Miracle-dz/UniFAR-FTUs huggingface dataset:
Intergalactic Photon Spectra from the Far-IR to the UV Lyman Limit for 0 < z < 6 and the Optical Depth of the Universe to High-Energy Gamma Rays

We calculate the intergalactic photon density as a function of both energy and redshift for 0 < z < 6 for photon energies from.003 eV to the Lyman limit cutoff at 13.6 eV in a ΛCDM universe with ΩΛ = 0.7 and Ωm = 0.3. The basic features of our backward-evolution model for galaxies were developed in earlier papers by Malkan & Stecker. With a few improvements, we find that this evolutionary model gives predictions of new deep number counts from Spitzer, as well as a calculation of the spectral energy distribution of the diffuse infrared background, which are in good agreement with the data. We then use our calculated intergalactic photon densities to extend previous work on the absorption of high-energy γ-rays in intergalactic space owing to interactions with low-energy photons and the 2.7 K cosmic microwave background radiation. We calculate the optical depth of the universe, τ, for γ-rays having energies from 4 GeV to 100 TeV emitted by sources at redshifts from 0 to 5. We also give an analytic fit with numerical coefficients for approximating τ(Eγ, z). As an example of the application of our results, we calculate the absorbed spectrum of the blazar PKS 2155-304 at z = 0.117 and compare it with the spectrum observed by the HESS air Cerenkov γ-ray telescope array.
[Evaluation of the antibiotic prescription in a paediatric intensive care unit].

UNLABELLED The antibiotic prescription in intensive care units is frequent using often broad-spectrum antibiotics; its quality has never been evaluated in paediatric intensive care units. OBJECTIVES To describe the modalities of antibiotic prescriptions in a paediatric intensive care unit and confront them to the literature guidelines and bacteriological data. METHODS From January 1st to March 31st 2005, 52 consecutive prescriptions regarding 45 children, with a total of 47 hospitalisations were prospectively analysed. RESULTS Confirmed diagnosis of bacterial infection was retained for 50 of the 52 patients: community acquired infection in 35 cases (70%) and a nosocomial infection in 15 cases. Ten children died during the antibiotic treatment (22%), with 5 deaths related to the infection (11%). Monotherapy represented 56% of the prescriptions of antibiotics. The initial antibiotic treatment was empirical in 42 of 52 cases (81%). The empirical prescriptions were documented afterward in 48% of cases. One or more microorganisms were isolated for 60% of the initial prescriptions. Misuses in antibiotic doses (in excess [10%] or by insufficiency [13%]), number of daily administration (4%), and way of administration and/or length of treatment were observed. Seventy-seven percent of the initial prescriptions seemed to be adapted to the identified or suspected bacteria, but only 63% adequate to recommendations. CONCLUSION Almost 2/3rd of the antibiotic prescriptions were adequate to the recommendations. The implementation of standardized and specific protocols should contribute to improve the quality of these prescriptions.
Rurality and Criminal History as Predictors of HIV Risk Among Drug-Involved Offenders

The current study examined rurality and criminality as predictors of the lifetime HIV risk behaviors of 661 male, drug-abusing state prisoners. HIV risk behaviors included the number of lifetime sex partners, the number of lifetime drug injections, the number of times had sex with an injection drug user, and the frequency with which a condom was used. Regression analyses showed that criminality was related to the number of lifetime injections, whereas rurality was related to fewer lifetime sex partners and less frequent condom use. A rurality by criminality interaction for sex with an injection drug user was found. Specifically, those from rural areas who had more extensive criminal histories reported relatively high numbers of sex partners who were IDUs. Results are discussed in the context of rural and criminal justice interventions for HIV risk behavior.
Phosphorylation Dependence of Hsp27 Multimeric Size and Molecular Chaperone Function*

The molecular chaperone Hsp27 exists as a distribution of large oligomers that are disassembled by phosphorylation at Ser-15, -78, and -82. It is controversial whether the unphosphorylated Hsp27 or the widely used triple Ser-to-Asp phospho-mimic mutant is the more active molecular chaperone in vitro. This question was investigated here by correlating chaperone activity, as measured by the aggregation of reduced insulin or α-lactalbumin, with Hsp27 self-association as monitored by analytical ultracentrifugation. Furthermore, because the phospho-mimic is generally assumed to reproduce the phosphorylated molecule, the size and chaperone activity of phosphorylated Hsp27 were compared with that of the phospho-mimic. Hsp27 was triply phosphorylated by MAPKAP-2 kinase, and phosphorylation was tracked by urea-PAGE. An increasing degree of suppression of insulin or α-lactalbumin aggregation correlated with a decreasing Hsp27 self-association, which was the least for phosphorylated Hsp27 followed by the mimic followed by the unphosphorylated protein. It was also found that Hsp27 added to pre-aggregated insulin did not reverse aggregation but did inhibit these aggregates from assembling into even larger aggregates. This chaperone activity appears to be independent of Hsp27 phosphorylation. In conclusion, the most active chaperone of insulin and α-lactalbumin was the Hsp27 (elongated) dimer, the smallest Hsp27 subunit observed under physiological conditions. Next, the Hsp27 phospho-mimic is only a partial mimic of phosphorylated Hsp27, both in self-association and in chaperone function. Finally, the efficient inhibition of insulin aggregation by Hsp27 dimer led to the proposal of two models for this chaperone activity.
Cak1 Is Required for Kin28 Phosphorylation and Activation In Vivo

ABSTRACT Complete activation of most cyclin-dependent protein kinases (CDKs) requires phosphorylation by the CDK-activating kinase (CAK). In the budding yeast, Saccharomyces cerevisiae, the major CAK is a 44-kDa protein kinase known as Cak1. Cak1 is required for the phosphorylation and activation of Cdc28, a major CDK involved in cell cycle control. We addressed the possibility that Cak1 is also required for the activation of other yeast CDKs, such as Kin28, Pho85, and Srb10. We generated three new temperature-sensitive cak1mutant strains, which arrested at the restrictive temperature with nonuniform budding morphology. All three cak1 mutants displayed significant synthetic interactions with loss-of-function mutations in CDC28 and KIN28. Loss of Cak1 function reduced the phosphorylation and activity of both Cdc28 and Kin28 but did not affect the activity of Pho85 or Srb10. In the presence of the Kin28 regulatory subunits Ccl1 and Tfb3, Kin28 was phosphorylated and activated when coexpressed with Cak1 in insect cells. We conclude that Cak1 is required for the activating phosphorylation of Kin28 as well as that of Cdc28.
Structure of a new nervous system glycoprotein, Nr-CAM, and its relationship to subgroups of neural cell adhesion molecules

We have identified and characterized a new glycoprotein in the chicken nervous system using immunological and molecular biological methods and we have examined its tissue distribution. Analysis revealed that this protein is very similar in structure to the chicken neuron-glia cell adhesion molecule, Ng-CAM, and to mouse L1. cDNA clones encompassing the entire coding sequence of this Ng-CAM related molecule, called Nr- CAM, have been isolated and sequenced. A glycoprotein containing one major component of Mr 145,000 on SDS-PAGE was purified from brain by lentil lectin affinity chromatography and FPLC, and its amino-terminal sequence was identical to that predicted from the Nr-CAM cDNA. The complete cDNA sequence encodes six Ig-like domains, five fibronectin type III repeats, a predicted transmembrane domain, and a short cytoplasmic domain. On Northern blots, nucleic acid probes for Nr-CAM recognized one major RNA species of approximately 7 kb and much lesser amounts of larger RNAs. Most of the same probes hybridized to single bands on genomic Southern blots, suggesting that Nr-CAM is encoded by a single gene that may be alternatively processed to yield several mRNAs. In support of this notion, two Nr-CAM cDNA clones had a 57-bp sequence located between the second and third Ig-like domains that was not found in two other Nr-CAM cDNA clones, and two other clones were isolated that lacked the 279-bp segment encoding the fifth fibronectin-like type III repeat. Antibodies against the purified protein and synthetic peptides in Nr-CAM both recognized a predominant Mr 145,000 species and a much less prevalent species of Mr 170,000 in neural tissues. Levels of Nr-CAM expression increased in the brain until approximately embryonic day (E) 12, followed by slightly lower levels of expression at E18 and after hatching. Immunofluorescent staining with anti-Nr-CAM antibodies showed that most neurons in the retina were positive at E7 and the pattern of expression became restricted to several layers on neuronal cell bodies and fibers during development. Anti-Nr-CAM antibodies labeled specifically cell surfaces on neurons in culture. Although the structure of Nr-CAM resembles that of chicken Ng-CAM and mouse L1, the identity with each of these neural CAMs does not exceed 40%. The differences indicate that Nr-CAM is distinct from Ng-CAM and L1, but there are sufficient similarities to suggest that all of these molecules are members of a subgroup of neural CAMs in the N-CAM superfamily. (ABSTRACT TRUNCATED AT 400 WORDS)
Combined Src and Aromatase Inhibition Impairs Human Breast Cancer Growth In vivo and Bypass Pathways Are Activated in AZD0530-Resistant Tumors

Purpose: Antiestrogens are used to treat estrogen receptor (ER)-α-positive breast cancers and cause a p27-dependent G1 arrest. Estrogen-bound ER recruits Src to mediate proteolysis of p27 and drive cell proliferation. Here, we tested the antitumor efficacy of combined Src and aromatase inhibition for ER-positive breast cancer. Experimental Design: Antiproliferative effects of the aromatase inhibitor, anastrozole, and Src inhibitor, AZD0530, alone or in combination were tested in vitro and in vivo on aromatase-transfected MCF-7Arom5 xenografts. Xenografts were analyzed by immunohistochemistry and proteomic analysis to identify potential biomarkers of drug response and resistance. Results: AZD0530 and anastrozole together increased p27 and caused greater G1 cell cycle arrest than either drug alone. AZD0530 monotherapy initially retarded xenograft growth in vivo, but drug resistance rapidly emerged. Combined anastrozole/AZD0530 reduced drug resistance and showed greater antitumor efficacy in vivo with greater Src and epidermal growth factor receptor inhibition and a greater increase in p27 and reduction of Ki-67 than either drug alone, supporting further evaluation of these putative predictors of response to combined Src/aromatase inhibition in vivo. Anastrozole alone stimulated Src activity both in vitro and in vivo. AZD0530-resistant tumors showed activation of bypass pathways including MEK and phosphatidylinositol 3-kinase (PI3K)/Akt/mammalian target of rapamycin, raising the possibility that MEK, mammalian target of rapamycin (mTOR), or PI3K inhibitors may augment Src inhibitor efficacy. Conclusions: These data support clinical investigation of anastrozole-AZD0530 therapy for postmenopausal ER-positive breast cancer. Loss of p27 and increased Ki-67 may predict response and further clinical studies should evaluate for activation of bypass pathways including MEK and PI3K pathways during Src inhibitor therapy.
Dissolved Concentrations, Sources, and Risk Evaluation of Selected Metals in Surface Water from Mangla Lake, Pakistan

The present study is carried out for the assessment of water quality parameters and selected metals levels in surface water from Mangla Lake, Pakistan. The metal levels (Ca, Cd, Co, Cr, Cu, Fe, K, Li, Mg, Mn, Na, Ni, Pb, Sr, and Zn) were determined by flame atomic absorption spectrophotometry. Average levels of Cd, Co, Cr, Ni, and Pb were higher than the allowable concentrations set by national and international agencies. Principal component analysis indicated significant anthropogenic contributions of Cd, Co, Cr, Ni, and Pb in the water reservoir. Noncarcinogenic risk assessment was then evaluated using Hazard Quotient (HQing/derm) and Hazard Index (HIing/derm) following USEPA methodology. For adults and children, Cd, Co, Cr, and Pb (HQing > 1) emerged as the most important pollutants leading to noncarcinogenic concerns via ingestion route, whereas there was no risk via dermal contact of surface water. This study helps in establishing pollutant loading reduction goal and the total maximum daily loads, and consequently contributes to preserve public health and develop water conservation strategy.
highlighted topics Signal Transduction in Smooth Muscle Invited Review: Cross-bridge regulation by thin ﬁlament-associated proteins

Invited Review: Cross-bridge regulation by thin ﬁlament-associated proteins. J Appl Physiol 91: 953–962, 2001. —This minireview will cover current concepts on the identity and mechanistic function of smooth muscle actin binding proteins that may regulate actin-myosin interactions. The po- tential roles of tropomyosin, caldesmon, calponin, and SM22 will be discussed. The review, for purposes of brevity, will be nonexhaustive but will give an overview of available information on the in vitro biochemistry and potential in vivo function of these proteins. Preterm labor is discussed as a possible example of where thin ﬁlament regulation may be relevant. Considerable controversy surrounds the putative physiological signiﬁcance of these proteins, and emphasis will be placed on the need for more experimental work to determine the degree to which tissue- and species-speciﬁc effects have clouded the interpretation of functional data.
Interestingness of frequent itemsets using Bayesian networks as background knowledge

The paper presents a method for pruning frequent itemsets based on background knowledge represented by a Bayesian network. The interestingness of an itemset is defined as the absolute difference between its support estimated from data and from the Bayesian network. Efficient algorithms are presented for finding interestingness of a collection of frequent itemsets, and for finding all attribute sets with a given minimum interestingness. Practical usefulness of the algorithms and their efficiency have been verified experimentally.
Processing Abstract Language Modulates Motor System Activity

Embodiment theory proposes that neural systems for perception and action are also engaged during language comprehension. Previous neuroimaging and neurophysiological studies have only been able to demonstrate modulation of action systems during comprehension of concrete language. We provide neurophysiological evidence for modulation of motor system activity during the comprehension of both concrete and abstract language. In Experiment 1, when the described direction of object transfer or information transfer (e.g., away from the reader to another) matched the literal direction of a hand movement used to make a response, speed of responding was faster than when the two directions mismatched (an action–sentence compatibility effect). In Experiment 2, we used single-pulse transcranial magnetic stimulation to study changes in the corticospinal motor pathways to hand muscles while reading the same sentences. Relative to sentences that do not describe transfer, there is greater modulation of activity in the hand muscles when reading sentences describing transfer of both concrete objects and abstract information. These findings are discussed in relation to the human mirror neuron system.
Enhancing Source-Based Clone Detection Using Intermediate Representation

Detecting software clones in large scale projects helps improve the maintainability of large code bases. The source code representation (e.g., Java or C files) of a software system has traditionally been used for clone detection. In this paper, we propose a technique that transforms the source code to an intermediate representation, and then reuses established source-based clone detection techniques to detect clones in the intermediate representation. The clones are mapped back to the source code and are used to augment the results reported by source-based clone detection. We demonstrate the performance of our new technique using systems from the Bellon clone evaluation benchmark. The result shows that our technique can detect Type 3 clones. Our technique has higher recall with minimal drop in precision using Bellon corpus. By examining the complete clone groups, our technique has higher precision than the standalone string based and token based clone detectors.
Chapter 5 Into the Land of Adolescent Metacognitive Knowledge During the Information Search Process: A Metacognitive Ethnography

This chapter examines adolescent metacognitive knowledge in a fresh light and answers some methodological questions related to the investigation of the deepest layers of thinking during the information search. It does so by presenting a study that used an ethnographic approach to investigate the metacognitive knowledge of 10 adolescents, aged 16 to 18, over the course of four months, and in a variety of settings –– home, school, public libraries –– as they searched for, collected, and then used information for a school project. The study was framed by Flavel's model of metacognition (1977) and Kuhlthau's information search process (ISP) model, a six-stage, multidimensional model of information problem solving (1991, 2004). The chapter begins with a discussion about the ISP, metacognitive knowledge, and its potential for information seeking. The chapter then presents the findings of the study as a set of gaps and strengths of adolescent metacognitive knowledge, and concludes with commentary about the challenges and rewards related to conducting research with young people and suggestions for future areas of research.
MAL2 Selectively Regulates Polymeric IgA Receptor Delivery from the Golgi to the Plasma Membrane in WIF‐B Cells

Myelin and lymphocyte protein 2 (MAL2) has been identified as a hepatic transcytotic regulator that mediates delivery from basolateral endosomes to the subapical compartment (SAC). However, overexpression of polymeric immunoglobulin A‐receptor (pIgA‐R) in polarized, hepatic WIF‐B cells led to the dramatic redistribution of MAL2 into the Golgi and all the transcytotic intermediates occupied by the receptor. Although overexpressed hemagglutinin and dipeptidylpeptidase IV (DPPIV) distributed to the same compartments, MAL2 distributions did not change indicating the effect is selective. Cycloheximide treatment led to decreased pIgA‐R and MAL2 intracellular staining, first in the Golgi then the SAC, suggesting they were apically delivered and that MAL2 was mediating the process. This was tested in Clone 9 cells (that lack endogenous MAL2). When expressed alone, pIgA‐R was restricted to the Golgi whereas when coexpressed with MAL2, it distributed to the surface, was internalized and delivered to MAL2‐positive puncta. In contrast, DPPIV distributions were independent of MAL2. Surface delivery of newly synthesized pIgA‐R, but not DPPIV, was enhanced greater than ninefold by MAL2 coexpression. In WIF‐B cells where MAL2 expression was knocked down, pIgA‐R, but not DPPIV, was retained in the Golgi and its basolateral delivery was impaired. Thus, in addition to its role in transcytosis, MAL2 also regulates pIgA‐R delivery from the Golgi to the plasma membrane.
Acceleration of α-Synuclein Aggregation by Exosomes*

Background: Cell-to-cell transmission of α-syn via exosomes has been proposed to propagate Parkinson disease pathology. Results: Exosomes contain gangliosides, several other lipid classes, and proteins. Exosomes and ganglioside vesicles accelerate α-syn aggregation. Vesicles made of other membrane lipids do not. Conclusion: Exosomes provide catalytic environments for nucleation of α-syn aggregation. Significance: Revealing factors that promote α-syn aggregation may provide insight into Parkinson disease pathogenesis. Exosomes are small vesicles released from cells into extracellular space. We have isolated exosomes from neuroblastoma cells and investigated their influence on the aggregation of α-synuclein, a protein associated with Parkinson disease pathology. Using cryo-transmission electron microscopy of exosomes, we found spherical unilamellar vesicles with a significant protein content, and Western blot analysis revealed that they contain, as expected, the proteins Flotillin-1 and Alix. Using thioflavin T fluorescence to monitor aggregation kinetics, we found that exosomes catalyze the process in a similar manner as a low concentration of preformed α-synuclein fibrils. The exosomes reduce the lag time indicating that they provide catalytic environments for nucleation. The catalytic effects of exosomes derived from naive cells and cells that overexpress α-synuclein do not differ. Vesicles prepared from extracted exosome lipids accelerate aggregation, suggesting that the lipids in exosomes are sufficient for the catalytic effect to arise. Using mass spectrometry, we found several phospholipid classes in the exosomes, including phosphatidylcholine, phosphatidylserine, phosphatidylethanolamine, phosphatidylinositol, and the gangliosides GM2 and GM3. Within each class, several species with different acyl chains were identified. We then prepared vesicles from corresponding pure lipids or defined mixtures, most of which were found to retard α-synuclein aggregation. As a striking exception, vesicles containing ganglioside lipids GM1 or GM3 accelerate the process. Understanding how α-synuclein interacts with biological membranes to promote neurological disease might lead to the identification of novel therapeutic targets.
West Nile Virus–Associated Mortality Events in Domestic Chukar Partridges (Alectoris chukar) and Domestic Impeyan Pheasants (Lophophorus impeyanus)

Abstract West Nile virus (WNV) infection was diagnosed in captive juvenile chukars (Alectoris chukar), and captive juvenile Impeyan pheasants (Lophophorus impeyanus) on the basis of necropsy, histopathology, polymerase chain reaction, and immunohistochemistry. The chukars were kept in a game bird farm that experienced two outbreaks with approximately 25% mortality in hundreds of chukars between September and October 2002 and during the same months in 2003. The submitted pheasants were part of a group of 15 juvenile Impeyan pheasants that all died within approximately 2 wk at the end of August 2002. The macroscopic lesions in the pheasants were dominated by mucosal hemorrhage at the proventricular to ventricular junction and cecal ulcers, whereas the gross lesions in the chukar partridges were nonspecific. The predominant microscopic lesion in the chukar partridges was myocardial necrosis, whereas fibrinous and necrotizing splenitis was prominent in the pheasants. Viral antigen was usually widespread in animals of both species. Spontaneously occurring WNV infection should be considered a differential diagnosis in cases of mortality among select species of galliform birds.