bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Sound of Rock Art. The Acoustics of the Rock Art of Southern Andalusia (Spain)
Authors: Díaz‐Andreu Margarita , García Benito Carlos , Lazarich María 
Published: January 2014

SummaryThis paper explores the potential of acoustics to interpret the prehistoric rock art of southern Andalusia (Spain). Tests undertaken in two areas, north of the Celemín river and the Bacinete area, will form the basis of our discussion. The results obtained at a selection of rock art sites show that the two key rock art sites, El Tajo de las Figuras and the large shelter at Bacinete, both with the majority of paintings in the earlier Laguna de la Janda style, had good resonance values. In contrast, at most of the other minor sites tested, the values for resonance were negative or insignificant, regardless of whether they were painted in Laguna de la Janda or schematic style. We conclude that the major rock art sites in southern Andalusia were chosen not only for their geological appearance and location in the landscape, but also for their acoustic properties.
Bacteria associated with yellow lupine grown on a metal‐contaminated soil: in vitro screening and in vivo evaluation for their potential to enhance Cd phytoextraction
Authors: Weyens N. , Gielen M. , Beckers B. , Boulet J. , van der Lelie D. , Taghavi S. , Carleer R. , Vangronsveld J. 
Published: January 2014

AbstractIn order to stimulate selection for plant‐associated bacteria with the potential to improve Cd phytoextraction, yellow lupine plants were grown on a metal‐contaminated field soil. It was hypothesised that growing these plants on this contaminated soil, which is a source of bacteria possessing different traits to cope with Cd, could enhance colonisation of lupine with potential plant‐associated bacteria that could then be inoculated in Cd‐exposed plants to reduce Cd phytotoxicity and enhance Cd uptake. All cultivable bacteria from rhizosphere, root and stem were isolated and genotypically and phenotypically characterised. Many of the rhizobacteria and root endophytes produce siderophores, organic acids, indole‐3‐acetic acid (IAA) and aminocyclopropane‐1‐carboxylate (ACC) deaminase, as well as being resistant to Cd and Zn. Most of the stem endophytes could produce organic acids (73.8%) and IAA (74.3%), however, only a minor fraction (up to 0.7%) were Cd or Zn resistant or could produce siderophores or ACC deaminase. A siderophore‐ and ACC deaminase‐producing, highly Cd‐resistant Rhizobium sp. from the rhizosphere, a siderophore‐, organic acid‐, IAA‐ and ACC deaminase‐producing highly Cd‐resistant Pseudomonas sp. colonising the roots, a highly Cd‐ and Zn‐resistant organic acid and IAA‐producing Clavibacter sp. present in the stem, and a consortium composed of these three strains were inoculated into non‐exposed and Cd‐exposed yellow lupine plants. Although all selected strains possessed promising in vitro characteristics to improve Cd phytoextraction, inoculation of none of the strains (i) reduced Cd phytotoxicity nor (ii) strongly affected plant Cd uptake. This work highlights that in vitro characterisation of bacteria is not sufficient to predict the in vivo behaviour of bacteria in interaction with their host plants.
Estimation after classification using lot quality assurance sampling: corrections for curtailed sampling with application to evaluating polio vaccination campaigns
Authors: Olives Casey , Valadez Joseph J. , Pagano Marcello 
Published: January 2014

AbstractObjectivesTo assess the bias incurred when curtailment of Lot Quality Assurance Sampling (LQAS) is ignored, to present unbiased estimators, to consider the impact of cluster sampling by simulation and to apply our method to published polio immunization data from Nigeria.MethodsWe present estimators of coverage when using two kinds of curtailedLQASstrategies: semicurtailed and curtailed. We study the proposed estimators with independent and clustered data using three field‐testedLQASdesigns for assessing polio vaccination coverage, with samples of size 60 and decision rules of 9, 21 and 33, and compare them to biased maximum likelihood estimators. Lastly, we present estimates of polio vaccination coverage from previously published data in 20 local government authorities (LGAs) from five Nigerian states.ResultsSimulations illustrate substantial bias if one ignores the curtailed sampling design. Proposed estimators show no bias. Clustering does not affect the bias of these estimators. Across simulations, standard errors show signs of inflation as clustering increases. Neither sampling strategy norLQASdesign influences estimates of polio vaccination coverage in 20 Nigerian LGAs. When coverage is low, semicurtailedLQASstrategies considerably reduces the sample size required to make a decision. CurtailedLQASdesigns further reduce the sample size when coverage is high.ConclusionsResults presented dispel the misconception that curtailedLQASdata are unsuitable for estimation. These findings augment the utility ofLQASas a tool for monitoring vaccination efforts by demonstrating that unbiased estimation using curtailed designs is not only possible but these designs also reduce the sample size.
Protein Domains of Unknown Function Are Essential in Bacteria
Authors: Goodacre Norman F. , Gerloff Dietlind L. , Uetz Peter 
Published: January 2014

ABSTRACT
More than 20% of all protein domains are currently annotated as “domains of unknown function” (DUFs). About 2,700 DUFs are found in bacteria compared with just over 1,500 in eukaryotes. Over 800 DUFs are shared between bacteria and eukaryotes, and about 300 of these are also present in archaea. A total of 2,786 bacterial Pfam domains even occur in animals, including 320 DUFs. Evolutionary conservation suggests that many of these DUFs are important. Here we show that 355 essential proteins in 16 model bacterial species contain 238 DUFs, most of which represent single-domain proteins, clearly establishing the biological essentiality of DUFs. We suggest that experimental research should focus on conserved and essential DUFs (eDUFs) for functional analysis given their important function and wide taxonomic distribution, including bacterial pathogens.

IMPORTANCE
The functional units of proteins are domains. Typically, each domain has a distinct structure and function. Genomes encode thousands of domains, and many of the domains have no known function (domains of unknown function [DUFs]). They are often ignored as of little relevance, given that many of them are found in only a few genomes. Here we show that many DUFs are essential DUFs (eDUFs) based on their presence in essential proteins. We also show that eDUFs are often essential even if they are found in relatively few genomes. However, in general, more common DUFs are more often essential than rare DUFs.
Transposon and Deletion Mutagenesis of Genes Involved in Perchlorate Reduction in
Azospira suillum
PS
Authors: Melnyk Ryan A. , Clark Iain C. , Liao Annette , Coates John D. 
Published: January 2014

ABSTRACT

Although much work on the biochemistry of the key enzymes of bacterial perchlorate reduction, chlorite dismutase, and perchlorate reductase has been published, understanding of the molecular mechanisms of this metabolism has been somewhat hampered by the lack of a clear model system amenable to genetic manipulation. Using transposon mutagenesis and clean deletions, genes important for perchlorate reduction in
Azospira suillum
PS have been identified both inside and outside the previously described perchlorate reduction genomic island (PRI). Transposon mutagenesis identified 18 insertions in 11 genes that completely abrogate growth via reduction of perchlorate but have no phenotype during denitrification. Of the mutants deficient in perchlorate reduction, 14 had insertions that were mapped to eight different genes within the PRI, highlighting its importance in this metabolism. To further explore the role of these genes, we also developed systems for constructing unmarked deletions and for complementing these deletions. Using these tools, every core gene in the PRI was systematically deleted; 8 of the 17 genes conserved in the PRI are essential for perchlorate respiration, including 3 genes that comprise a unique histidine kinase system. Interestingly, the other 9 genes in the PRI are not essential for perchlorate reduction and may thus have unknown functions during this metabolism. We present a model detailing our current understanding of perchlorate reduction that incorporates new concepts about this metabolism.

IMPORTANCE
Although perchlorate is generated naturally in the environment, groundwater contamination is largely a result of industrial activity. Bacteria capable of respiring perchlorate and remediating contaminated water have been isolated, but relatively little is known about the biochemistry and genetics of this process. Here we used two complementary approaches to identify genes involved in perchlorate reduction. Most of these genes are located on a genomic island, which is potentially capable of moving between organisms. Some of the genes identified are known to be directly involved in the metabolism of perchlorate, but other new genes likely regulate the metabolism in response to environmental signals. This work has uncovered new questions about the regulation, energetics, and evolution of perchlorate reduction but also presents the tools to address them.
Highly Infectious Prions Generated by a Single Round of Microplate-Based Protein Misfolding Cyclic Amplification
Authors: Moudjou Mohammed , Sibille Pierre , Fichet Guillaume , Reine Fabienne , Chapuis Jérôme , Herzog Laetitia , Jaumain Emilie , Laferrière Florent , Richard Charles-Adrien , Laude Hubert , Andréoletti Olivier , Rezaei Human , Béringue Vincent 
Published: January 2014

ABSTRACT

Measurements of the presence of prions in biological tissues or fluids rely more and more on cell-free assays. Although protein misfolding cyclic amplification (PMCA) has emerged as a valuable, sensitive tool, it is currently hampered by its lack of robustness and rapidity for high-throughput purposes. Here, we made a number of improvements making it possible to amplify the maximum levels of scrapie prions in a single 48-h round and in a microplate format. The amplification rates and the infectious titer of the PMCA-formed prions appeared similar to those derived from the
in vivo
laboratory bioassays. This enhanced technique also amplified efficiently prions from different species, including those responsible for human variant Creutzfeldt-Jakob disease. This new format should help in developing ultrasensitive, high-throughput prion assays for cognitive, diagnostic, and therapeutic applications.

IMPORTANCE
The method developed here allows large-scale, fast, and reliable cell-free amplification of subinfectious levels of prions from different species. The sensitivity and rapidity achieved approach or equal those of other recently developed prion-seeded conversion assays. Our simplified assay may be amenable to high-throughput, automated purposes and serve in a complementary manner with other recently developed assays for urgently needed antemortem diagnostic tests, by using bodily fluids containing small amounts of prion infectivity. Such a combination of assays is of paramount importance to reduce the transfusion risk in the human population and to identify asymptomatic carriers of variant Creutzfeldt-Jakob disease.
Quorum Sensing-Mediated, Cell Density-Dependent Regulation of Growth and Virulence in Cryptococcus neoformans
Authors: Albuquerque Patrícia , Nicola André M. , Nieves Edward , Paes Hugo Costa , Williamson Peter R. , Silva-Pereira Ildinete , Casadevall Arturo 
Published: January 2014

ABSTRACT

Quorum sensing (QS) is a cell density-dependent mechanism of communication between microorganisms, characterized by the release of signaling molecules that affect microbial metabolism and gene expression in a synchronized way. In this study, we investigated cell density-dependent behaviors mediated by conditioned medium (CM) in the pathogenic encapsulated fungus
Cryptococcus neoformans
. CM produced dose-dependent increases in the growth of planktonic and biofilm cells, glucuronoxylomannan release, and melanin synthesis, important virulence attributes of this organism. Mass spectrometry revealed the presence of pantothenic acid (PA) in our samples, and commercial PA was able to increase growth and melanization, although not to the same extent as CM. Additionally, we found four mutants that were either unable to produce active CM or failed to respond with increased growth in the presence of wild-type CM, providing genetic evidence for the existence of intercellular communication in
C. neoformans
.
C. neoformans
CM also increased the growth of
Cryptococcus albidus
,
Candida albicans
, and
Saccharomyces cerevisiae
. Conversely, CM from
Cryptococcus albidus
,
C. albicans
,
S.
cerevisiae, and
Sporothrix schenckii
increased
C. neoformans
growth. In summary, we report the existence of a new QS system regulating the growth and virulence factor expression of
C. neoformans in vitro
and, possibly, also able to regulate growth in other fungi.

IMPORTANCE
Quorum sensing is a strategy of communication used by pathogenic microorganisms to coordinate the expression of attributes necessary to cause disease. In this work, we describe a quorum sensing system in
Cryptococcus neoformans
, a yeast that can cause severe central nervous system infections. Adding conditioned medium—culture medium in which
C. neoformans
has previously grown—to fresh cultures resulted in faster growth of
C. neoformans
both as isolated cells and in microbial communities called biofilms. The addition of conditioned medium also increased the secretion of capsule carbohydrates and the formation of melanin pigment, two tools used by this microorganism to thrive in the host. This remarkable example of microbial communication shows that
C. neoformans
cells can act in unison when expressing attributes necessary to survive in the host, a finding that could point the way to improvements in the treatment of cryptococcosis.
Redaction of Sensitive Data in the Publication of Dual Use Research of Concern
Authors: Casadevall Arturo , Enquist Lynn , Imperiale Michael J. , Keim Paul , Osterholm Michael T. , Relman David A. 
Published: January 2014

ABSTRACT
The publication of scientific information that derives from dual use research of concern (DURC) poses major problems for journals because it brings into conflict the benefits of free access to data and the need to prevent misuse of that information by others. Recently, a group of authors and a major scientific journal addressed the issue of publishing information on a newly discovered, highly lethal toxin that can be delivered to large populations and for which there are no available countermeasures. The journal addressed this conflict by permitting the redaction of information that is normally considered essential for publication. This action establishes a precedent for redaction of sensitive data that also provides an example of responsible scientific publishing. However, this precedent leaves many questions unanswered and suggests a need for a discussion by all stakeholders of scientific information so as to derive normative standards for the publication of DURC.
Detection ofChlamydia trachomatisandNeisseria gonorrhoeaein an STI population: performances of the Presto CT-NG assay, the Lightmix Kit 480 HT CT/NG and the COBAS Amplicor with urine specimens and urethral/cervicovaginal samples
Authors: Schuurs T A , Verweij S P , Weel J F L , Ouburg S , Morré S A 
Published: January 2014

ObjectivesThis study assessed the performances of the Presto CT-NG assay, the Lightmix Kit 480 HT CT/NG and the COBAS Amplicor forChlamydia trachomatisandNeisseria gonorrhoeaedetection.DesignA cross-sectional study design.SettingIzore, Centre for Diagnosing Infectious Diseases in Friesland, the Netherlands, tested samples sent from regional sexually transmitted infection (STI) outpatient clinics and regional hospitals from the province Friesland, the Netherlands.ParticipantsSamples were collected from 292 men and 835 women. These samples included 560 urine samples and 567 urethral/cervicovaginal samples.Primary and secondary outcome measuresThe primary outcome measure isC trachomatisinfection. No secondary outcome measures are available.ResultsThe sensitivity, specificity, positive predicative value (PPV) and negative predictive value (NPV) forC trachomatisdetection in urine samples using the Presto CT-NG assay were 100%, 99.8%, 98.1% and 100%, respectively; for the Lightmix Kit 480 HT CT/NG: 94.2%, 99.8%, 96.1% and 99.4%, respectively; for the COBAS Amplicor: 92.3%, 99.6%, 96% and 99.2%, respectively. The sensitivity, specificity, PPV and NPV forC trachomatisdetection in urethral/cervicovaginal swabs using the Presto CT-NG assay and the COBAS Amplicor were 100%, 99.8%, 97.7% and 100%, respectively; for the Lightmix Kit 480 HT CT/NG: 100%, 99.6%, 97.7% and 100%, respectively. Calculations forN gonorrhoeaecould not be made due to a low prevalence.ConclusionsAll three assays had a high sensitivity, specificity, PPV and NPV forC trachomatis, with best performance for the Presto CT-NG assay.
Consultations for sexually transmitted infections in the general practice in the Netherlands: an opportunity to improve STI/HIV testing
Authors: Trienekens Suzan C M , van den Broek Ingrid V F , Donker Gé A , van Bergen Jan E A M , van der Sande Marianne A B 
Published: January 2014

ObjectivesIn the Netherlands, sexually transmitted infection (STI) care is provided by general practitioners (GPs) as well as by specialised STI centres. Consultations at the STI centres are monitored extensively, but data from the general practice are limited. This study aimed to examine STI consultations in the general practice.DesignProspective observational patient survey.SettingGeneral practices within the nationally representative Dutch Sentinel GP network (n=125 000 patient population), 2008–2011.Outcome measuresGPs were asked to fill out a questionnaire at each STI consultation addressing demographics, sexual behaviour and laboratory test results. Patient population, testing practices and test positivity are reported.ParticipantsPatients attending a consultation concerning an STI/HIV-related issue.ResultsOverall, 1 in 250 patients/year consulted their GP for STI/HIV-related problems. Consultations were concentrated among young heterosexuals of Dutch origin. Laboratory testing was requested for 83.3% of consultations. Overall consult positivity was 33.4%, highest for chlamydia (14.7%), condylomata (8.7%) and herpes (6.4%). 32 of 706 positive patients (4.5%) were diagnosed with multiple infections. Main high-risk groups were patients who were <25 years old (for chlamydia), >25 years old (syphilis), men who have sex with men (MSM; for gonorrhoea/syphilis/HIV) or having symptoms (for any STI). Adherence to guideline-recommendations to test for multiple STI among high-risk groups varied from 15% to 75%.ConclusionsThis study found that characteristics of patients who consulted a GP for STIs were comparable to those of patients attending STI centres regarding age and ethnicity; however, consultations of high-risk groups like MSM and (clients of) commercial sex workers were reported less by the general practice. Where the STI centres routinely test all patients for chlamydia/syphilis/HIV/gonorrhoea, GPs tested more selectively, even more restricted than advised by GP guidelines. Test positivity was, therefore, higher in general practice, although it is unknown how many STIs are missed (particularly among high-risk groups). Opportunities for a more proactive role in STI/HIV testing at general practices in line with current guidelines should be explored.
Subjective symptoms related to GSM radiation from mobile phone base stations: a cross-sectional study
Authors: Gómez-Perretta Claudio , Navarro Enrique A , Segura Jaume , Portolés Manuel 
Published: January 2014

ObjectivesWe performed a re-analysis of the data from Navarroet al(2003) in which health symptoms related to microwave exposure from mobile phone base stations (BSs) were explored, including data obtained in a retrospective inquiry about fear of exposure from BSs.DesignCross-sectional study.SettingLa Ñora (Murcia), Spain.ParticipantsParticipants with known illness in 2003 were subsequently disregarded: 88 participants instead of 101 (in 2003) were analysed. Since weather circumstances can influence exposure, we restricted data to measurements made under similar weather conditions.Outcomes and methodsA statistical method indifferent to the assumption of normality was employed: namely, binary logistic regression for modelling a binary response (eg, suffering fatigue (1) or not (0)), and so exposure was introduced as a predictor variable. This analysis was carried out on a regular basis and bootstrapping (95% percentile method) was used to provide more accurate CIs.ResultsThe symptoms most related to exposure were lack of appetite (OR=1.58, 95% CI 1.23 to 2.03); lack of concentration (OR=1.54, 95% CI 1.25 to 1.89); irritability (OR=1.51, 95% CI 1.23 to 1.85); and trouble sleeping (OR=1.49, 95% CI 1.20 to 1.84). Changes in –2 log likelihood showed similar results. Concerns about the BSs were strongly related with trouble sleeping (OR =3.12, 95% CI 1.10 to 8.86). The exposure variable remained statistically significant in the multivariate analysis. The bootstrapped values were similar to asymptotic CIs.ConclusionsThis study confirms our preliminary results. We observed that the incidence of most of the symptoms was related to exposure levels—independently of the demographic variables and some possible risk factors. Concerns about adverse effects from exposure, despite being strongly related with sleep disturbances, do not influence the direct association between exposure and sleep.
Factors associated with being overweight among Inner Mongolia medical students in China
Authors: Chen Jie , Yi He , Liu Zhiyue , Fan Yancun , Bian Jiang , Guo Wenfang , Chang Wulantuya , Sun Juan 
Published: January 2014

ObjectivesA major goal of our study was to identify the associations between lifestyle factors and obesity in adolescents and young adults at risk by surveying students in Inner Mongolia Medical University. A second goal was to determine these factors differed by gender.DesignCross-sectional study.SettingStudents grade 1–3 in Inner Mongolia Medical University.Participants5471 grade 1–3 medical students, composed of 3891 female and 1580 male students. Students with body mass index (BMI) ≥25 were defined as overweight.ResultsBMI for male students was 22.1±2.9 and 21.2±2.2 for female students. The prevalence of overweight was 7.6%, with the prevalence being higher for male students compared with females, urban higher than rural and being an only child higher than having sibling children. For male students, urban residence was a risk factor, while for female students being an only child and staying up at night were risk factors, with physical activity a protective factor. A dose-dependency relationship was found between physical fitness and overweight prevalence.ConclusionsThis study shows that being an only child and resident in an urban area are risk factors; staying up late and lack of physical activities increased the risk of being overweight. BMI was associated with declines in physical fitness. Our study provides more insight into adolescent obesity problems.