bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Abstract
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.
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

AbstractMotivation: 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.comSupplementary 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

Abstract
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

Abstract
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

Abstract
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

ABSTRACTObjective: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.
The mandibular gland inNasonia vitripennis(Hymenoptera: Pteromalidae)
Authors: Mikó István , Deans Andrew R. 
Published: June 2014

ABSTRACTThe 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 proliferationSummaryKey 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

Summary

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

Summary

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

SummaryAn 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.
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

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

SummaryImaging 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

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

AbstractAimTo 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.MethodThe 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.ResultsTo 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.ConclusionThe 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.