Miracle-dz/UniFAR-FTUs huggingface dataset:
Contributions of the N- and C-Terminal Domains of Surfactant Protein D to the Binding, Aggregation, and Phagocytic Uptake of Bacteria

ABSTRACT Collectins play important roles in host defense against infectious microorganisms. We now demonstrate that the serum collectins mannose-binding lectin (MBL) and conglutinin have less ability to bind to, aggregate, and enhance neutrophil uptake of several strains of gram-negative and gram-positive bacteria than pulmonary surfactant protein D (SP-D). Collectins are composed of four major structural domains (i.e., N-terminal, collagen, and neck and carbohydrate recognition domains). To determine which domains of SP-D are responsible for its greater bacterial binding or aggregating activity, activities of chimeric collectins containing the N-terminal and collagen domains of SP-D coupled to the neck recognition domains and carbohydrate recognition domains (CRD) of MBL or conglutinin (SP-D/Congneck+CRD and SP-D/MBLneck+CRD) were tested. The SP-D/Congneck+CRD and SP-D/MBLneck+CRD chimeras bound to and aggregated the bacteria more strongly than did wild-type MBL or conglutinin. SP-D/MBLneck+CRD also enhanced neutrophil uptake of bacteria more so than MBL. Hence, the SP-D N-terminal and/or collagen domains contribute to the enhanced bacterial binding and aggregating activities of SP-D. In prior studies, SP-D/Congneck+CRD and SP-D/MBLneck+CRD had increased ability to bind to influenza virus compared not only with that of conglutinin or MBL but with that of wild-type SP-D as well. In contrast, the chimeras had either reduced or unchanged ability to bind to or aggregate bacteria compared to that of wild-type SP-D. Hence, although replacement of the neck recognition domains and CRDs of SP-D with those of MBL and conglutinin conferred increased viral binding activity, it did not favorably affect bacterial binding activity, suggesting that requirements for optimal collectin binding to influenza virus and bacteria differ.
Verapamil, a Ca2+ Entry Blocker, Targets the Pore-Forming Subunit of Cardiac Type KATP Channel (Kir6.2)

This study investigated the mechanism by which verapamil, which blocks 10R1, l-type Ca2+ channel and the HERG channel, blocks ATP-sensitive K+ (KATP) channels. In whole cell patch experiments, verapamil reversibly inhibited cardiac type KATP (Kir6.2/SUR2A) channels previously activated by 100-&mgr;mol/L pinacidil. In inside-out patch experiments, verapamil inhibited the C-terminal truncated form of Kir6.2 (Kir6.2&Dgr;C36) in a concentration-dependent manner; half-maximal inhibition (IC50) was obtained at 11.5 ± 2.8 &mgr;mol/L when Kir6.2&Dgr;C36 was expressed without SUR2A. Verapamil also inhibited Kir6.2/SUR2A with a similar potency; IC50 was 8.9 ± 2.1 &mgr;mol/L for Kir6.2/SUR2A (not statistically different from the value for Kir6.2&Dgr;C36 alone). Thus, verapamil appeared to target the pore-forming subunit Kir6.2 rather than SUR2A, a member of ABC superfamily. Verapamil did not decrease the single-channel conductance, but increased the closed time of Kir6.2/SUR2A. The mutations of Kir6.2&Dgr;C36 (Kir6.2&Dgr;C36-R50G, -K185Q, -G334D), which have much lower ATP sensitivity, had no significant effect on verapamil block, suggesting that the site at which verapamil mediates KATP channel inhibition is not identical with that involved in ATP block.
Molecular Cloning and Transcript Expression of Genes Encoding Two Types of Lipoprotein Lipase in the Ovary of Cutthroat Trout, Oncorhynchus clarki

Large amounts of neutral lipids (NLs) are stored as lipid droplets in the ooplasm of fish oocytes, providing an essential energy resource for developing embryos and larvae. However, little is known about the origin of such lipids or about mechanisms underlying their uptake and accumulation in oocytes. We have proposed a model for this lipidation of teleost oocytes, as follows: very low density lipoprotein (Vldl) is metabolized by lipoprotein lipase (Lpl) outside and/or inside of the oocyte and the resulting fatty acids (FAs) are then utilized for de novo biosynthesis of NLs. As a first step toward verification of this model, cDNAs for genes encoding two types of Lpl, lpl and lpl2, were cloned from the ovary of cutthroat trout, Oncorhynchus clarki. Examination of Lpl polypeptide sequences deduced from the cDNAs revealed features similar to LPLs/Lpls in other species, including several conserved structural and functional domains. Both types of lpl mRNA were highly expressed in lipid storage tissues (e.g., adipose tissue, muscle, and ovary) and were predominantly expressed in the granulosa cells of ovarian follicles. Ovarian lpl1 mRNA levels showed a remarkable peak in April (early oocyte lipid droplet stage) and then decreased to low values sustained until November (mid-vitellogenesis), after which time a small peak in lpl1 gene expression was observed in December (late vitellogenesis). The mRNA levels of lpl2 also were elevated in April and were highest in June (late lipid droplet stage), but did not show other pronounced changes. These results suggest that, in the cutthroat trout, Vldl is metabolized by the action of Lpls in the granulosa cell layer to generate free FAs for uptake and biosynthesis of neutral lipids by growing oocytes.
CcpA-Independent Regulation of Expression of the Mg2+-Citrate Transporter Gene citM by Arginine Metabolism in Bacillus subtilis

ABSTRACT Transcriptional regulation of the Mg2+-citrate transporter, CitM, the main citrate uptake system of Bacillus subtilis, was studied during growth in rich medium. Citrate in the growth medium was required for induction under all growth conditions. In Luria-Bertani medium containing citrate, citM expression was completely repressed during the exponential growth phase, marginally expressed in the transition phase, and highly expressed in the stationary growth phase. The repression was relieved when the cells were grown in spent Luria-Bertani medium. The addition of a mixture of 18 amino acids restored repression. l-Arginine in the mixture appeared to be solely responsible for the repression, and ornithine appeared to be an equally potent repressor of citM expression. Studies of mutant strains deficient in RocR and SigL, proteins required for the expression of the enzymes of the arginase pathway, confirmed that uptake into the cell and, most likely, conversion of arginine to ornithine were required for repression. Arginine-mediated repression was independent of a functional CcpA, the global regulator protein in carbon catabolite repression (CCR). Nevertheless, CCR-mediated repression was the major mechanism controlling the expression during exponential growth, while the newly described, CcpA-independent arginine-mediated repression was specifically apparent during the transition phase of growth.
Confocal microscopy of the mitochondrial permeability transition in necrotic cell killing, apoptosis and autophagy

Onset of the cyclosporin‐A‐sensitive mitochondrial permeability transition (MPT) in individual mitochondria within living cells can be visualized by laser scanning confocal microscopy. The MPT is a causative event in many types of necrotic and apoptotic cell death, including oxidative stress, ischemia/reperfusion injury, Ca2+ ionophore toxicity and tumor necrosis factor alpha (TNFα) induced apoptosis, and may contribute to Reye's‐related drug toxicity. Pyridine nucleotide oxidation, mitochondrial generation of reactive oxygen species, and increased mitochondrial Ca2+ and pH can each promote onset of the MPT in situ. The MPT can also be directly visualized during TNFα‐induced apoptosis to hepatocytes. Mitochondria spontaneously depolarize in situ after nutrient deprivation before entering an acidic lysosomal compartment, suggesting that the MPT precedes the normal process of mitochondrial autophagy. We propose a model in which onset of the MPT to increasing numbers of mitochondria leads progressively to autophagy, apoptosis and necrotic cell death.
Regulation of L-asparaginase in a Chlamydomonas species in response to ambient concentrations of combined nitrogen

Cellular levels of an L-asparaginase in a Chlamydomonas species were found to be greater in nitrogen-limited batch cultures than in batch cultures grown in ample nitrogen. Cells grown in high nitrogen medium (5 mM NH4Cl) and suspended in nitrogen-free medium showed a 2- to 3.5-fold increase in activity after 24 to 48 h. This increase in activity was inhibited by cycloheximide and by the addition of high levels of combined nitrogen (5 mM NH4Cl, NaNO3, or L-asparagine), suggesting repression by ambient nitrogen levels as the mode of regulation of this enzyme. Derepressed L-asparaginase activity did not disappear in the presence of high concentrations of medium nitrogen, indicating the absence of an asparaginase-degrading system. Derepression of asparaginase by this organism was light dependent and inhibited by 3-(3',4'-dichlorophenyl)-1,1-dimethylurea suggesting a requirement for photosynthetic energy.
A novel SVR parameter selection base on bi-level programming problem

The selection of parameters plays an important role to the performance of support vector regression (SVR). In this paper, a novel parameter selection method for SVR is presented based on the bi-level programming problem. The proposed method does not need priori knowledge the value of the parameter ε. At the same time, the parameter ε can be calculated by the new SVR. And the number of the support vector will be controlled by the parameter C, even if the value of the parameter C is too big, the regression function still adapts to real function. And then, the complexity doesn't increase. Experimental results show that the better performance could be obtained by using the new SVR than the standard SVR.
Time trends, ethnicity and risk factors for eczema in New Zealand children: ISAAC Phase Three

Background Eczema is a common chronic disease which has significant morbidity and costs for children and their families. Phase One (1993) of the International Study of Asthma and Allergies in Childhood (ISAAC) found a high prevalence of symptoms of eczema in New Zealand. Objective In Phase Three (2001-3) we aimed to answer these three questions: Is the prevalence of eczema changing over time? ; Are there ethnic differences in prevalence? ; and What are the risk factors for eczema? Methods Five New Zealand centres participated in ISAAC Phases One and Three using the same methodology. Questionnaires about ethnicity, symptoms of eczema and environmental factors were completed by parents of 6-7 year olds (children) and self-completed by 13-14 year olds (adolescents). Prevalence and change per year were calculated by centre, ethnicity and gender. Prevalence differences between centres and associations with environmental factors were examined using logistic regression. Results There was little change in prevalence over time for the children, and a decrease in prevalence for the adolescents. Prevalence was higher among Māori and even higher among Pacific participants than among European children. Positive associations with current eczema symptoms were found for both age groups for truck traffic in the street of residence, and current paracetamol consumption, and for children only, antibiotics or paracetamol in the 1st year of life. Inverse associations were found with residence in New Zealand less than 5 years, consumption of milk, seafood, and eggs, and presence of a dog in the home. Conclusion Eczema remains a significant problem, particularly for young Māori and Pacific New Zealanders in whom less recognition of eczema and poorer access to effective, sustained eczema management may be contributing factors. Reverse causation may explain all the environmental findings apart from truck traffic which is increasing in New Zealand.
The curious perspective : literary and pictorial wit in the seventeenth century

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Complete Genome Sequence of a Peste des Petits Ruminants Virus Recovered from an Alpine Goat during an Outbreak in Morocco in 2008

ABSTRACT Here, we announce the first complete genome sequence of a field isolate of a peste des petits ruminants virus (PPRV) from northern Africa. This isolate is derived from an Alpine goat that suffered from severe clinical disease during the 2008 outbreak in Morocco. The full genome sequence of this isolate clusters phylogenetically with the lineage IV isolates of PPRV, sharing high levels of sequence identity with other lineage IV isolates.
Genetic analysis of sequences in maltoporin that contribute to binding domains and pore structure

Maltoporin (LamB protein) is a maltodextrin transport protein in the outer membrane of Escherichia coli with binding sites for bacteriophage lambda and maltosaccharides. Binding of starch by bacteria was found to inhibit swarming of Escherichia coli in soft agar plates; the inhibition was dependent on the maltodextrin affinity of maltoporin. On the basis of this observation, chemotactic cell-sorting techniques were developed for the isolation and analysis of mutants with an altered starch-binding phenotype. Fifteen lamB mutations generated by hydroxylamine and linker mutagenesis, as well as spontaneous mutations, were analyzed. The effects of the mutations on starch and lambda-binding, as well as transport specificity, were assayed. Mutations that affect residues near 8 to 18, 74 to 82, and 118 to 121 were found to affect starch binding and maltodextrin-selective functions strongly, confirming and extending previous results with substitutions at these regions. Substitutions and insertions in two previously undefined regions in the protein, in or near residues 194 and 360, also resulted in defects in maltodextrin-specific functions and indicate that C-terminal parts of the protein also contribute to the discontinuous binding and pore domains. There was a detectable transport defect in all binding-affected mutants, and one mutation caused near-total pore blocking towards both maltose and nonmaltoside. The highly discontinuous phage lambda-binding site was affected by mutations near residues 9 and 10 and 194, as well as previously established regions near residues 18, 148 to 165, 245 to 259, and 380 to 400. The significance of these mutations is discussed in the context of a model of the functional topology of maltoporin. The additional role of regions near residues 10 and 120 in maltoporin assembly, as well as starch binding, was suggested by the temperature-sensitive biogenesis of maltoporin in strains with one- or two-codon insertion at these sites.
Investigation of the antigen recognition and presentation capacity of pecteneal hyalocytes in the chicken (gallus gallus domesticus)

We investigated at different developmental stages the antigen recognition and presentation capacity of pecteneal hyalocytes that adhere to the pecten oculi in the eye of domestic chickens. Forty-eight fertilized eggs were used to investigate embryonic stages and 12 6-week-old chickens were used to investigate adults. Tissue samples from both embryos and adults were stained with monoclonal antibodies against MHC-II, TLR2/CD282 and TLR4, and also with RCA-1, WGA and SNA lectins. The developmental stage of the pecteneal hyalocytes was determined using Masson's triple staining. Pecteneal hyalocytes first appeared at Hamburger-Hamilton stages 30 34 and remained unchanged from their first appearance to adulthood. Chicken pecteneal hyalocytes were stained by monoclonal antibodies against TLR2 and TLR4, and were unstained by monoclonal antibodies for MHC-II. Hyalocytes were positive for RCA-I, WGA and SNA lectins. We found that pecteneal hyalocytes that adhere to the pecten oculi in domestic chickens recognized antigens, but could not present them. These cells have been assumed to be of monocyte/macrophage lineage; their functions in the immune response are not fully understood.
Flexible clap and fling in tiny insect flight

SUMMARY Of the insects that have been filmed in flight, those that are 1 mm in length or less often clap their wings together at the end of each upstroke and fling them apart at the beginning of each downstroke. This `clap and fling' motion is thought to augment the lift forces generated during flight. What has not been highlighted in previous work is that very large forces are required to clap the wings together and to fling the wings apart at the low Reynolds numbers relevant to these tiny insects. In this paper, we use the immersed boundary method to simulate clap and fling in rigid and flexible wings. We find that the drag forces generated during fling with rigid wings can be up to 10 times larger than what would be produced without the effects of wing–wing interaction. As the horizontal components of the forces generated during the end of the upstroke and beginning of the downstroke cancel as a result of the motion of the two wings, these forces cannot be used to generate thrust. As a result, clap and fling appears to be rather inefficient for the smallest flying insects. We also add flexibility to the wings and find that the maximum drag force generated during the fling can be reduced by about 50%. In some instances, the net lift forces generated are also improved relative to the rigid wing case.
Analysis of the Implicit Euler Local Uniform Grid Refinement Method

Attention is focused on parabolic problems having solutions with sharp moving transitions in space and time. An adaptive grid method is analysed that refines the space grid locally around sharp spatial transitions, so as to avoid discretization on a very fine grid over the entire physical domain. This method is based on static-regridding and local uniform grid refinement. Static-regridding means that for evolving time the space grid is adapted at discrete times. Local uniform grid refinement means that the actual adaptation of the space grid takes place using nested locally and uniformly refined grids. The present paper concentrates on stability and error analysis while using the implicit Euler method for time integration. Maximum norm stability and convergence results are proved for a certain class of linear and nonlinear partial differential equations. The central issue is a refinement condition with a strategy that distributes spatial interpolation and discretization errors in such a way that the spati.
A flexible architecture for multi-standard LDPC decoders

Since Low-Density Parity-Check codes have near-capacity decoding performance and very high decoding throughput, they have been employed as FEC coding scheme in many transmission standards for wireless communication, such as IEEE 802.22n, IEEE 802.16e, DVB-S2, and DTMB. This trend triggers the need for so-called multi-standard LDPC decoders. In this paper, a flexible architecture that supports multiple code rates, variable block sizes and is code independent for block-LDPC codes is proposed, based on rearranged TPMP algorithm,. By implementing a dynamically reconfigurable RPPU, our proposed architecture can be configured into row update or column update mode by time-division multiplexing. Consequently, the decoder achieves a high area and power efficiency. To verify our proposed architecture, a novel LDPC decoder which supports IEEE802.16e standard has been implemented. The results on a 0.18 um CMOS process show that the decoder occupies an area of approximately 13.7 mm2 and runs correctly at an maximum operating frequency of 110 MHz, resulting in 98 Mbps decoding throughput1.
Preliminary investigation of the radiosensitizing activity of guduchi (Tinospora Cordifolia) in tumor‐bearing mice

The radiosensitizing activity of dichloromethane extract of guduchi [Tinospora cordifolia (WILLD.) MIERS ex HOOK. F. & THOMS. Family: Menispermaceae (TCE)] in the mice transplanted with Ehrlich ascites carcinoma (EAC) was investigated. The EAC mice received 0, 25, 30, 40, 50 or 100 mg/kg b.wt. TCE 1 h before exposure to 6 Gy hemi‐body γ‐radiation and then once daily for another eight consecutive days after irradiation.
Comparison of high-energy photon and electron dosimetry for various dosimetry protocols.

The American Association of Physicists in Medicine Task Group 51 (TG-51) and the International Atomic Energy Agency (IAEA) published a new high-energy photon and electron dosimetry protocol, in 1999 and 2000, respectively. These protocols are based on the use of an ion chamber having an absorbed-dose to water calibration factor with a 60Co beam. These are different from the predecessors, the TG-21 and IAEA TRS-277 protocols, which require a 60Co exposure or air-kerma calibration factor. The purpose of this work is to present the dose comparison between various dosimetry protocols and the AAPM TG-51 protocol for clinical reference dosimetry of high-energy photon and electron beams. The absorbed-dose to water calculated according to the Japanese Association of Radiological Physics (JARP), International Atomic Energy Agency Technical Report Series No. 277 (IAEA TRS-277) and No. 398 (IAEA TRS-398) protocols is compared to that calculated using the TG-51 protocol. For various Farmer-type chambers in photon beams, TG-51 is found to predict 0.6-2.1% higher dose than JARP. Similarly, TG-51 is found to be higher by 0.7-1.7% than TRS-277. For electron beams TG-51 is higher than JARP by 1.5-3.8% and TRS-277 by 0.2-1.9%. The reasons for these differences are presented in terms of the cavity-gas calibration factor, Ngas, and a dose conversion factor, Fw, which converts the absorbed-dose to air in the chamber to the absorbed-dose to water. The ratio of cavity-gas calibration factors based on absorbed-dose to water calibration factors, N60Co(D,w), in TG-51 and cavity-gas calibration factors which are equivalent to absorbed-dose to air chamber factors, N(D,air), based on the IAEA TRS-381 protocol is 1.008 on average. However, the estimated uncertainty of the ratio between the two cavity-gas calibration factors is 0.9% (1 s.d.) and consequently, the observed difference of 0.8% is not significant. The absorbed-dose to water and exposure or air-kerma calibration factors are based on standards traceable to the National Institute of Standards and Technology (NIST). In contrast, the absorbed-dose to water determined with TRS-398 is in good agreement with TG-51 within about 0.5% for photon and electron beams.
Robust predictive control design for automatic steering

This paper presents a feasibility study of the robust predictive control for the design of an automatic steering system. The involved vehicle is a full-scale nonlinear model of a BMW520i and the feedback is only on the lateral displacement. The robustness feature is particularly motivated by variations in velocity, tyre-road contact and vehicle mass. The control design is performed using a sensitivity function shaping procedure that heavily borrows from the robust control culture. Intensive simulations are carried out to emphasize the performance of the proposed automatic steering system.
Exploring Civic Engagement at an Urban Commuter Campus: Pathways and Barriers

Universities have traditionally had a vested interest in the civic preparation of students. In order to understand the unique situation of this population of students in a university serving non-traditional community students, qualitative data was used to identify pathways and barriers associated with their civic engagement. Results suggest themes associated with time, knowledge, and access.