bluuebunny/crossref_metadata_2025 huggingface dataset:
Paediatric oropharyngeal and cutaneous candidiasis with special reference to Candida dubliniensis
Authors: Bhai Niti , Tendolkar Uma , Baradkar Vasant , Mathur Meenakshi , Kulkarni Madhuri
Published: January 2014

Mucocutaneous and cutaneous candidiasis, though common in children, is often under-reported. The prevalence ofCandida dubliniensisin causing these infections in this age group is also largely unknown. A prospective epidemiological cross-sectional study for candidiasis was performed in paediatric patients clinically suspected of candidiasis with oropharyngeal lesions (75 patients), cutaneous lesions (18 patients) and lesions at both sites (2 patients).Candidaspecies were identified by conventional tests. ForC. dubliniensis, chlamydospore production, growth on tobacco agar and growth at 45 °C were performed. Nine isolates were confirmed at a reference centre. The rates of candidiasis were 77.3 % (58 out of 75 patients clinically suspected of candidiasis) and 83.3 % (15/18) in oropharyngeal and cutaneous lesions respectively, and 1 of the 2 children with lesions at both sites was diagnosed as having chronic mucocutaneous candidiasis due toC. dubliniensis. The commonest species isolated wasCandida albicans, in 41 (70.7 %) patients with oropharyngeal candidiasis and 11 (73.3 %) with cutaneous lesions;C. dubliniensiswas isolated from 11 and 3 children respectively. In the paediatric population,C. albicanspredominates in mucocutaneous and cutaneous candidiasis, withC. dubliniensisalso contributing substantially.
Chlamydia psittaci exposure in pet birds
Authors: Cong W. , Huang S. Y. , Zhang X. X. , Zhou D. H. , Xu M. J. , Zhao Q. , Qian A. D. , Zhu X. Q.
Published: January 2014

Chlamydia psittaci is a zoonotic pathogen with a wide range of avian hosts and may be transmitted to humans and cause severe disease. To assess the risk of psittacosis posed by pet birds, the seroprevalence of Chlamydia psittaci antibodies in 360 Eurasian siskins (Carduelis spinus), 289 oriental skylarks (Alauda arvensis) and 36 black-tailed grosbeaks (Coccothraustes migratorius) in Gansu province, north-western China was detected by an indirect haemagglutination assay. Twenty-seven out of 289 (9.34 %) Alauda arvensis, 45 out of 360 (12.50 %) Carduelis spinus and 2 out of 36 (5.56 %) Coccothraustes migratorius were positive for Chlamydia psittaci infection at a cut-off dilution of 1 : 16. The prevalence of Chlamydia psittaci was higher in Carduelis spinus (12.5 %) than in Alauda arvensis (9.34 %) and Coccothraustes migratorius (5.56 %); however, the differences were not statistically significant (P>0.05). Statistical analysis indicated that Chlamydia psittaci seroprevalence in adult pet birds (12.4 %, 67/540) was significantly higher than that in juvenile pet birds (4.83 %, 7/145) (P<0.01). There was no statistical difference in Chlamydia psittaci seroprevalence between male (12.4 %) and female (8.27 %) birds. To our knowledge, this is the first report indicating the seroprevalence of Chlamydia psittaci exposure in pet birds in China. Our results indicate that close contact with pet birds poses the risk of zoonotic transmission of Chlamydia psittaci.
Predictive value of direct nitrate reductase assay and its clinical performance in the detection of multi- and extensively drug-resistant tuberculosis
Authors: Imperiale Belén R. , Morcillo Nora S. , Palomino Juan C. , Vandamme Peter , Martin Anandi
Published: January 2014

Conventional culture and drug susceptibility testing (DST) methods for Mycobacterium tuberculosis are laborious and time consuming. For this reason alternative rapid culture and DST techniques are urgently needed to shorten the time for drug-resistance detection. A total of 222 smear-positive sputum samples were evaluated by the direct nitrate reductase assay (D-NRA) on Lowenstein–Jensen medium, for the rapid and simultaneous detection of resistance to isoniazid, rifampicin, kanamycin and ofloxacin. p-Nitrobenzoic acid was also included for identification of the M. tuberculosis complex. Results were compared with the BACTEC MGIT 960 as gold standard. The general performance of the D-NRA was very good, reaching a global value of 97 %. D-NRA had a turn-around time of 16.9 days to obtain results while that of the indirect MGIT 960 system was 29 days. D-NRA is a low-cost technology, easy to set up in clinical laboratories and suitable to be used for DST of M. tuberculosis in all smear-positive samples.
Comparative proteomic analysis of Clostridium difficile isolates of varying virulence
Authors: Chilton C. H. , Gharbia S. E. , Fang M. , Misra R. , Poxton I. R. , Borriello S. P. , Shah H. N.
Published: January 2014

The soluble proteome of three Clostridium difficile strains of varying pathogenic potential, designated B-1, Tra 5/5 and 027 SM, were compared using differential in-gel electrophoresis in which the proteins of each strain were labelled with CyDyes. This enabled visual inspection of the 2D profiles of strains and identification of differentially expressed proteins using image analysis software. Unlabelled protein reference maps of the predominant proteins were then generated for each strain using 2D gel electrophoresis followed by protein sequencing of each spot using a Reflectron matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometer. Increased coverage of the proteome was achieved using 1D gel electrophoresis in a bottom-up approach using LC-MS/MS of 1 cm gel slices. A total of 888 different proteins were detected by comparative analysis of isolates grown in parallel for 64 h on blood agar plates. Of these, only 38 % were shared between all isolates. One hundred and ten proteins were identified as showing ≥2-fold difference in expression between strains. Differential expression was shown in a number of potential virulence and colonization factors. Toxin B was detected in the more virulent strains B-1 and 027 SM, but not in the lower virulent strain Tra 5/5, despite all strains possessing an intact pathogenicity locus. The S-layer protein (Cwp2) was identified in strains 027 SM and Tra 5/5 but not strain B-1, and differences in the post-translational modification of SlpA were noted for strain B-1. The variant S-layer profile of strain B-1 was confirmed by genomic comparison, which showed a 58 kb insertion in the S-layer operon of strain B-1. Differential post-translation modification events were also noted in flagellar proteins, thought to be due to differential glycosylation. This study highlights genomic and proteomic variation of different Clostridium difficile strains and suggests a number of factors may play a role in mediating the varying virulence of these different strains.
Coalescence 2.0: a multiple branching of recent theoretical developments and their applications
Authors: Tellier Aurelien , Lemaire Christophe
Published: January 2014

Population genetics theory has laid the foundations for genomics analyses including the recent burst in genome scans for selection and statistical inference of past demographic events in many prokaryote, animal and plant species. Identifying SNPs under natural selection and underpinning species adaptation relies on disentangling the respective contribution of random processes (mutation, drift, migration) from that of selection on nucleotide variability. Most theory and statistical tests have been developed using the Kingmans coalescent theory based on the Wright-Fisher population model. However, these theoretical models rely on biological and life-history assumptions which may be violated in many prokaryote, fungal, animal or plant species. Recent theoretical developments of the so called multiple merger coalescent models are reviewed here (Λ-coalescent, beta-coalescent, Bolthausen-Snitzman, Ξ-coalescent). We explicit how these new models take into account various pervasive ecological and biological characteristics, life history traits or life cycles which were not accounted in previous theories such as 1) the skew in offspring production typical of marine species, 2) fast adapting microparasites (virus, bacteria and fungi) exhibiting large variation in population sizes during epidemics, 3) the peculiar life cycles of fungi and bacteria alternating sexual and asexual cycles, and 4) the high rates of extinction-recolonization in spatially structured populations. We finally discuss the relevance of multiple merger models for the detection of SNPs under selection in these species, for population genomics of very large sample size and advocate to potentially examine the conclusion of previous population genetics studies.
A TIN2 dyskeratosis congenita mutation causes telomerase-independent telomere shortening in mice
Authors: Frescas David , de Lange Titia
Published: January 2014

The progressive bone marrow failure syndrome dyskeratosis congenita (DC) is often caused by mutations in telomerase or the factors involved in telomerase biogenesis and trafficking. However, a subset of DC patients is heterozygous for mutations in the shelterin component TIN2. To determine how the TIN2-DC mutations affect telomere function, we generated mice with the equivalent of the TIN2 K280E DC allele (TIN2DC) by gene targeting. Whereas homozygous TIN2DC/DC mice were not viable, first-generation TIN2+/DC mice were healthy and fertile. In the second and third generations, the TIN2+/DC mice developed mild pancytopenia, consistent with hematopoietic dysfunction in DC, as well as diminished fecundity. Bone marrow telomeres of TIN2+/DC mice shortened over the generations, and immortalized TIN2+/DC mouse embryonic fibroblasts (MEFs) showed telomere shortening with proliferation. Unexpectedly, telomere shortening was accelerated in TIN2+/DC mTR−/− mice and MEFs compared with TIN2+/+ mTR−/− controls, establishing that the TIN2DC telomere maintenance defect was not solely due to diminished telomerase action. The TIN2DC allele induced mild ATR kinase signaling at telomeres and a fragile telomere phenotype, suggestive of telomere replication problems. These data suggest that this TIN2-DC mutation could induce telomeric dysfunction phenotypes in telomerase-negative somatic cells and tissues that further exacerbate the telomere maintenance problems in telomerase-positive stem cell compartments.
Cellular senescence and its effector programs
Authors: Salama Rafik , Sadaie Mahito , Hoare Matthew , Narita Masashi
Published: January 2014

Cellular senescence is a stress response that accompanies stable exit from the cell cycle. Classically, senescence, particularly in human cells, involves the p53 and p16/Rb pathways, and often both of these tumor suppressor pathways need to be abrogated to bypass senescence. In parallel, a number of effector mechanisms of senescence have been identified and characterized. These studies suggest that senescence is a collective phenotype of these multiple effectors, and their intensity and combination can be different depending on triggers and cell types, conferring a complex and diverse nature to senescence. Series of studies on senescence-associated secretory phenotype (SASP) in particular have revealed various layers of functionality of senescent cells in vivo. Here we discuss some key features of senescence effectors and attempt to functionally link them when it is possible.
Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of the LRR domain of the LePRK1 receptor-like kinase from tomato
Authors: Xu Anbi , Huang Laiqiang
Published: January 2014

LePRK1 is a receptor-like kinase involved in successful fertilization in Lycopersicon esculentum (tomato). Importantly, the extracellular leucine-rich repeat (LRR) domain of LePRK1 mediates transmembrane signal transduction for pollen-tube growth and pollen germination. In this study, the N-terminal extracellular LRR domain of L. esculentum-derived LePRK1 was purified using an insect-cell secretion expression system and was crystallized by the vapour-diffusion method. The crystals diffracted X-rays to a resolution of 2.75 Å using synchrotron radiation. The crystals belonged to space group C2, with unit-cell parameters a = 136.53, b = 56.01, c = 62.93 Å, β = 108.99° and two molecules per asymmetric unit.
Expression, purification and crystallization of a dye-decolourizing peroxidase from Dictyostelium discoideum
Authors: Rai Amrita , Fedorov Roman , Manstein Dietmar J.
Published: January 2014

Dye-decolourizing peroxidases are haem-containing peroxidases with broad substrate specificity. Using H2O2 as an electron acceptor, they efficiently decolourize various dyes that are of industrial and environmental relevance, such as anthraquninone- and azo-based dyes. In this study, the dye-decolourizing peroxidase DdDyP from Dictyostelium discoideum was overexpressed in Escherichia coli strain Rosetta(DE3)pLysS, purified and crystallized using the vapour-diffusion method. A native crystal diffracted to 1.65 Å resolution and belonged to space group P41212, with unit-cell parameters a = b = 141.03, c = 95.56 Å, α = β = γ = 90°. The asymmetric unit contains two molecules.
Distribution of essential and non‐essential elements on the surface of roadside leaves and in the bulk of various fruits by atomic absorption spectrophotometry
Authors: Ahmad Fiaz , Munir Arshad , Zafar‐uz‐Zaman  , Zafar Ali Naveed
Published: January 2014

Purpose

The purpose of this paper is to establish some acceptable trends in the contamination of roadside vegetation and to define a safety limit regarding the effects of metal contamination arising from various toxic metals deposited on leaves of the plants and in the bulk of the fruits.

Design/methodology/approach

Distribution of essential and non‐essential elements on the surface of leaves and in bulk of fruits of specific areas of Multan (Pakistan) was estimated and correlated with World Health Organization (WHO) standards. The metal concentrations are expressed as X ± SD for triplicate sub samples with the SD of ± 1.0‐1.5 per cent. The maximum metal levels in bulk of various fruits were calculated for FE, followed by Cu, Zn and Co.

Findings

In samples from roadside leaves Fe (823 mg/kg) was found to be the dominant metal, whereas the observed threshold level was found for Co (17.25 mg/kg). The non‐essential elements in various fruits, the Cr was found to be the dominate (16 mg/kg) on mean basis as compared with other metals in fruits. The increasing order of non‐essential metals on the surface of roadside leaves was Li < Ni < Sr < Pb < Cr. The results revealed that metal concentration decreases with increase in distance from roadside (10, 30 and 50 m) with negative correlation coefficient.

Originality/value

This paper shows that the metals concentration in case of all fruit samples fall within the permissible safe limit, whereas the metal concentrations on the surface of roadside leaves were found to surpass the safe limits laid down by the WHO. It is consequently suggested that edible portions of vegetation and fruits near highways should be consumed cautiously.
Slimming students survey
Authors: Auckland John N , Hunt Clive , MPhil  , Whelbourn Yvette
Published: January 2014

John N Auckland BSc, PhD, Clive Hunt BSc, MPhil and Yvette Whelbourn describe an investigation they carried out to discover how much a certain group of students knew about some aspects of nutrition. The students, from The Polytechnic, Huddersfield, had made a voluntary decision to slim and were also self catering. The authors found that, in general, female students were nutritionally more knowledgeable than males, having a better idea of relative energy values and which foods it is necessary to reduce in order to slim. However, the intake of several vitamins and minerals fell substantially below UK recommended levels during slimming and the results therefore suggest that self‐catering students would benefit from nutritional advice and possibly access to specifically formulated slimming diets
Profiling gene expression to distinguish the likely active diazotrophs from a sea of genetic potential in marine sediments
Authors: Brown S. M. , Jenkins B. D.
Published: January 2014

Nitrogen (N) cycling microbial communities in marine sediments are extremely diverse, and it is unknown whether this diversity reflects extensive functional redundancy. Sedimentary denitrifiers remove significant amounts of N from the coastal ocean and diazotrophs are typically regarded as inconsequential. Recently, N fixation has been shown to be a potentially important source of N in estuarine and continental shelf sediments. Analysis of expressed genes for nitrite reductase (nirS) and a nitrogenase subunit (nifH) was used to identify the likely active denitrifiers and nitrogen fixers in surface sediments from different seasons in Narragansett Bay (Rhode Island, USA). The overall diversity of diazotrophs expressing nifH decreased along the estuarine gradient from the estuarine head to an offshore continental shelf site. Two groups of sequences related to anaerobic sulphur/iron reducers and sulphate reducers dominated libraries of expressed nifH genes. Quantitative polymerase chain reaction (qPCR) and quantitative reverse transcription polymerase chain reaction (qRT‐PCR) data shows the highest abundance of both groups at a mid bay site, and the highest nifH expression at the head of the estuary, regardless of season. Several potential environmental factors, including water temperature, oxygen concentration and metal contamination, may influence the abundance and nifH expression of these two bacterial groups.
The commodification of patient opinion: the digital patient experience economy in the age of big data
Authors: Lupton Deborah
Published: January 2014

As part of the digital health phenomenon, a plethora of interactive digital media platforms have been established in recent years to elicit lay people's experiences of illness and health care. The overt function of these platforms is to provide forums where patients and caregivers can share their experiences with others, benefit from the support and knowledge of other users and contribute to large aggregated data archives as part of developing better medical treatments and services and conducting medical research. However, what may not always be readily apparent to the users of these platforms are the growing commercial uses by many of the platforms’ owners of the data they contribute. This article examines this phenomenon of what I term ‘the digital patient experience economy’. Such aspects of this economy as prosumption (the combination of content consumption and production that is characteristic of the use of Web 2.0 technologies), the valorising of big data, the discourse and ethic of sharing and the commercialisation of affective labour are discussed. It is argued that via these online platforms patients’ opinions and experiences may be expressed in more diverse and accessible forums than ever before, but simultaneously they have become exploited in novel ways.
Functional dental occlusion: an anthropological perspective and implications for practice
Authors: Kaidonis JA , Ranjitkar S , Lekkas D , Brook AH , Townsend GC
Published: January 2014

Physiologic changes occur in dental occlusion throughout life, resulting from the interplay between functional demands and reciprocating adaptive responses. These changes have been reported in the anthropological literature and they reflect evolutionary changes in the human stomatognathic system during the Paleolithic, hunter‐gatherer period. Specific occlusal changes occur in response to different environments, leading to extensive variation within and between extinct and extant human populations. For example, functional demands can cause occlusal and interproximal tooth wear, resulting in shortening of the dental arch, continual tooth eruption and changes in masticatory patterns.

Since the advent of farming through to our current industrialized culture, functional demands on the human masticatory system, and its adaptive responses to these demands, have been reduced considerably. Indeed, it is only occasionally that functional demands are severe enough to lead to obvious pathology in the modern human dentition. In contrast to normal masticatory activity, ‘modern‐day conditions’ such as dental caries, periodontal disease and erosion, can lead to significant changes in dental occlusion that are pathological and need to be treated.

The masticatory system is a dynamic, functional unit that displays considerable change over a lifetime. In this concept paper, it is proposed that modern human populations living in industrialized environments display dental occlusions that can be considered to be ‘neotenous’; that is, our dentitions tend to reflect an unworn stage of our ancestors that was only seen in infants, juveniles and young adults. Clinicians can draw on both phylogenetic and ontogenetic perspectives of ‘functional dental occlusion’ to differentiate continual physiological changes occurring over time that require ongoing review, from pathological responses that require intervention.
Worldwide frequency distribution of the ‘Gait keeper’ mutation in the DMRT3 gene
Authors: Promerová M. , Andersson L. S. , Juras R. , Penedo M. C. T. , Reissmann M. , Tozaki T. , Bellone R. , Dunner S. , Hořín P. , Imsland F. , Imsland P. , Mikko S. , Modrý D. , Roed K. H. , Schwochow D. , Vega‐Pla J. L. , Mehrabani‐Yeganeh H. , Yousefi‐Mashouf N. , G. Cothran E. , Lindgren G. , Andersson L.
Published: January 2014

For centuries, domestic horses have represented an important means of transport and served as working and companion animals. Although their role in transportation is less important today, many horse breeds are still subject to intense selection based on their pattern of locomotion. A striking example of such a selected trait is the ability of a horse to perform additional gaits other than the common walk, trot and gallop. Those could be four‐beat ambling gaits, which are particularly smooth and comfortable for the rider, or pace, used mainly in racing. Gaited horse breeds occur around the globe, suggesting that gaitedness is an old trait, selected for in many breeds. A recent study discovered that a nonsense mutation in DMRT3 has a major impact on gaitedness in horses and is present at a high frequency in gaited breeds and in horses bred for harness racing. Here, we report a study of the worldwide distribution of this mutation. We genotyped 4396 horses representing 141 horse breeds for the DMRT3 stop mutation. More than half (2749) of these horses also were genotyped for a SNP situated 32 kb upstream of the DMRT3 nonsense mutation because these two SNPs are in very strong linkage disequilibrium. We show that the DMRT3 mutation is present in 68 of the 141 genotyped horse breeds at a frequency ranging from 1% to 100%. We also show that the mutation is not limited to a geographical area, but is found worldwide. The breeds with a high frequency of the stop mutation (>50%) are either classified as gaited or bred for harness racing.
Quantitative trait loci for magnitude of the plasma cortisol response to confinement in rainbow trout
Authors: Quillet E. , Krieg F. , Dechamp N. , Hervet C. , Bérard A. , Le Roy P. , Guyomard R. , Prunet P. , Pottinger T. G.
Published: January 2014

Better understanding of the mechanisms underlying interindividual variation in stress responses and their links with production traits is a key issue for sustainable animal breeding. In this study, we searched for quantitative trait loci (QTL) controlling the magnitude of the plasma cortisol stress response and compared them to body size traits in five F2 full‐sib families issued from two rainbow trout lines divergently selected for high or low post‐confinement plasma cortisol level. Approximately 1000 F2 individuals were individually tagged and exposed to two successive acute confinement challenges (1 month interval). Post‐stress plasma cortisol concentrations were determined for each fish. A medium density genome scan was carried out (268 markers, overall marker spacing less than 10 cM). QTL detection was performed using qtlmap software, based on an interval mapping method (http://www.inra.fr/qtlmap). Overall, QTL of medium individual effects on cortisol responsiveness (<10% of phenotypic variance) were detected on 18 chromosomes, strongly supporting the hypothesis that control of the trait is polygenic. Although a core array of QTL controlled cortisol concentrations at both challenges, several QTL seemed challenge specific, suggesting that responses to the first and to a subsequent exposure to the confinement stressor are distinct traits sharing only part of their genetic control. Chromosomal location of the steroidogenic acute regulatory protein (STAR) makes it a good potential candidate gene for one of the QTL. Finally, comparison of body size traits QTL (weight, length and body conformation) with cortisol‐associated QTL did not support evidence for negative genetic relationships between the two types of traits.
The Limits of Financial Imagination: Free Investors, Efficient Markets, and Crisis
Authors: Ortiz Horacio
Published: January 2014

Fieldwork with a team of investment managers investing in credit derivatives in Paris in 2004 shows how the concepts of “investor” and “market efficiency” are central in the technicalities of their procedures, in diverse and contradictory ways. The employees refer to their moral and political contents, as they are articulated in liberal philosophy and in financial regulation, to make sense of their careers and of the social role of finance. “Crisis” is then defined as a deviation from market efficiency, itself expected to lead to an optimal allocation of credit. These concepts thus constitute the limited repertoire of the meaning of practical rules followed by employees for a remuneration, within a bureaucratic commercial network, in a setting very different from the utopias from which the concepts stem. Therefore, anthropologists must not use them as analytic tools; rather, such concepts should be understood as part of the object of study.
Effects of ropivacaine concentration on the spread of sensory block produced by continuous thoracic paravertebral block: a prospective, randomised, controlled, double‐blind study
Authors: Yoshida T. , Fujiwara T. , Furutani K. , Ohashi N. , Baba H.
Published: January 2014

Factors affecting the distribution of continuous thoracic paravertebral block have never been examined. We designed this prospective, double‐blind study to check whether continuous thoracic paravertebral block with a higher ropivacaine concentration would provide a wider segmental sensory block spread. Sixty consecutive patients undergoing pulmonary lobectomy or segmentectomy were randomly allocated to receive continuous paravertebral infusion of either 0.2% or 0.5% ropivacaine (6 ml.h−1). The primary outcome was the number of anaesthetised dermatomes as determined by loss of cold sensation 24 h after surgery. Twenty‐seven patients per group were included in the final analysis. The median (IQR [range]) number of anaesthetised dermatomes 24 h after surgery was 4 (3–6 [1–9]) with ropivacaine 0.2% and 4 (3–6 [2–11]) with ropivacaine 0.5% (p = 0.66). Contrary to our expectation, the segmental spread of sensory block produced by continuous thoracic paravertebral block does not depend on ropivacaine concentration.
Preliminary Safety Evaluation of Photodynamic Therapy for Blood Purification: An Animal Study
Authors: Yin Huijuan , Zhang Guorong , Chen Hongli , Wang Weichao , Kong Deling , Li Yingxin
Published: January 2014

Photodynamic therapy (PDT) has been shown to inactivate blood‐borne pathogenic microorganisms in vitro. The method may be used to purify blood in the body, kill pathogenic microorganisms, and treat difficult diseases. Our aim was to investigate the safety of photodynamic blood purification (PBP) therapy using an in vivo blood circulation experiment in an animal model. Twenty‐four New Zealand rabbits were used as experimental subjects; 12 received PDT and 12 served as negative controls. Extracorporeal blood bypass was established using the femoral artery and vein. A sterile disposable irradiation chamber was connected in the bypass pathway. Hematoporphyrin monomethyl ether was injected intravenously as a photosensitizer with an initial bolus of 3.7 mg, followed by a continuous infusion at 24 mg/h during PDT administration. Five minutes after initial injection, a laser beam was vertically focused on the irradiation chamber side wall, with a 9.5 cm2 spot area, 1 h exposure time, and 20 mW/cm2 power density. Six animals received a single PDT application, and six received PDT every other day for three applications. The 12 control group animals underwent extracorporeal blood circulation but did not receive the photosensitizer or light treatment. Blood samples were taken 20 min, 1 day, 4 days, and 7 days after PDT treatment for analysis of cell counts, coagulation, liver and renal function, and other biochemical changes. On the 7th day, animals were sacrificed, and parenchymal organs were evaluated for morphological changes. There were no significant differences in white blood cells, red blood cells, or destroyingplatelets after PDT compared with the control group. There was a little significant difference in alanine aminotransferase, aspartate aminotransferase, alkaline phosphatase, γ‐glutamyl transpeptidase, uric acid, blood urea nitrogen, and creatinine in the PDT group compared with the control group, except at individual time points. We found no significant damage in the heart, liver, spleen, lungs, kidneys, or other organs after PDT. This short‐duration, fixed‐strength PBP method did not cause changes in blood parameters or in the structure or function of major organs in an animal model. These findings suggest that PBP is safe in vivo and has potential as a new therapy for inactivating blood‐borne microorganisms.
Fever survey highlights significant variations in how infants aged ≤60 days are evaluated and underline the need for guidelines
Authors: Yarden‐Bilavsky Havatzelet , Ashkenazi Shai , Amir Jacob , Schlesinger Yechiel , Bilavsky Efraim
Published: January 2014

Aim

To assess the common practices for evaluating and treating febrile infants aged ≤60 days in a nationwide survey.

Methods

Questionnaires were administrated to inpatient paediatric departments in all 25 hospitals in Israel.

Results

Of the 25 centres surveyed (100% response rate), only 36% had written protocols concerning the approach to young febrile infants. The existence of a written protocol was significantly associated with the level of medical centre (tertiary versus primary and secondary, p = 0.041) and with the number of local paediatric infectious disease specialists (p = 0.034). In 13 (52%) hospitals, a normal white blood cell count was defined as 5000–15 000 cells/mL and 20 (80%) centres use C‐reactive protein. Hospitalisation was mandatory in most (96%) centres for all neonates aged ≤28 days. Low‐risk infants aged 29–60 days were hospitalised in 68.4% of the primary and secondary hospitals, compared with 33.3% tertiary centres. Ampicillin and gentamicin was the routine empiric antibiotic treatment for febrile infant in 92% of centres.

Conclusion

Significant differences exist among centres in the evaluation of febrile infants aged ≤60 days exist. These differences reflect the lack of, and highlight the need for, national or international guidelines for the evaluation of fever in this age group.
Repeated fear‐induced diurnal rhythm disruptions predict PTSD‐like sensitized physiological acute stress responses in F344 rats
Authors: Thompson R. S. , Strong P. V. , Clark P. J. , Maslanik T. M. , Wright K. P. , Greenwood B. N. , Fleshner M.
Published: January 2014

Aim

To identify objective factors that can predict future sensitized stress responses, thus allowing for effective intervention prior to developing sensitization and subsequent stress‐related disorders, including post‐traumatic stress disorder (PTSD).

Methods

Adult male F344 rats implanted with biotelemetry devices were exposed to repeated conditioned fear or control conditions for 22 days followed by exposure to either no, mild or severe acute stress on day 23. Diurnal rhythms of locomotor activity (LA), heart rate (HR) and core body temperature (CBT) were biotelemetrically monitored throughout the study. In a subset of rat not implanted, corticosterone and indices of chronic stress were measured immediately following stress.

Results

Rats exposed to repeated fear had fear‐evoked increases in behavioural freezing and HR/CBT during exposure to the fear environment and displayed indices of chronic stress. Repeated fear produced flattening of diurnal rhythms in LA, HR and CBT. Repeated fear did not sensitize the corticosterone response to acute stress, but produced sensitized HR/CBT responses following acute stress, relative to the effect of acute stress in the absence of a history of repeated fear. Greater diurnal rhythm disruptions during repeated fear predicted sensitized acute stress‐induced physiological responses. Rats exposed to repeated fear also displayed flattened diurnal LA and basal increases in HR.

Conclusions

Exposure to repeated fear produces outcomes consistent with those observed in PTSD. The results suggest that diurnal rhythm disruptions during chronic stressors may help predict sensitized physiological stress responses following traumatic events. Monitoring diurnal disruptions during repeated stress may thus help predict susceptibility to PTSD.
Systematic review with meta‐analysis: malignancies with anti‐tumour necrosis factor‐α therapy in inflammatory bowel disease
Authors: Williams C. J. M. , Peyrin‐Biroulet L. , Ford A. C.
Published: January 2014

Background

Anti‐tumour necrosis factor‐α (TNFα) antibodies are efficacious in inflammatory bowel disease (IBD). These drugs carry the theoretical risk of malignancy, particularly lymphoma, but no systematic review and meta‐analysis has examined this issue.

Aim

To pool data from all available placebo‐controlled studies to estimate risk of malignancy with anti‐TNFα therapy in IBD.

Methods

MEDLINE, EMBASE and the Cochrane central register of controlled trials were searched to November 2013. Randomised controlled trials (RCTs) comparing anti‐TNFα therapy with placebo in adults with Crohn's disease (CD) or ulcerative colitis (UC) were eligible. Data were pooled to obtain a relative risk (RR) of malignancy with a 95% confidence interval (CI).

Results

The search strategy identified 25 338 citations, of which 22 RCTs were eligible (11 infliximab, six adalimumab, four certolizumab and one golimumab) involving 7054 patients (4566 CD and 2488 UC). In total, there were 16 (0.39%) malignancies in 4135 IBD patients allocated to anti‐TNFα, compared with 13 (0.45%) in 2919 patients randomised to placebo. There were no cases of lymphoma in the active treatment group, compared with three (0.1%) in the control group. The RR of malignancy for patients receiving anti‐TNFα therapy compared with placebo was 0.77 (95% CI 0.37–1.59). When seven individuals with nonmelanoma skin cancer were excluded from the analysis, the RR was 0.90 (95% CI 0.40–2.02).

Conclusions

Anti‐TNFα therapy was not associated with an increased risk of malignancy in patients with IBD. However, no trials provided data for risk of malignancy beyond 1 year of treatment, meaning that an increased risk in the longer term cannot be excluded.
Cargoes of Iron Semi‐Products Recovered from Shipwrecks off the Carmel Coast, Israel
Authors: Galili E. , Bauvais S. , Rosen B. , Dillmann P.
Published: January 2014

Underwater surveys along the Israeli Carmel coast have revealed six cargoes of iron semi‐products associated with shipwrecks. They are described and dated according to the associated artefacts. Metallographic and chemical analyses on samples from the biggest cargo have determined the stages of the chaîne opératoire, identified the properties of the iron and characterized the iron trade along the Israeli coast. The new discoveries contribute to our understanding of the circulation of iron in the South Levant, which was characterized by an almost complete absence of local iron production. During the Byzantine and Crusader periods, this absence was compensated by long‐distance sea trade, depending on political circumstances and restrictions. Three main types of iron semi‐products were identified: (a) partly consolidated blooms, (b) short pointed bars and (c) elongated pointed bars. The cargoes discovered represent a time period of nearly a millennium. Altogether, 148 iron semi‐products were studied. Of these, 166 were from cargo a, which was dated by coins to around 1130–1200 ce. Those coins could have been imported from Europe for Crusader military and civil uses in the Levant. The iron from cargoes b, d and f, dated perhaps to the Byzantine period, could have been imported from Anatolia or Venice for military and civil purposes.
Zakat as a Poverty Reduction Mechanism Among the Muslim Community: Case Study of Bangladesh, Malaysia, and Indonesia
Authors: Ali Isahaque , Hatta Zulkarnain A.
Published: January 2014

Poverty reduction remains the most important challenge for policy makers in Islamic communities. The World Bank (2010: Poverty profile in Muslim world, from http://www.worldbank.org) estimates that approximately 3 billion people are living in poverty and 46 million more people will come under the income level of US$1.25 a day due to the recent global economic meltdown and slow economic growth rates. Thirty‐five percent of these people are Muslims from Islamic countries. The global Muslim community has an essential role to play in addressing the injustice of global poverty through zakat. Zakat is an Islamic faith‐based institution and is being underutilized for poverty reduction in many of these poor Muslim countries. Since zakat constitutes one of the pillars of Islam, it is logical to assume that policy makers among Muslims should pay serious attention to it. However, that is not the case for many Muslim countries and this paper will show that not all Muslim countries are seriously applying zakat in its strategy of combating poverty. This paper will specifically examine the role and effect of zakat in three Muslim countries (Bangladesh, Malaysia and Indonesia) providing the facts of countries that practise zakat in comparison with those that do not.
Red Lists and conservation prioritization of plant communities – a methodological framework
Authors: Berg Christian , Abdank Anja , Isermann Maike , Jansen Florian , Timmermann Tiemo , Dengler Jürgen
Published: January 2014

Aims

Red Lists of threatened species are a well‐established conservation tool throughout the world. In contrast, Red Lists of ecosystems, habitats or plant community types have only recently found interest at the global level, although they have a longer tradition in Central Europe. We contribute to the debate by presenting and discussing a comprehensive conservation assessment methodology for plant communities that was developed within the framework of the project ‘The plant communities of Mecklenburg‐Vorpommern and their vulnerability’.

Location

Mecklenburg‐Vorpommern, Northeast Germany (23,174 km²).

Approach

Our approach adopts various concepts from modern red listing and prioritization at various organizational levels of biodiversity, and combines them into a methodological framework applicable for regional to continental Red Lists of plant communities. For each distinguished plant community, three steps are carried out, i.e. (1) assessment of endangerment (scientific part, using the three criteria ‘past trend’, ‘current status’ and ‘prognosis’), (2) assessment of conservation value (normative part, using the three criteria ‘degree of naturalness’, ‘relevance for species conservation’ and ‘global relevance’), and (3) a combination of (1) and (2) to derive a need for action (conservation prioritization). These steps are all based on the successive aggregation of quantitative criteria via decision matrices, which makes the assessment process transparent, avoids definition gaps and allows easy adjustment of the decision rules.

Conclusions

Plant community types derived from well‐documented classifications of extensive vegetation‐plot databases in combination with a transparent conservation assessment methodology have great potential in nature conservation and environmental monitoring. We suggest that the presented methodology is an improvement on traditional expert judgments as it separates the scientific and normative parts of the evaluation and uses clear, quantitative criteria and explicit rules to connect these into aggregated measures. It worked effectively and yielded meaningful results for a German federal state. By adjusting the scaling of the criteria, the approach can be adapted, as a whole or in part, to other regions or higher levels of ecosystem typology.
Grassland vegetation of the Molinio‐Arrhenatheretea class in the NW Balkan Peninsula
Authors: Šilc Urban , Aćić Svetlana , Škvorc Željko , Krstonošić Daniel , Franjić Jozo , Dajić Stevanović Zora
Published: January 2014

Questions

How does the floristic composition of plant species of meadows and mesic pastures vary along a broad geographical gradient in the NW Balkans? How does the current phytosociological classification of the Molinio‐Arrhenatheretea vegetation differ among the NW Balkan countries?

Location

NW Balkans (Slovenia, Croatia, Bosnia and Herzegovina, Serbia).

Methods

3635 relevés originally assigned to the class Molinio‐Arrhenatheretea were classified with a beta flexible method, and the crispness of classification was checked. DCA ordination with Pignatti indicator values and climate data were applied to show the influence of site conditions on species composition.

Results

The classification was best interpreted at the level of 13 clusters, but could also be interpreted at the level of three groups of clusters. The first division was according to geography and climate: the first and third groups were concentrated in the NW part, while the second was restricted to the eastern part of the study area. The most important variable was site moisture, followed by nutrients and altitude, which corresponded with a west–east direction. The first group was very diverse and included communities on the wettest and most nutrient‐rich sites (Potentillion anserinae, Cynosurion cristati, Calthion palustris, Molinion caeruleae, Molinio‐Hordeion). The second group comprised mesophilous continental grasslands (Trifolio‐Ranunculion pedati, Trifolion pallidi, Trifolion resupinati), while the third group consisted of grasslands from regions with abundant precipitation (Arrhenatherion elatioris, Deschampsion cespitosae, Pancicion serbicae, Triseto flavescentis‐Polygonion bistortae).

Conclusions

Our analysis can be used to unify different phytosociological classifications in different countries, also showing the transitional forms of well‐known Central European vegetation types that have a different floristic composition and ecology in the Balkans. This knowledge will enable classification of the same vegetation types in neighbouring Balkan countries that are less studied.
Identification of causal effects in the presence of nonignorable missing outcome values
Authors: Mattei Alessandra , Mealli Fabrizia , Pacini Barbara
Published: January 2014

We consider a new approach to identify the causal effects of a binary treatment when the outcome is missing on a subset of units and dependence of nonresponse on the outcome cannot be ruled out even after conditioning on observed covariates. We provide sufficient conditions under which the availability of a binary instrument for nonresponse allows us to derive tighter identification intervals for causal effects in the whole population and to partially identify causal effects in some latent subgroups of units, named Principal Strata, defined by the nonresponse behavior in all possible combinations of treatment and instrument. A simulation study is used to assess the benefits of the presence versus the absence of an instrument for nonresponse. The simulation design is based on real health data, coming from a randomized trial on breast self‐examination (BSE) affected by a large proportion of missing outcome data. An instrument for nonresponse is simulated considering alternative scenarios to discuss the key role of the instrument for nonresponse in identifying average causal effects in presence of nonignorable missing outcomes. We also investigate the potential inferential gains from using an instrument for nonresponse adopting a Bayesian approach for inference. In virtue of our theoretical and empirical results, we provide some recommendations on study designs for causal inference.
Estimation of stage duration distributions and mortality under repeated cohort censuses
Authors: Knape Jonas , Daane Kent M. , de Valpine Perry
Published: January 2014

Many processes in nature can be viewed as arising from subjects progressing through sequential stages and may be described by multistage models. Examples include disease development and the physiological development of plants and animals. We develop a multistage model for sampling designs where a small set of subjects is followed and the number of subjects in each stage is assessed repeatedly for a sequence of time points, but for which the subjects cannot be identified. The motivating problem is the laboratory study of developing arthropods through stage frequency data. Our model assumes that the same individuals are censused at each time, introducing among sample dependencies. This type of data often occur in laboratory studies of small arthropods but their detailed analysis has received little attention. The likelihood of the model is derived from a stochastic model of the development and mortality of the individuals in the cohort. We present an MCMC scheme targeting the posterior distribution of the times of development and times of death of individuals. This is a novel type of MCMC that uses customized proposals to explore a posterior with disconnected support arising from the fact that individual identities are unknown. The MCMC algorithm may be used for inference about parameters governing stage duration distributions and mortality rates. The method is demonstrated by fitting the development model to stage frequency data of a mealybug cohort placed on a grape vine.
Assessing the significance of global and local correlations under spatial autocorrelation: A nonparametric approach
Authors: Viladomat Júlia , Mazumder Rahul , McInturff Alex , McCauley Douglas J. , Hastie Trevor
Published: January 2014

We propose a method to test the correlation of two random fields when they are both spatially autocorrelated. In this scenario, the assumption of independence for the pair of observations in the standard test does not hold, and as a result we reject in many cases where there is no effect (the precision of the null distribution is overestimated). Our method recovers the null distribution taking into account the autocorrelation. It uses Monte‐Carlo methods, and focuses on permuting, and then smoothing and scaling one of the variables to destroy the correlation with the other, while maintaining at the same time the initial autocorrelation. With this simulation model, any test based on the independence of two (or more) random fields can be constructed. This research was motivated by a project in biodiversity and conservation in the Biology Department at Stanford University.