bluuebunny/crossref_metadata_2025 huggingface dataset:
Corrigendum to: Impacts of level of utilisation by grazing on an Astrebla (Mitchell grass) grassland in north-western Queensland between 1984 and 2010. 1. Herbage mass and population dynamics of Astrebla spp.
Authors: Orr D. M. , Phelps D. G.
Published: June 2014

Managing large variations in herbage production, resulting from highly variable seasonal rainfall, provides a major challenge for the sustainable management of Astrebla (Mitchell grass) grasslands in Australia. A grazing study with sheep was conducted between 1984 and 2010 on an Astrebla grassland in northern Queensland to describe the effects of a range of levels of utilisation of the herbage at the end of the summer growing season (April–May in northern Australia) on the sustainability of these grasslands. In unreplicated paddocks, sheep numbers were adjusted annually to achieve 0, 10, 20, 30, 50 and 80% utilisation of the herbage mass at the end of the summer over the ensuing 12 months. Higher levels of utilisation reduced both total and Astrebla spp. herbage mass because of the effects of higher utilisation on Astrebla spp. and this effect was accentuated by drought. The tussock density of Astrebla spp. varied widely among years but with few treatment differences until 2005 when density was reduced at the 50% level of utilisation. A major change in density resulted from a large recruitment of Astrebla spp. in 1989 that influenced its density for the remainder of the study. Basal area of the tussocks fluctuated among years, with increases due to rainfall and decreases during droughts. Seasonal rainfall was more influential than level of utilisation in changes to the basal area of perennial grasses. Drought resulted in the death of Astrebla spp. tussocks and this effect was accentuated at higher levels of utilisation. A series of three grazing exclosures were used to examine the recovery of the density and basal area of Astrebla spp. after it had been reduced by 80% utilisation over the preceding 9 years. This recovery study indicated that, although grazing exclusion was useful in the recovery of Astrebla spp., above-average rainfall was the major factor driving increases in the basal area of perennial grasses. Spring values of the Southern Oscillation Index and associated rainfall probabilities were considered to have potential for understanding the dynamics of Astrebla spp. It was concluded that Astrebla grassland remained sustainable after 26 years when grazed at up to 30% utilisation, while, at 50% utilisation, they became unsustainable after 20 years. Results from this study emphasised the need to maintain the population of Astrebla spp. tussocks.
Corrigendum to: Impacts of level of utilisation by grazing on an Astrebla (Mitchell grass) grassland in north-western Queensland between 1984 and 2010. 2. Plant species richness and abundance
Authors: Orr D. M. , Phelps D. G.
Published: June 2014

The occurrence of interstitial species in Astrebla grasslands in Australia are influenced by grazing and seasonal rainfall but the interactions of these two influences are complex. This paper describes three studies aimed at determining and explaining the changes in plant species richness and abundance of the interstitial species in a long-term sheep utilisation experiment in an Astrebla grassland in northern Queensland. In the first study, increasing utilisation increased the frequency of Dactyloctenium radulans (Button grass) and Brachyachne convergens (Downs couch) and reduced that of Streptoglossa adscendens (Mint bush). In the second study, seasonal rainfall variation between 1984 and 2009 resulted in large annual differences in the size of the seed banks of many species, but increasing utilisation consistently reduced the seed bank of species such as Astrebla spp. and S. adscendens and increased that of species such as B. convergens, D. radulans, Amaranthus mitchellii (Boggabri) and Boerhavia sp. (Tar vine). In the third study, the highest species richness occurred at the lightest utilisation because of the presence of a range of palatable forbs, especially legumes. Species richness was reduced as utilisation increased. Species richness in the grazing exclosure was low and similar to that at the heaviest utilisation where there was a reduction in the presence of palatable forb species. The pattern of highest species richness at the lightest grazing treatment was maintained across three sampling times, even with different amounts of seasonal rainfall, but there was a large yearly variation in both the density and frequency of many species. It was concluded that the maintenance of highest species richness at the lightest utilisation was not aligned with other data from this grazing experiment which indicated that the maximum sustainable wool production occurred at moderate utilisation.
Nutrient and microbial loss in relation to timing of rainfall following surface application of dairy farm manure slurries to pasture
Authors: Laurenson S. , Houlbrooke D. J.
Published: June 2014

This study investigated nutrient and faecal microbe (Escherichia coli) loss in surface runoff following application of dairy manure slurry to intact soil monoliths. Time between manure slurry application and first simulated rainfall event varied from 0 to 20 days. Manure slurries of varying dry matter (DM) content, ranging from 3 to 14%, were also investigated. Results indicated that phosphorus (P), nitrogen (N) and E. coli concentrations decreased with time since application because of chemical and physical breakdown of the manure. Greatest risk to water quality occurred when rainfall was received within 2 days of manure slurry application. When the period between manure slurry application and first rainfall event was ≥10 days, concentrations of N, P and faecal microbes was generally similar to those from dairy grazed pasture. Variation in slurry DM content appears to have little effect on measured runoff concentrations. Results suggest that manure slurries should be applied ≥2 days before rainfall events likely to cause surface runoff in order to limit nutrient and faecal microbe loss when applying manure slurries.
Biological charge transfer via flickering resonance
Authors: Zhang Yuqi , Liu Chaoren , Balaeff Alexander , Skourtis Spiros S. , Beratan David N.
Published: June 2014

Significance

Electron transport through DNA plays a central role in nucleic acid damage and repair, and it is usually modeled using a carrier tunneling mechanism (at short distances) and a hopping mechanism (at longer distances). We find that fluctuations into transient geometries that bring multiple bases into electronic degeneracy may support band-like transport during the resonance lifetimes over a distance of ≲15 Å, obviating the need to invoke electron tunneling at short distances. This line of research may help to reveal mechanisms of charge transport in multiheme proteins, bacterial nanowires, and synthetic nanowires, and may also assist in framing the mechanisms of coherent multipigment excitonic transport in light-harvesting proteins.
The
B2
flowering time locus of beet encodes a zinc finger transcription factor
Authors: Dally Nadine , Xiao Ke , Holtgräwe Daniela , Jung Christian
Published: June 2014

Significance

Flowering must be strictly avoided in crop plants whose vegetative parts (such as leaves or roots) are harvested. A new flowering time regulator has been cloned from a root crop (sugar beet) which acts epistatically to a recently identified bolting gene. Mutations in each of the two genes resulted in a loss of competence to flower without vernalization. This offers a perspective to breed “never bolting” hybrids by combining two mutations in each of both genes. Those cultivars would have a higher yield potential because they could be grown over winter or early in spring.
On Language Distribution in Ilam Province, Iran
Authors: Aliakbari Mohammad , Gheitasi Mojtaba , Anonby Erik
Published: June 2014

As is still the case in many parts of Iran, the distribution of languages and dialects in Ilam Province, western Iran, is unevenly documented. There have been several studies on specific language varieties spoken throughout the province but, in large part because of conflicting perspectives on the relationship between language and ethnicity, the situation for the region as a whole has until now remained unclear. The present study first of all brings together existing sociolinguistic and demographic data on language distribution and highlight areas of uncertainty. The main part of the study provides an overview of local perceptions of language distribution and language use based on field research and interviews conducted in each of the province's ten regions (shahrestān) and their twenty-five districts (bakhsh). Here, respondents' assessments of the geographic extent of the province's four main languages—Kurdish, Luri, Laki and Arabic—as well as more minor languages spoken by immigrants from elsewhere in Iran are summarized. For Kurdish in particular, which is the major of the four languages, the article shows the perceived geographic distribution of each major dialect and its affiliation within one of two major Kurdish dialect groups: Ilāmi (or “Feyli”) and Kalhōri. This analysis is followed by a brief discussion of multilingualism. The results of the study are brought together in a map of the province's languages.
Movement with Touch and Sound in the Sesame Approach: Bringing the Bones to the Flesh
Authors: Porter Rachel
Published: June 2014

Movement with Touch and Sound (MTS), a specific element of the Sesame approach to dramatherapy, is often said to be indescribable. This paper investigates the experience of a small but varied group of Sesame-trained dramatherapists. Similarities between interviewees’ descriptions tie together the data through corresponding themes. A thread throughout is the idea of paradox and how it makes it hard to pin the subject down. Despite its mercurial quality, key elements of MTS are found and techniques identified. This work attempts to bring together the flesh of change in contemporary practice with what remains unchanged in the essence of the subject – the so-called bones.
Urine 3-hydroxykynurenine is higher during the postovulatory phase than in the preovulatory phase indicating a higher vitamin B6 requirement
Authors: Shibata Katsumi
Published: June 2014

The relationship between l-tryptophan to nicotinamide metabolism and the menstrual cycle of Japanese women was investigated. Nine metabolism intermediates from urine samples collected during the preovulatory and postovulatory phases were measured. Only urine 3-hydroxykynurenine was higher in the postovulatory phase than in the preovulatory phase. This increase in 3-hydroxykynurenine suggests a decreased reaction of 3-hydroxykynurenine → 3-hydroxyanthranilic acid catalyzed by kynureninase, a vitamin B6 enzyme.
Enhancement of exercise endurance capacity by fermented deer antler in BALB/c mice
Authors: Jang Seongho , Park Eu Ddeum , Suh Hyung Joo , Lee Sang Hun , Kim Jin Soo , Park Yooheon
Published: June 2014

To investigate the activity of fermented deer antler on exercise endurance capacity, we evaluated endurance capacity in five-week-old male BALB/c mice by administering the fermented deer antler extract (FA) or the non-fermented deer antler extract (NFA) and then subjected the mice to exercise in the form of swimming. The mice administered 500 mg/kg/day of FA showed a significant increase in swimming time compared with mice administered placebo (16.55 min vs. 21.64 min, P < 0.05). Serum lactate dehydrogenase (LDH), the marker of the liver and muscle damage, was significantly lower in FA groups. However, NFA groups did not show significantly different swimming time or serum LDH from that of the control group. Moreover, the FA-500 group had significantly higher hepatic superoxide dismutase (SOD) activity after forced swimming than the control and NFA groups (P < 0.05). These findings suggest that fermentation may increase the exercise endurance capacity of the deer antler.
Fungal colonization and enzyme-mediated metabolism of waste coal by Neosartorya fischeri strain ECCN 84
Authors: Sekhohola Lerato Mary , Isaacs Michelle Louise , Cowan Ashton Keith
Published: June 2014

Colonization and oxidative metabolism of South African low-rank discard coal by the fungal strain ECCN 84 previously isolated from a coal environment and identified as Neosartorya fischeri was investigated. Results show that waste coal supported fungal growth. Colonization of waste coal particles by N. fischeri ECCN 84 was associated with the formation of compact spherical pellets or sclerotia-like structures. Dissection of the pellets from liquid cultures revealed a nucleus of “engulfed” coal which when analyzed by energy dispersive X-ray spectroscopy showed a time-dependent decline in weight percentage of elemental carbon and an increase in elemental oxygen. Proliferation of peroxisomes in hyphae attached to coal particles and increased extracellular laccase activity occurred after addition of waste coal to cultures of N. fischeri ECCN 84. These results support a role for oxidative enzyme action in the biodegradation of coal and suggest that extracellular laccase is a key component in this process.
The Art Therapy Practice Research Network: Hurdles, pitfalls and achievements
Authors: Huet Val , Springham Neil , Evans Chris
Published: June 2014

Aim: This article gives an overview of the setting up of the Art Therapy Practice Research Network (ATPRN) in 2000, amidst a culture resistant to research. The authors discuss their experiences in changing this culture and encouraging art therapists to become practitioner/researchers. They identify learning points that may be helpful for other professionals who want to form new practice research networks (PRNs). Context: The research and practice context contemporary to the ATPRN foundation is outlined and identified as a significant influence on its inception and development. Key events in the 14 years of the PRN's life and articles on art therapy and psychotherapy research published at the time of the ATPRN foundation are used to illuminate the historical context. ATPRN newsletters and symposium reports were consulted to identify themes and issues across 14 years of development and growth. Learning points: Several learning points are identified and listed as useful factors to address when setting up and maintaining a PRN and include: shape the culture from the start; review and revise; get practical together; encourage members' presentations; build synergy with professional body; embed the ATPRN around all aspects of research publication. Conclusions: Successful PRNs depend on making practitioners feel included from the start by acknowledging fear and anxiety about research. Providing practical projects helped practitioners to feel less isolated by being part of a meaningful and productive network. Maintaining and developing PRNs is an iterative process that demands constant reviewing and revising.
Therapist orientation, supervisor match, and therapeutic interventions: Implications for session quality in a psychotherapy training PRN
Authors: Mcaleavey Andrew A. , Castonguay Louis G. , Xiao Henry
Published: June 2014

Background: Theoretical orientation is a multifaceted construct that is integral to the process of psychotherapy and psychotherapy training. While some research has been conducted on personal identification with particular schools of psychotherapy, techniques used in psychotherapy sessions, and match between trainees and supervisors in training, there is insufficient information regarding how these may interact with one another. Aim: This study, conducted in a practice research network of trainee therapists, was designed to test whether these variables may be related to one another in predicting session quality. Method: The sample comprised 328 sessions from 26 clients and 11 therapists, with the clients completing session quality measures and therapists completing measures of technique immediately post‐session. Results: Using multilevel linear modelling, the data showed varied results. For behavioural therapy and person‐centred therapy, techniques and orientation were unrelated to session quality in the sample. However, process‐experiential, psychodynamic, and cognitive therapy techniques were all involved in interactions with therapist and/or supervisor orientations. Conclusions: These results suggest that the impact of specific psychotherapy techniques sometimes depends on the orientation of the therapist and/or supervisor. For instance, sessions high in cognitive therapy techniques were only associated with positive outcome when both the therapist and supervisor were highly cognitively oriented. Though preliminary, these results suggest that orientation may be an important variable to consider in training and supervision, especially in the context of other variables.
LIM kinase regulation of cytoskeletal dynamics is required for salivary gland branching morphogenesis
Authors: Ray Shayoni , Fanti Joseph A. , Macedo Diego P. , Larsen Melinda
Published: June 2014

Coordinated actin microfilament and microtubule dynamics is required for salivary gland development, although the mechanisms by which they contribute to branching morphogenesis are not defined. Because LIM kinase (LIMK) regulates both actin and microtubule organization, we investigated the role of LIMK signaling in mouse embryonic submandibular salivary glands using ex vivo organ cultures. Both LIMK 1 and 2 were necessary for branching morphogenesis and functioned to promote epithelial early- and late-stage cleft progression through regulation of both microfilaments and microtubules. LIMK-dependent regulation of these cytoskeletal systems was required to control focal adhesion protein–dependent fibronectin assembly and integrin β1 activation, involving the LIMK effectors cofilin and TPPP/p25, for assembly of the actin- and tubulin-based cytoskeletal systems, respectively. We demonstrate that LIMK regulates the early stages of cleft formation—cleft initiation, stabilization, and progression—via establishment of actin stability. Further, we reveal a novel role for the microtubule assembly factor p25 in regulating stabilization and elongation of late-stage progressing clefts. This study demonstrates the existence of multiple actin- and microtubule-dependent stabilization steps that are controlled by LIMK and are required in cleft progression during branching morphogenesis.
VEGF-A isoforms differentially regulate ATF-2–dependent VCAM-1 gene expression and endothelial–leukocyte interactions
Authors: Fearnley Gareth W. , Odell Adam F. , Latham Antony M. , Mughal Nadeem A. , Bruns Alexander F. , Burgoyne Nicholas J. , Homer-Vanniasinkam Shervanthi , Zachary Ian C. , Hollstein Monica C. , Wheatcroft Stephen B. , Ponnambalam Sreenivasan
Published: June 2014

Vascular endothelial growth factor A (VEGF-A) regulates many aspects of vascular physiology. VEGF-A stimulates signal transduction pathways that modulate endothelial outputs such as cell migration, proliferation, tubulogenesis, and cell–cell interactions. Multiple VEGF-A isoforms exist, but the biological significance of this is unclear. Here we analyzed VEGF-A isoform–specific stimulation of VCAM-1 gene expression, which controls endothelial–leukocyte interactions, and show that this is dependent on both ERK1/2 and activating transcription factor-2 (ATF-2). VEGF-A isoforms showed differential ERK1/2 and p38 MAPK phosphorylation kinetics. A key feature of VEGF-A isoform–specific ERK1/2 activation and nuclear translocation was increased phosphorylation of ATF-2 on threonine residue 71 (T71). Using reverse genetics, we showed ATF-2 to be functionally required for VEGF-A–stimulated endothelial VCAM-1 gene expression. ATF-2 knockdown blocked VEGF-A–stimulated VCAM-1 expression and endothelial–leukocyte interactions. ATF-2 was also required for other endothelial cell outputs, such as cell migration and tubulogenesis. In contrast, VCAM-1 was essential only for promoting endothelial–leukocyte interactions. This work presents a new paradigm for understanding how soluble growth factor isoforms program complex cellular outputs and responses by modulating signal transduction pathways.
H 3 M 2 : detection of runs of homozygosity from whole-exome sequencing data
Authors: Magi Alberto , Tattini Lorenzo , Palombo Flavia , Benelli Matteo , Gialluisi Alessandro , Giusti Betti , Abbate Rosanna , Seri Marco , Gensini Gian Franco , Romeo Giovanni , Pippucci Tommaso
Published: June 2014

Motivation: Runs of homozygosity (ROH) are sizable chromosomal stretches of homozygous genotypes, ranging in length from tens of kilobases to megabases. ROHs can be relevant for population and medical genetics, playing a role in predisposition to both rare and common disorders. ROHs are commonly detected by single nucleotide polymorphism (SNP) microarrays, but attempts have been made to use whole-exome sequencing (WES) data. Currently available methods developed for the analysis of uniformly spaced SNP-array maps do not fit easily to the analysis of the sparse and non-uniform distribution of the WES target design.

Results: To meet the need of an approach specifically tailored to WES data, we developed H3M2 , an original algorithm based on heterogeneous hidden Markov model that incorporates inter-marker distances to detect ROH from WES data. We evaluated the performance of H3M2 to correctly identify ROHs on synthetic chromosomes and examined its accuracy in detecting ROHs of different length (short, medium and long) from real 1000 genomes project data. H3M2 turned out to be more accurate than GERMLINE and PLINK, two state-of-the-art algorithms, especially in the detection of short and medium ROHs.

Availability and implementation : H3M2 is a collection of bash, R and Fortran scripts and codes and is freely available at https://sourceforge.net/projects/h3m2/ .

Contact : albertomagi@gmail.com

Supplementary information : Supplementary data are available at Bioinformatics online.
Executive Summary: Practice Guidelines for the Diagnosis and Management of
Skin and Soft Tissue Infections: 2014 Update by the Infectious Diseases Society of
America
Authors: Stevens Dennis L. , Bisno Alan L. , Chambers Henry F. , Dellinger E. Patchen , Goldstein Ellie J. C. , Gorbach Sherwood L. , Hirschmann Jan V. , Kaplan Sheldon L. , Montoya Jose G. , Wade James C.
Published: June 2014

A panel of national experts was convened by the Infectious Diseases Society of America (IDSA) to update the 2005 guidelines for the treatment of skin and soft tissue infections (SSTIs). The panel's recommendations were developed to be concordant with the recently published IDSA guidelines for the treatment of methicillin-resistant Staphylococcus aureus infections. The focus of this guideline is the diagnosis and appropriate treatment of diverse SSTIs ranging from minor superficial infections to life-threatening infections such as necrotizing fasciitis. In addition, because of an increasing number of immunocompromised hosts worldwide, the guideline addresses the wide array of SSTIs that occur in this population. These guidelines emphasize the importance of clinical skills in promptly diagnosing SSTIs, identifying the pathogen, and administering effective treatments in a timely fashion.
A sea change: Johan Hjort and the natural fluctuations in the fish stocks
Authors: Schwach Vera
Published: June 2014

That recruitment of juveniles to the stocks of fish is subject to natural variations is considered a scientific truth, if not a truism, in marine science. However, in 1914, when the zoologist Johan Hjort (1869–1948) published the notion, it meant a basic change in the understanding of the biology of the sea fish. A century later, his insight is a topic still at the centre of interest in fish biology. Hjort based his concept largely on investigations of herring (Clupea harengus) and cod (Gadus morhua) in the North Atlantic. He was the mastermind, but worked with a small group at the Directorate of Fisheries in Bergen, Norway, and in cooperation with the International Council for the Exploration of the Sea (ICES). The theory of natural fluctuations prompted an important step from migration thinking to population thinking, and gave the emerging fish biology and multidisciplinary marine science a theoretical basis. The article aims to explore the set of important facts and reasoned ideas intended to explain the causes for variations in year classes, and in this the fluctuations in the recruitment to the stocks. It argues that in addition to scientific factors, economic and political circumstances had an important say in the shaping of the understanding of stock fluctuations. The mere existence of a theory does not alone account for a breakthrough, and the article draws attention to the acceptance of scientific results.
The first analytical expression to estimate photometric redshifts suggested by a machine
Authors: Krone-Martins A. , Ishida E. E. O. , de Souza R. S.
Published: June 2014

We report the first analytical expression purely constructed by a machine to determine photometric redshifts (zphot) of galaxies. A simple and reliable functional form is derived using 41 214 galaxies from the Sloan Digital Sky Survey Data Release 10 (SDSS-DR10) spectroscopic sample. The method automatically dropped the u and z bands, relying only on g, r and i for the final solution. Applying this expression to other 1417 181 SDSS-DR10 galaxies, with measured spectroscopic redshifts (zspec), we achieved a mean 〈(zphot − zspec)/(1 + zspec)〉 ≲ 0.0086 and a scatter σ(zphot − zspec)/(1 + zspec) ≲ 0.045 when averaged up to z ≲ 1.0. The method was also applied to the PHAT0 data set, confirming the competitiveness of our results when faced with other methods from the literature. This is the first use of symbolic regression in cosmology, representing a leap forward in astronomy-data-mining connection.
Anastomotic Ulcerations After Intestinal Resection in Infancy
Authors: Charbit‐Henrion Fabienne , Chardot Christophe , Ruemmele Frank , Talbotec Cécile , Morali Alain , Goulet Olivier , Colomb Virginie
Published: June 2014

Objective:

Anastomotic ulceration (AU) is a rare complication after intestinal resection and anastomosis, described mostly in children. The main symptom is occult bleeding, leading to iron‐deficiency anemia, which is life threatening.

Methods:

The present survey reports a series of patients with AU after intestinal resection in infancy, focusing on predictive factors, medical and surgical treatment options, and long‐term outcomes. Eleven patients (7 boys) born between 1983 and 2005 with AU after an intestinal resection and anastomosis in infancy were included in this retrospective review.

Results:

The diagnosis of AU was often delayed for several years. No predictive factor (including the primary disease, the length of the remnant bowel, and the loss of the ileocaecal valve) could be identified. Numerous treatment options, including antibiotics and anti‐inflammatory drugs, proved to be ineffective to induce prolonged remission. Even after surgical resection, relapses were observed in 5/7 children.

Conclusions:

The mechanism leading to AU remains unknown. Contrary to previous reports with limited follow‐up, no medical or surgical treatment could prevent recurrences. Because relapses may occur several years after treatment, long‐term follow‐up is needed.
Sulfurovum aggregans sp. nov., a hydrogen-oxidizing, thiosulfate-reducing chemolithoautotroph within the Epsilonproteobacteria isolated from a deep-sea hydrothermal vent chimney, and an emended description of the genus Sulfurovum
Authors: Mino Sayaka , Kudo Hideaki , Arai Takayuki , Sawabe Tomoo , Takai Ken , Nakagawa Satoshi
Published: June 2014

A novel mesophilic, strictly hydrogen-oxidizing, sulfur-, nitrate- and thiosulfate-reducing bacterium, designated strain Monchim33T, was isolated from a deep-sea hydrothermal vent chimney at the Central Indian Ridge. The non-motile, rod-shaped cells were Gram-stain-negative and non-sporulating. Growth was observed between 15 and 37 °C (optimum 33 °C; 3.2 h doubling time) and between pH 5.4 and 8.6 (optimum pH 6.0). The isolate was a strictly anaerobic chemolithoautotroph capable of using molecular hydrogen as the sole energy source and carbon dioxide as the sole carbon source. The G+C content of the genomic DNA was 42.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the novel isolate belonged to the genus

Sulfurovum

and was closely related to

Sulfurovum sp.
NBC37-1 and

Sulfurovum lithotrophicum

42BKT (95.6 and 95.4 % similarity, respectively). DNA–DNA hybridization demonstrated that the novel isolate could be differentiated genotypically from

Sulfurovum sp.
NBC37-1 and

Sulfurovum lithotrophicum

. On the basis of the molecular and physiological traits of the new isolate, the name Sulfurovum aggregans sp. nov. is proposed, with the type strain Monchim33T ( = JCM 19824T = DSM 27205T).
Rapid identification of Acinetobacter baumannii, Acinetobacter nosocomialis and Acinetobacter pittii with a multiplex PCR assay
Authors: Chen Te-Li , Lee Yi-Tzu , Kuo Shu-Chen , Yang Su-Pen , Fung Chang-Phone , Lee Shou-Dong
Published: June 2014

Acinetobacter baumannii, Acinetobacter nosocomialis and Acinetobacter pittii are clinically relevant members of the Acinetobacter calcoaceticus–A. baumannii (Acb) complex and important nosocomial pathogens. These three species are genetically closely related and phenotypically similar; however, they differ in their epidemiology, antibiotic resistance and pathogenicity. In this study, we investigated the use of a multiplex PCR-based assay designed to detect internal fragments of the 16S–23S rRNA intergenic region and the gyrB and recA genes. The assay was capable of differentiating A. baumannii, A. nosocomialis and A. pittii in a reliable manner. In 23 different reference strains and 89 clinical isolates of Acinetobacter species, the assay accurately identified clinically relevant Acb complex species except those ‘between 1 and 3’ or ‘close to 13TU’. None of the non-Acb complex species was misidentified. In an analysis of 1034 positive blood cultures, the assay had a sensitivity of 92.4 % and specificity of 98.2 % for Acb complex identification. Our results show that a single multiplex PCR assay can reliably differentiate clinically relevant Acb complex species. Thus, this method may be used to better understand the clinical differences between infections caused by these species.
The mandibular gland inNasonia vitripennis(Hymenoptera: Pteromalidae)
Authors: Mikó István , Deans Andrew R.
Published: June 2014

The mandibular gland ofNasonia vitripennis(Hymenoptera: Pteromalidae) is visualized for the first time, using Confocal Laser Scanning Microscopy and dissection. The gland was previously hypothesized to exist, based on observations of the wasp’s courtship behaviors, but its presence had never been confirmed.
ADP-ribose derived Nuclear ATP is Required for Chromatin Remodeling and Hormonal Gene Regulation (97 charact)
Authors: Wright Roni H. G. , LeDily Francois , Soronellas Daniel , Pohl Andy , Bonet Jaume , Nacht A. S. , Vicent Guillermo P. , Wierer Michael , Oliva Baldo , Beato Miguel
Published: June 2014

Highlights

–

Hormonal gene regulation requires synthesis of PAR and its degradation to ADP-ribose by PARG

–

ADP-ribose is converted to ATP in the cell nuclei by hormone-activated NUDIX5/NUDT5

–

Blocking nuclear ATP formation precludes hormone-induced chromatin remodeling, gene regulation and cell proliferation

Key nuclear processes in eukaryotes including DNA replication or repair and gene regulation require extensive chromatin remodeling catalyzed by energy consuming enzymes. How the energetic demands of such processes are ensured in response to rapid stimuli remains unclear. We have analyzed this question in the context of the massive gene regulation changes induced by progestins in breast cancer cells and found that ATP is generated in the cell nucleus via the hydrolysis of poly-ADP-ribose to ADP-ribose. Nuclear ATP synthesis requires the combined enzymatic activities of PARP1, PARG and NUDIX5/NUDT5. Although initiated via mitochondrial derived ATP, the nuclear source of ATP is essential for hormone induced chromatin remodeling, gene regulation and cell proliferation and may also participate in DNA repair. This novel pathway reveals exciting avenues of research for drug development.
Exclusion of herbivores slows down recovery after experimental warming and nutrient addition in an alpine plant community
Authors: Olsen Siri L. , Klanderud Kari
Published: June 2014

Global change, such as climate warming and nitrogen deposition, has been predicted to induce non‐reversible regime shifts in natural ecosystems. However, we lack knowledge of the potential for recovery from global change perturbations and factors influencing the recovery rate.

We examined the recovery of an alpine plant community from a combined warming and nutrient addition experiment, which initially caused profound changes in plant community composition and diversity. We also examined whether the recovery process was affected by herbivory, as the presence of herbivores has been shown to modify the response of plant communities to global change.

Many aspects of the alpine plant community had not recovered from experimental warming and nutrient addition 6 years after cessation of the treatments. A persistent shift in vascular plant species composition seemed to inhibit recovery and maintain a community dominated by highly competitive grasses at the expense of the previously dominating dwarf shrub Dryas octopetala, lichens and bryophytes.

The exclusion of herbivores decreased the community recovery rate by maintaining unfavourable conditions for lichens and bryophytes.

Synthesis. Our findings suggest that a shift in dominance hierarchies in arctic and alpine plant communities due to global change is not readily reversible. Herbivory may, however, facilitate plant community recovery.
Phylogenetic tree shape and the structure of mutualistic networks
Authors: Chamberlain Scott , Vázquez Diego P. , Carvalheiro Luisa , Elle Elizabeth , Vamosi Jana C.
Published: June 2014

Species community composition is known to alter the network of interactions between two trophic levels, potentially affecting its functioning (e.g. plant pollination success) and the stability of communities. Phylogenies vary in shape with regard to the rate of evolutionary change across a tree (influencing tree balance) and variation in the timing of branching events (affecting the distribution of node ages in trees), both of which may influence the structure of species interaction networks. Because related species are likely to share many of the traits that regulate interactions, the shape of phylogenetic trees may provide some insights into the distribution of traits within communities, and hence the likelihood of interaction among species. However, little attention has been paid to the potential effects of changes in phylogenetic diversity (PD) on interaction networks.

Phylogenetic diversity is influenced by species diversity within a community, but also how distantly‐related the constituent species are from one another. Here, we evaluate the relationship between two important measures of phylogenetic diversity (tree shape and age of nodes) and the structure of plant–pollinator interaction networks using empirical and simulated data. Whereas the former allows us to evaluate patterns in real communities, the latter allows us to evaluate more systematically the relationship between tree shape and network structure under three different models of trait evolution.

In empirical networks, less balanced plant phylogenies were associated with lower connectance in interaction networks indicating that communities with the descendants of recent radiations are more diverged and specialized in their partnerships. In simulations, tree balance and the distribution of nodes through time were included in the best models for modularity, and the second best models for connectance and nestedness. In models assuming random evolutionary change through time (i.e. Brownian motion), less balanced trees and trees with nodes near the tips exhibited greater modularity, whereas in models with an early burst of radiation followed by relative stasis (i.e. early‐burst models) more balanced trees and trees with nodes near roots had greater modularity.

Synthesis. Overall, these results suggest that the shape of phylogenies can influence the structure of plant–pollinator interaction networks. However, the mismatch between simulations and empirical data indicate that no simple model of trait evolution mimics that observed in real communities.
Genome of the halotolerant green alga Picochlorum sp. reveals strategies for thriving under fluctuating environmental conditions
Authors: Foflonker Fatima , Price Dana C. , Qiu Huan , Palenik Brian , Wang Shuyi , Bhattacharya Debashish
Published: June 2014

An expected outcome of climate change is intensification of the global water cycle, which magnifies surface water fluxes, and consequently alters salinity patterns. It is therefore important to understand the adaptations and limits of microalgae to survive changing salinities. To this end, we sequenced the 13.5 Mbp genome of the halotolerant green alga Picochlorum SENEW3 (SE3) that was isolated from a brackish water pond subject to large seasonal salinity fluctuations. Picochlorum SE3 encodes 7367 genes, making it one of the smallest and most gene dense eukaryotic genomes known. Comparison with the pico‐prasinophyte Ostreococcus tauri, a species with a limited range of salt tolerance, reveals the enrichment of transporters putatively involved in the salt stress response in Picochlorum SE3. Analysis of cultures and the protein complement highlight the metabolic flexibility of Picochlorum SE3 that encodes genes involved in urea metabolism, acetate assimilation and fermentation, acetoin production and glucose uptake, many of which form functional gene clusters. Twenty‐four cases of horizontal gene transfer from bacterial sources were found in Picochlorum SE3 with these genes involved in stress adaptation including osmolyte production and growth promotion. Our results identify Picochlorum SE3 as a model for understanding microalgal adaptation to stressful, fluctuating environments.
Taking Evolution Seriously, or Metaphorically? A Review of Interactions between Historical Institutionalism and Darwinian Evolutionary Theory
Authors: Ma Shu-Yun
Published: June 2014

Since the mid-1980s, political scientists, in particular historical institutionalists, have employed evolutionary theory to study institutional stasis and change. More recently, there have been calls for ‘taking evolution seriously’. This article will frame the earlier uses of evolutionary theory by historical institutionalists, and the recent calls for ‘taking evolution seriously’ into a hierarchy of levels of interaction between natural and social sciences. Put in this perspective, the earlier efforts can be seen as limiting the use of evolutionary theory at the lowest, metaphorical level. On the other hand, the recent calls are striving to advance political science’s interaction with biological science to analogous and homologous levels, and even make it part of the larger project of generalizing Darwinism. These are noble scientiﬁc explorations. However, they should not lead to an impression that using evolutionary theory metaphorically is necessarily unserious.
Numb chin syndrome: A case series of a clinical syndrome associated with malignancy
Authors: Tejani Neetu , Cooper Adam , Rezo Angela , Pranavan Gane , Yip Desmond
Published: June 2014

Introduction

Information regarding the appropriate work‐up and outcomes in patients receiving palliative treatment for numb chin syndrome (NCS) in the setting of malignancy is sparse. This study aims to describe NCS in malignancy and evaluate the disease trajectory, significance of diagnostic modalities and outcomes with palliative treatment.

Methods

A retrospective study was performed on patients presenting with NCS between March 2007 and October 2013 at the Capital Region Cancer Service, Canberra.

Results

Thirteen patients were identified who presented with numbness of the chin between March 2007 and October 2013. Seven patients had breast cancer, two had prostate cancer, two had multiple myeloma, one had medulloblastoma and one had an adenoid cystic salivary gland tumour. The mean interval from initial cancer diagnosis to development of the syndrome was 4.32 years. Twelve out of 13 patients had had prior chemotherapy with two or more lines of treatment (with a median of two lines), indicating this condition tended to present late in the course of disease in our patients. Four patients developed bilateral symptoms, and in two of these cases the metastatic lesion was in the base of the skull. Eleven out of 13 patients had positive signs on imaging. Nine out of 13 patients received palliative radiotherapy, with clinical response in eight patients.

Conclusion

Patients with malignancy presented with NCS late in the disease trajectory, often after multiple lines of treatment. In our cohort of patients, 84% had positive imaging signs to aid diagnosis, and 77% had resolution of numbness with palliative treatment.
‘Do not touch’ lesions of the skull base
Authors: Dobre Mircea C , Fischbein Nancy
Published: June 2014

Imaging of the skull base presents many challenges due to its anatomical complexity, numerous normal variants and lack of familiarity to many radiologists. As the skull base is a region which is not amenable to physical examination and as lesions of the skull base are generally difficult to biopsy and even more difficult to operate on, the radiologist plays a major role in directing patient management via accurate image interpretation. Knowledge of the skull base should not be limited to neuroradiologists and head and neck radiologists, however, as the central skull base is routinely included in the field of view when imaging the brain, cervical spine, or head and neck with computed tomography or magnetic resonance imaging, and hence, its nuances should be familiar to general radiologists as well. We herein review the imaging findings of a subcategory of lesions of the central skull base, the ‘do not touch’ lesions.
Safety of less frequent monitoring of liver transaminases levels in rheumatic patients treated with low‐dose methotrexate
Authors: Khabbazi Alireza , Kolahi Sousan , Dastgiri Saeed , Hajialiloo Mehrzad , Nazeri Mahshid , Nazeri Leila , Sheikholeslami Salmasi Arefe , Gader Sevda , Bak Mohammad Zadeh Shagayegh , Ghasemi Aisan , Poormohammad Arezu
Published: June 2014

Aim

Consideration of the safety of liver transaminases monitoring every 12 weeks in patients with inflammatory connective tissue disorders who are treated with methotrexate (MTX).

Methods

In a retrospective study, the data from rheumatic patients receiving MTX were analyzed. Alanine aminotransferase (ALT) and aspartate aminotransferase (AST) were measured every 12 weeks. Based on the physician's final decision about the continuation of MTX, the patients were classified into one of the following groups: continuation of MTX without MTX dose reduction, MTX dose reduction, MTX discontinuation due to liver complication and MTX discontinuation due to other reasons.

Results

A total of 809 patients who were on MTX were included in the study. The mean follow‐up duration and the mean duration of treatment with MTX were 31.22 and 19.76 months, respectively. The mean accumulation dose of MTX was 865.85 mg. Due to the increase in the level of transaminases in 3.2% of the patients, MTX dose was reduced; and in 1.1% of the cases it was temporarily discontinued. In the follow‐up of the patients with elevated transaminases, they returned to normal limits in 99.5% of patients; and only in four cases (0.5%) they remained elevated and MTX was discontinued. The probability of the patients remaining on MTX for 5 years without discontinuation for liver complications was 98.5%

Conclusion

Liver transaminase monitoring every 12 weeks for MTX‐treated patients is safe.
Translation, cultural adaptation and validation of the WHO fracture risk assessment tool (FRAX®) into Bengali
Authors: Islam Md. Nazrul , Ferdous Nira , ten Klooster Peter M. , Uddin M. Sheikh Giash , Nasrin Salma , Pal Bipasha , Rasker Johannes J.
Published: June 2014

Aim

To develop a translated and culturally adapted Bengali version of the WHO Fracture Risk Assessment Tool (FRAX®) and to test its feasibility, content validity and reliability.

Method

The English FRAX was translated and culturally adapted for use in Bangladeshi populations following established forward–backward translation methods and being extensively field‐tested. The final version was interviewer‐administered to 130 consecutive osteoporotic patients between 40 and 90 years of age. For test–retest reliability, the questionnaire was re‐administered after 14 days in 60 odd serial‐numbered patients.

Results

To better match with the Bengali culture, several adaptations were made to the FRAX items, including replacements and additions for tobacco, prednisolone and alcohol use. The response rate of the pre‐final Bengali version of FRAX was 100% and all patients could understand the questions. Test–retest reliability (Pearson's r) in osteoporotic patients was > 0.93 for all items.

Conclusion

The culturally adapted Bengali version of the FRAX appears to be an acceptable and reliable instrument. Further studies are needed to confirm the ability of the tool to accurately predict the 10‐year probability of hip and major osteoporotic fractures in the Bengali population.
Transport and release procedures in reintroduction programs: stress and survival in grey partridges
Authors: Jenni L. , Keller N. , Almasi B. , Duplain J. , Homberger B. , Lanz M. , Korner‐Nievergelt F. , Schaub M. , Jenni‐Eiermann S.
Published: June 2014

During translocations, stress, as measured by the increase of glucocorticoids, cannot be avoided, but has been suspected to exacerbate the vulnerability to many causes of mortality after release. Therefore, measures to reduce stress have been proposed, such as keeping animals in pens before release (soft release). In this study, we investigated two open questions in translocations: (1) whether stress caused by the translocation procedure has an effect on survival; (2) whether soft release allows recovering from stress induced by capture and transportation. Hand‐raised grey partridges showed a moderate adrenocortical response to transportation and kept the capacity to mount a stress response to a new acute stressor, partly by a decrease of corticosteroid‐binding globulin capacity. In contrast to studies demonstrating a pervasive effect of capture and transport by virtual elimination of a proper stress response, we demonstrated a robust stress response and a return of baseline levels to pre‐transport levels after 33 h of acclimatization. Possibly captive‐bred birds may be less sensitive to capture and transportation than wild‐caught birds. During the first month after release, birds held 33 h in release pens survived better when their corticosterone levels were lower. However, survival beyond the first month did not differ between birds held 9 or 33 h in acclimatization pens. Elevated glucocorticoids, as induced by the translocation procedure, likely affect short‐term survival after release. We recommend glucocorticoid stress levels be surveyed in an appropriate subsample and minimized during translocations.