and our understanding of the prognostic implications of MRD at different phases of treatment have significantly improved over the past decade. As a result, definitions of treatment failure based on bone marrow morphology by light microscopy are becoming increasingly inadequate for clinical care and trial design. In addition, novel therapies that may have increased efficacy and decreased toxicity in the setting of MRD compared to overt disease are changing clinical practice and challenging investigators to redefine treatment failure, the role of disease surveillance in remission, and clinical trial eligibility in the era of MRD.
Ciliary neurotrophic factor induces cholinergic differentiation of rat sympathetic neurons in culture

Ciliary neurotrophic factor (CNTF) influences the levels of choline acetyltransferase (ChAT) and tyrosine hydroxylase (TH) in cultures of dissociated sympathetic neurons from newborn rats. In the presence of CNTF both the total and specific activity of ChAT was increased 7 d after culture by 15- and 18-fold, respectively, as compared to cultures kept in the absence of CNTF. Between 3 and 21 d in culture in the presence of CNTF the total ChAT activity increased by a factor of greater than 100. Immunotitration demonstrated that the elevated ChAT levels were due to an increased number of enzyme molecules. In contrast to the increase in ChAT levels, the total and specific activity levels of TH were decreased by 42 and 36%, respectively, after 7 d in culture. Half-maximal effects for both ChAT increase and TH decrease were obtained at CNTF concentrations of approximately 0.6 ng and maximal levels were reached at 1 ng of CNTF per milliliter of medium. The effect of CNTF on TH and ChAT levels were seen in serum-containing medium as well as in serum-free medium. CNTF was shown to have only a small effect on the long-term survival of rat sympathetic neurons. We therefore concluded that the effects of CNTF on ChAT and TH are not due to selective survival of cells that acquire cholinergic traits in vitro, but are rather due to the induction of cholinergic differentiation of noradrenergic sympathetic neurons.
The role of intermediate vesicles in the adsorptive endocytosis and transport of ligand to lysosomes by human fibroblasts

Recent work from several laboratories has suggested the participation of intermediate structures in the delivery of adsorbed ligands from the plasma membrane to lysosomes. This report presents subcellular fractionation studies bearing on the role of these structures in adsorptive pinocytosis of epidermal growth factor (EGF), beta- hexosaminidase, and low density lipoprotein (LDL) by human fibroblasts. Using a two-step Percoll density gradient fractionation, we identified newly internalized (5 min) EGF in two intermediate density structures that are essentially negative for plasma membrane marker, and more bouyant than secondary lysosomes. Continued incubation for 20 min resulted in transfer to (or conversion to) vesicles sedimenting with secondary lysosomes. Internalized beta-hexosaminidase and LDL behaved similarly, appearing first in structures of intermediate density, and later appearing in association with secondary lysosomes. Two drugs, NH4Cl and monensin, were found to inhibit ligand transfer to the secondary lysosome peak, although they did not inhibit entry of bound ligands into intermediate density structures. Upon removal of both inhibitors, internalized ligands were quickly transferred to the secondary lysosome peak. This "transfer process" was faster for EGF, than for the other two ligands studied. We interpret these data to indicate that the endocytosis of these three ligands, and their delivery to lysosomes in fibroblasts, proceeds through a common pathway, involving intermediate nonlysosomal structures.
HUMAN CYTOCHROME P450 2S1: LACK OF ACTIVITY IN THE METABOLIC ACTIVATION OF SEVERAL CIGARETTE SMOKE CARCINOGENS AND IN THE METABOLISM OF NICOTINE

Cytochrome P450 (P450) enzymes play a critical role in the metabolic activation of a wide variety of environmental carcinogens. Recently, a novel human P450 enzyme, CYP2S1, has been identified. It is inducible by dioxin and other classical aryl hydrocarbon receptor ligands. However, little is known regarding the substrates and the functional role of CYP2S1. Since CYP2S1 is predominantly expressed in human lung and trachea, it is reasonable to speculate that CYP2S1 may play an important role in metabolizing the environmental chemicals to which human respiratory tissues are exposed. In the present study, we examined the activity of human CYP2S1 in the metabolism of nicotine and in the activation of three potent carcinogens in cigarette smoke, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK), benzo[a]pyrene (BaP), and 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP). The full-length CYP2S1 cDNA was amplified by nested polymerase chain reaction from a human lung cDNA library and was expressed in both Chinese hamster ovary (CHO) cells and Sf9 insect cells. In contrast to the positive controls, i.e., CHO cells expressing human CYP2A13 (for NNK activation) or human CYP1A1 (for BaP activation), there was no increase in NNK- or BaP-induced toxicity in the CHO cells expressing CYP2S1. The heterologously expressed CYP2S1 proteins showed no detectable activity in metabolizing nicotine and PhIP. These results clearly demonstrate that CYP2S1 does not catalyze the metabolism of nicotine and the metabolic activation of these lung carcinogens.
Theobromine Inhibits Uric Acid Crystallization. A Potential Application in the Treatment of Uric Acid Nephrolithiasis

Purpose To assess the capacity of methylxanthines (caffeine, theophylline, theobromine and paraxanthine) to inhibit uric acid crystallization, and to evaluate their potential application in the treatment of uric acid nephrolithiasis. Materials and Methods The ability of methylxathines to inhibit uric acid nucleation was assayed turbidimetrically. Crystal morphology and its modification due to the effect of theobromine were evaluated by scanning electron microscopy (SEM). The ability of theobromine to inhibit uric acid crystal growth on calculi fragments resulting from extracorporeal shock wave lithotripsy (ESWL) was evaluated using a flow system. Results The turbidimetric assay showed that among the studied methylxanthines, theobromine could markedly inhibit uric acid nucleation. SEM images showed that the presence of theobromine resulted in thinner uric acid crystals. Furthermore, in a flow system theobromine blocked the regrowth of post-ESWL uric acid calculi fragments. Conclusions Theobromine, a natural dimethylxanthine present in high amounts in cocoa, acts as an inhibitor of nucleation and crystal growth of uric acid. Therefore, theobromine may be clinically useful in the treatment of uric acid nephrolithiasis.
The chemokine SLC is expressed in T cell areas of lymph nodes and mucosal lymphoid tissues and attracts activated T cells via CCR7

Secondary lymphoid‐tissue chemokine, SLC, also known as exodus‐2 and 6Ckine, is a novel CC chemokine with selectivity for T lymphocytes and preferential expression in lymphoid tissues. We have studied its production, receptor usage and biological activities. High levels of SLC mRNA were detected in lymph nodes, the gastrointestinal tract and several gland tissues, but no expression was found by Northern blot analysis in freshly isolated or stimulated blood monocytes and lymphocytes, or neutrophils and eosinophils. In situ hybridization revealed constitutive expression of SLC in the T cell areas and the marginal zone of follicles in lymph nodes and the mucosa‐associated lymphoid tissue, but not in B cell areas or sinuses. Comparison with immunocytochemical staining showed similarity between the in situ expression of SLC and the distribution of interdigitating dendritic cells but not with sinus‐lining dendritic cells, macrophages or T lymphocytes. SLC induced chemotaxis of T lymphocytes and its activity increased considerably when the cells were conditioned with IL‐2 or phytohemagglutinin (PHA). Under optimal conditions SLC had unusually high efficacy and induced the migration of up to 50 % of input T lymphocytes. SLC also induced Ca2+ mobilization in these cells. Similar responses were obtained with EBI1 ligand chemokine (ELC), and sequential stimulation with both chemokines led to cross‐desensitization, suggesting that SLC acts via the ELC receptor, CCR7. This was confirmed using murine pre‐B cells stably transfected with CCR7 which bound SLC with high affinity and showed chemotaxis and Ca2+ mobilization in response to both SLC and ELC. In T lymphocytes PHA and IL‐2, which enhanced chemotactic responsiveness, also markedly enhanced CCR7 expression. In contrast to all known chemokine receptors, up‐regulation of CCR7 by IL‐2 was transient. A maximum was reached in 2 – 3 days and expression returned to initial levels within 8 – 10 days. The present study shows that SLC is constitutively produced within the T cell areas of secondary lymphoid organs and attracts T lymphocytes via CCR7.
Culture and CEO Compensation

The theory and research on chief executive officer (CEO) compensation tends to be dominated by assumptions and values reflective of those dominant in the national culture of the United States, where most of this work is done. This suggests that an underlying theme focuses on how CEO compensation is related to instrumental choices made in a competitive, capitalist culture. This study seeks to expand the understanding of CEO compensation by examining it in the context of other cultures, based on the premise that national culture plays a significant part in the nature of compensation strategies.We relate cultural dimensions (uncertainty avoidance, power distance, individualism, and masculinity-femininity) developed by Hofstede (Hofstede 1980a, 2001) to several dimensions of CEO compensation. These dimensions are total CEO pay, the proportion of variable pay to total compensation, and the ratio of CEO pay to the lowest level employees. The main findings of our paper are (1) all of the different dimensions of CEO pay were related to power distance, leading us to infer that CEO pay in a culture is most reflective of the strength of the power structure in a society, and (2) total compensation and the ratio of variable pay to total pay are related to individualism.We conclude that cultural dimensions can contribute to understanding cross-national CEO compensation. The implication of this conclusion is that there are different ways that CEO compensation fits into the cognitive schema of various cultures and, furthermore, that these cognitive schema vary across societies that affect the nature of the "cultural matrix into which [money] is incorporated" (Bloch and Parry 1989, p. 1). Moreover, our results imply that particular forms of CEO compensation do not mean the same thing in different cultures, but rather carry different symbolic connotations depending on the values dominant in a society. Thus, not only does the compensation structure of a firm within a culture have a symbolic meaning within organizations (e.g., Trice and Beyer 1993), but it can also be seen as an expression of deeper social values (Hofstede et al. 1990) that may differ across countries.