bluuebunny/crossref_metadata_2025_split huggingface dataset:
Covalent immobilization of Drosophila acetylcholinesterase for biosensor applications
Authors: Barshan‐Tashnizi Mohammad , Ahmadian Shahin , Niknam Kaveh , Torabi Seyed‐Fakhreddin , Ranaei‐Siadat Seyed‐Omid 
Published: June 2008

The synthesized cDNA coding for AChE (acetylcholinesterase) was subcloned in pENTR™/D‐TOPO® plasmid and expressed using baculovirus expression vector and Sf9 insect cells as host. Purified enzyme (specific activity 36374 μmol·min−1·mg−1) was immobilized on pre‐activated perlite (a porous silica matrix) by silanization and glutaraldehyde treatment. The total enzyme immobilized was then measured, and total and specific activity of immobilized AChE was compared with that of soluble enzyme. Using this perlite support not only resulted in a great amount of maintained immobilized enzyme activity (more than 70%, specific activity 26238 μmol·min−1·mg−1), but also significantly improved stability against temperature (8.7‐ and 17.7‐fold at 50 and 60 °C respectively), urea (2.7‐fold) and acetonitrile (1.7‐fold). Kinetic studies showed that the Km value for immobilized enzyme is very similar to the soluble one (0.088 and 0.081 mM respectively). In addition, immobilized enzymes retained 80% of their initial activity after 16 consecutive reactor batch cycles. A comparison of the inhibitory effect of paraoxon on soluble and immobilized AChE showed that immobilization increased the linearity of the inhibition plot particularly in the range 0.1 nM–0.1 μM.
Oxford Journals' adventures in open access
Authors: BIRD Claire 
Published: June 2008

ABSTRACTIn 2004, Oxford Journals began experimenting with an ‘author‐side payment’ open access model for its flagship molecular biology journal, Nucleic Acids Research (NAR). Since then, around 70 of its approximately 200 journals have adopted an open access model of some kind, providing a unique perspective on the practicalities involved and the potential impact of open access on established academic journals. Under NAR's full open access model, submissions and author satisfaction remain encouragingly stable, and most NAR authors are paying the open access charges. NAR's income per article declined in 2005, but increased once more in 2007. The journal remains financially viable under the new model. Uptake of the optional ‘Oxford Open’ model varies by discipline. It is highest in the life sciences: in the region of 17–25% for some molecular and computational biology journals. It is too soon to tell whether the ‘Oxford Open’ model will have an impact on subscriptions, usage, and citations, but further research is under way.
Author perceptions of journal quality
Authors: REGAZZI John J. , AYTAC Selenay 
Published: June 2008

ABSTRACTOne of the most important issues facing scholarly communication today is what constitutes quality in the publishing and dissemination of research findings; the aim of this exploratory research study was to investigate author‐perceived quality characteristics of science, technology and medicine journals. We triangulated data from a small number of volunteer full‐time faculty members of Long Island University, using three different research techniques: (1) questionnaire survey, (2) focus groups, and (3) semi‐structured face‐to‐face interviews. The study identified some significant differences by discipline, gender, and tenure status. Overall, the three most important attributes were the reputation of the journal, the estimated length of time to article publication, and the readership of the journal. Our findings bring new insight into this area for the scholarly research community as a whole.
Giving new life to out‐of‐print books: when publishers' and libraries' interests meet
Authors: VANDOOREN Françoise , GASS Cécile 
Published: June 2008

ABSTRACTThe Library of the Université Libre de Bruxelles and Editions de l'Université de Bruxelles (EUB), the University's publishing imprint, have recently agreed to collaborate to provide free online access to recent out‐of‐print books published by EUB. The e‐books are available on the Digithèque website, a collection of digital copies of printed books created by the Library. This initiative is valuable for the scientific community and the general public who can freely access the books online, for the authors whose books have been digitized and widely disseminated, and for the publisher whose collections become more visible on the Internet, thereby generating more traffic on its website and potentially increasing sales of its other books. Around 20 books have been made available online so far. This article describes the context of the agreement, how the collaboration operates, the options of file conversion vs. book scanning, issues relating to copyright and users' rights, how access is provided to the digital copies, and future collaborative projects of the Library and EUB.
Library systems in the electronic era
Authors: BLEY Robert 
Published: June 2008

ABSTRACTThe ‘traditional’ academic library system model – i.e. a central system constructed around a common catalogue record that also dictated the end‐users' view – is breaking down. Systems that were constructed to handle the processing and lending of printed items are no longer capable, on their own, of dealing with the variety of different information resources handled by modern academic libraries. A great deal has been written about how end‐users expect more ‘Web 2.0’ features than library catalogues currently provide. New front‐end services have been designed by libraries and library system providers to cater for this need. However, not much has been written about the needs of internal library staff who struggle with processing, handling, and supporting the huge volume of electronic resources subscribed to by libraries. Electronic resource management systems have been developed to cater for these needs, and new standards for data interchange with such systems have been developed. Just as standards were important in encouraging electronic data interchange (orders, invoices, claims, etc.) between libraries, publishers, and agents in the last century, so new standards are evolving for such transactions in the electronic era.
PoooL: an efficient method for estimating haplotype frequencies from large DNA pools
Authors: Zhang Han , Yang Hsin-Chou , Yang Yaning 
Published: June 2008

Abstract
Motivation: Pooling DNA is a cost-effective alternative to individual genotyping method. It is often used for initial screening in genome-wide association analysis. In some studies, large pools with sizes up to several hundreds were applied in order to significantly reduce genotyping cost. However, method for estimating haplotype frequencies from large DNA pools has not been available due to computational complexity involved.
Methods: We propose a novel constrained EM algorithm, PoooL, to estimate frequencies of single-nucleotide polymorphism (SNP) haplotypes from DNA pools. A quantity called importance factor is introduced to measure the contribution of a haplotype to the likelihood. Under the assumption of asymptotic normality of the estimated allele frequencies and a system of linear constraints on haplotype frequencies the importance factor remains a constant in the iterative maximization process. The maximization problem in the EM algorithm is then formulated into a constrained maximum entropy model and solved by the improved iterative scaling method.
Results: Simulation study shows that our algorithm can efficiently estimate haplotype frequencies from DNA pools with arbitrarily large sizes. The algorithm works equally well for large pools with sizes up to hundreds or thousands and for pools with sizes as small as one or two individuals. The computational complexity of the PoooL algorithm is independent of pool sizes, and the computational efficiency for large pools is thus substantially improved over existing estimating methods. Simulation results also show that the proposed method is robust to genotype errors and population admixture.
Availability: http://staff.ustc.edu.cn/~ynyang/poool
Contact: zhanghan@mail.ustc.edu.cn; ynyang@ustc.edu.cn
Exploring the impact of polyproline II (PII) conformational bias on the binding of peptides to the SEM‐5 SH3 domain
Authors: Whitten Steven T. , Yang Huan‐Wang , Fox Robert O. , Hilser Vincent J. 
Published: June 2008

AbstractThe left‐handed polyproline II helical structure (PII) is observed to be a dominant conformation in the disordered states of protein and small polypeptide chains, even when no prolines are present in the sequence. Recently, in work by Ferreon and Hilser, the energetics associated with Ala and Gly substitutions at a surface exposed proline site were determined calorimetrically by measuring the binding energetics of Sos peptide variants to the C‐terminal Src Homology 3 domain of SEM‐5. The results were interpreted as a significant conformational bias toward the bound conformation (i.e., PII), even when the ligand is unbound. That study was not able to determine, however, whether the conformational bias of the peptides could be explained in terms other than that of a PII preference. Here, we test, using a computer algorithm based on the hard sphere collision (HSC) model, the notion of whether a bias in the unbound states of the peptide ligands is specific for the PII conformation, or if a bias to any other region of (φ, ψ) space can also result in the same observed binding energetics. The results of these computer simulations indicate that, of the regions of (φ, ψ) modeled for bias in the small peptides, only the bias to the PII conformation, and at rates of bias similar to the experimentally observed rates, quantitatively reproduced the experimental binding energetics.
Number, distribution and concentration of Australian veterinarians in 2006, compared with 1981, 1991 and 2001
Authors: Heath TJ 
Published: June 2008

Objective  To determine the number, concentration and distribution of veterinarians working in Australia in 2006, and compare with data from 1981, 1991 and 2001.Procedure  Data on each veterinarian who was registered, resident and apparently working in each Australian state and territory were obtained from relevant veterinary board lists, entered into an Excel spreadsheet and analysed with SAS System for Windows 8. Other data were obtained from the Official Australian Postcode Map, and the Australian Bureau of Statistics.Results  A total of 7510 veterinarians, of whom 46% were female, were working in Australia in 2006. The rate of increase (230/year) between 2001 and 2006 was greater than for the previous 20 years. The number per million people (360) was 73% higher than in 1981, and more than 30% higher than in the USA and UK. With the establishment of three new veterinary schools the number of graduates, and the total number of veterinarians, will increase further. By 2011 the number of veterinarians is likely to be three‐fold greater, and the number per million people two‐fold greater than in 1981. The number of veterinarians per million dogs and cats will increase at a greater rate if dog and cat numbers continue to fall. As more than 75% of Australian veterinary work involves dogs and cats this has serious implications for the profession.Conclusions  Progressively increasing numbers of veterinarians will compete for a constant or diminishing resource – the dogs and cats of Australia. It seems likely that overt signs of oversupply will appear before sufficient numbers of veterinarians enter alternative forms of employment.
Surgical treatment of uterine torsion using a ventral midline laparotomy in 19 mares
Authors: Jung C , Hospes R , Bostedt H , Litzke LF 
Published: June 2008

Objective  To report on the outcome of surgical treatment of uterine torsion in preterm mares.Design  Retrospective case series of pregnant mares with uterine torsion presented to the Clinic for Obstetrics, Gynaecology and Andrology of Large and Small Animals.Methods  Hospital records of all pregnant mares that underwent ventral midline laparotomy for uterine torsion between 1998 and 2004 were reviewed. The signalment, history, clinical signs, results of diagnostic procedures, direction and degree of the uterine twist, treatment and outcome were retrieved from each case record.Results  This study comprised 19 mares between months 5 and 11 of pregnancy (8.7 ± 1.9) and suffering from uterine torsion. In all cases ventromedian laparotomy was carried out under general anaesthesia. Gastrointestinal disorders were also present in 52.6% of horses. Postoperative complications included subcutaneous seromas (five mares), peritonitis (one mare) and abortion (two mares). In four mares (21%) the operation was unsuccessful (i.e. these mares had to be euthanased intra‐ or postoperatively). Of the surviving 15 mares, 13 (86.6%) gave birth to viable foals at full term. The foals developed normally. Only two mares aborted.Conclusions  Because of its versatility the ventral midline approach should be considered for correction of uterine torsion. The approach has many advantages, including rapid and clear access to the abdominal cavity, safety, visual assessment of uterine wall viability, correction of concomitant gastrointestinal tract problems, and performance of hysterotomy or hysterectomy, if indicated. In this study, managing uterine torsion in this way resulted in a high percentage of cases (86.6%) in which pregnancy was maintained, with the birth of a viable, mature foal.
Toxin Targets T Cells
Authors: Ray L. Bryan 
Published: June 2008

The compound 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD, also referred to as dioxin) is a highly toxic environmental pollutant that acts by regulating a ligand-activated transcription factor known as the aryl hydrocarbon receptor (AHR), for which the endogenous regulatory ligand or ligands remain uncertain. Two papers report that the AHR has an important role in controlling T cell differentiation that could help explain increased prevalence of autoimmune diseases in industrialized countries in which exposure to environmental toxins may be a factor. T cells can differentiate into T
reg
cells, which help keep inflammation in check by inhibiting proliferation of effector cells and secretion of inflammatory cytokines, or T
H
17 cells, which generally promote inflammation. Dioxin exposure suppresses immune responses, but the mechanism has been unclear. Quintana
et al
. made the connection of the AHR to T cell differentiation because the regulatory region near a gene that is highly expressed in T
reg
cells (Foxp3) contained an evolutionarily conserved binding site for the AHR. Veldhoen
et al
. noted that T
H
17 cells specifically expressed AHRs. The latter group showed that activation of AHR increased expression of cytokines by T
H
17 cells in vitro and that, in AHR-deficient mice, production of T
H
17 cells was diminished when they induced experimental autoimmune encephalitis in the animals. Quintana
et al
. went on to show that AHR indeed directly regulated expression of Foxp3. Furthermore, in mice, their experiments showed that the AHR could promote either differentiation of T
reg
or T
H
17 cells, depending on the ligand that was used to activate it. The authors note that this ligand-specific modulation of inflammatory responses could make AHR a particularly valuable therapeutic target for modulation of immune function. Stevens and Bradfield provide commentary.

F. J. Quintana, A. S. Basso, A. H. Iglesias, T. Korn, M. F. Farez, E. Bettelli, M. Caccamo, M. Oukka, H. L. Weiner, Control of T
reg
and T
H
17 cell differentiation by the aryl hydrocarbon receptor.
Nature
453
, 65-71 (2008).
[PubMed]

M. Veldhoen, K. Hirota, A. M. Westendorf, J. Buer, L. Dumoutier, J.-C. Renauld, B. Stockinger, The aryl hydrocarbon receptor links T
H
17-cell-mediated autoimmunity to environmental toxins.
Nature
453
, 106-109 (2008).
[PubMed]

E. A. Stevens, C. A. Bradfield, T cells hang in the balance.
Nature
453
, 46-47 (2008).
[PubMed]
Cooperation between Prokaryotic (Lde) and Eukaryotic (MRP) Efflux Transporters in J774 Macrophages Infected withListeria monocytogenes: Studies with Ciprofloxacin and Moxifloxacin
Authors: Lismond Ann , Tulkens Paul M. , Mingeot-Leclercq Marie-Paule , Courvalin Patrice , Van Bambeke Françoise 
Published: June 2008

ABSTRACTAntibiotic efflux is observed in both eukaryotic and prokaryotic cells, modulating accumulation and resistance. The present study examines whether eukaryotic and prokaryotic fluoroquinolone transporters can cooperate in the context of an intracellular infection. We have used (i) J774 macrophages (comparing a ciprofloxacin-resistant cell line overexpressing an MRP-like transporter with wild-type cells with basal expression), (ii)Listeria monocytogenes(comparing a clinical isolate [CLIP21369] displaying ciprofloxacin resistance associated with overexpression of the Lde efflux system with a wild-type strain [EGD]), (iii) ciprofloxacin (substrate of both Lde and MRP) and moxifloxacin (nonsubstrate), and (iv) probenecid and reserpine (preferential inhibitors of MRP and Lde, respectively). The ciprofloxacin MICs for EGD were unaffected by reserpine, while those for CLIP21369 were decreased approximately fourfold (and made similar to those of EGD). Neither probenecid nor reserpine affected the moxifloxacin MICs against EGD or CLIP21369. In dose-response studies (0.01× to 100× MIC) in broth, reserpine fully restored the susceptibility of CLIP21369 to ciprofloxacin (no effect on EGD) but did not influence the activity of moxifloxacin. In studies with intracellular bacteria, reserpine, probenecid, and their combination increased the activity of ciprofloxacin in wild-type and ciprofloxacin-resistant macrophages in parallel with an increase in ciprofloxacin accumulation in macrophages for EGD and an increase in accumulation and decrease in MIC (in broth) for CLIP21369. Moxifloxacin accumulation and intracellular activity were consistently not affected by the inhibitors. A bacterial efflux pump may thus actively cooperate with a eukaryotic efflux transporter to reduce the activity of a common substrate (ciprofloxacin) toward an intracellular bacterial target.
Effects of Minocycline and Valproic Acid Coadministration on Atazanavir Plasma Concentrations in Human Immunodeficiency Virus-Infected Adults Receiving Atazanavir-Ritonavir
Authors: DiCenzo Robert , Peterson Derick R. , Cruttenden Kim , Mariuz Peter , Rezk Naser L. , Hochreiter Jill , Gelbard Harris , Schifitto Giovanni 
Published: June 2008

ABSTRACT

Minocycline and valproic acid are potential adjuvant therapies for the treatment of human immunodeficiency virus (HIV)-associated cognitive impairment. The purpose of this study was to determine whether minocycline alone or in combination with valproic acid affected atazanavir plasma concentrations. Twelve adult HIV-infected subjects whose regimen included atazanavir (300 mg)-ritonavir (100 mg) daily for at least 4 weeks were enrolled. Each subject received atazanavir-ritonavir on day 1, atazanavir-ritonavir plus 100 mg minocycline twice daily on days 2 to 15, and atazanavir-ritonavir plus 100 mg minocycline twice daily and 250 mg valproic acid twice daily on days 16 to 30 with meals. The subjects had 11 plasma samples drawn over a dosing interval on days 1, 15, and 30. The coadministration of minocycline and valproic acid with atazanavir-ritonavir was well tolerated in all 12 subjects (six male; mean [± standard deviation] age was 43.1 [8.2] years). The geometric mean ratios (GMRs; 95% confidence interval [CI]) for the atazanavir area under the concentration-time curve from 0 to 24 h at steady state (AUC
0-24
), the plasma concentration 24 h after the dose (
C
min
), and the maximum concentration during the dosing interval (
C
max
) with and without minocycline were 0.67 (0.50 to 0.90), 0.50 (0.28 to 0.89), and 0.75 (0.58 to 0.95), respectively. Similar decreases in atazanavir exposure were seen after the addition of valproic acid. The GMRs (95% CI) for atazanavir AUC
0-24
,
C
min
, and
C
max
with and without minocycline plus valproic acid were 0.68 (0.43 to 1.06), 0.50 (0.24 to 1.06), and 0.66 (0.41 to 1.06), respectively. Coadministration of neither minocycline nor minocycline plus valproic acid appeared to influence the plasma concentrations of ritonavir (
P
> 0.2). Minocycline coadministration resulted in decreased atazanavir exposure, and there was no evidence that the addition of valproic acid mediated this effect.
Accelerated Control of VisceralLeishmania donovaniInfection in Interleukin-6-Deficient Mice
Authors: Murray Henry W. 
Published: June 2008

ABSTRACTIn patients with visceral leishmaniasis, increased levels of circulating interleukin-6 (IL-6) regularly accompany fully expressed, progressive infections (kala-azar). To experimentally test the role of IL-6, responses to an intracellularLeishmania donovaniinfection in the livers of IL-6−/−and wild-type mice were compared. IL-6−/−mice showed an enhanced control of the infection and earlier, rapid parasite killing along with additional evidence of a stimulated antileishmanial Th1-cell-type response: increased levels of circulating gamma interferon, accelerated granuloma assembly, and heightened responsiveness to chemotherapy. In this model of visceral leishmaniasis, IL-6 appears to act in a suppressive, macrophage-deactivating fashion, which identifies it as a potential target for therapeutic blockade.
Feasibility of increased biogas production from the co-digestion of agricultural, municipal, and agro-industrial wastes in rural communities
Authors: McDonald Tanya , Achari Gopal , Abiola Abimbola 
Published: June 2008

In rural communities, such as Olds, Alberta (population 7248) energy may be produced through anaerobic co-digestion of municipal, agricultural, and agro-industrial wastes. An inventory within a 20 km radius of Olds revealed that 291 000 tonnes of wet organic waste are generated annually (96.8% manure) with an electrical potential of 42 GWh (1 GWh = 106 kWh). Analysis of feedlot, hog, dairy and poultry manure, offal, food, grass, and biosolids identified the potential for waste blending to optimize solids content, nutrient balance, and pH level. In laboratory tests, biogas yield increased from 0.382 m3/kg volatile solid (VS) for feedlot manure alone to 0.513, 0.517, and 0.500 m3/kg VS with co-digestion of 30% hog manure, 15% offal, and 30% offal, respectively. Methane content of biogas increased from 75.8% in feedlot manure digestion to 78.8, 79.5, and 80.9% with co-digestion of 30% hog manure, 15% offal, and 30% offal, respectively.
Heterogeneous modeling of an anaerobic sequencing batch biofilm reactor (ASBBR)
Authors: Cabrera Padilla Rebeca Yndira , Miqueleto Ana Paula , Zaiat Marcelo , Kwong Wu Hong 
Published: June 2008

The objective of this study was to estimate the first-order intrinsic kinetic constant (k1) and the liquid-phase mass transfer coefficient (kc) in a bench-scale anaerobic sequencing batch biofilm reactor (ASBBR) fed with glucose. A dynamic heterogeneous mathematical model, considering two phases (liquid and solid), was developed through mass balances in the liquid and solid phases. The model was adjusted to experimental data obtained from the ASBBR applied for the treatment of glucose-based synthetic wastewater with approximately 500 mg L–1 of glucose, operating in 8 h batch cycles, at 30 °C and 300 rpm. The values of the parameters obtained were 0.8911 min–1 for k1 and 0.7644 cm min–1 for kc. The model was validated utilizing the estimated parameters with data obtained from the ASBBR operating in 3 h batch cycles, with a good representation of the experimental behavior. The solid-phase mass transfer flux was found to be the limiting step of the overall glucose conversion rate.