bluuebunny/crossref_metadata_2025_split huggingface dataset:
Joint analysis of expression profiles from multiple cancers improves the identification of microRNA–gene interactions
Authors: Chen Xiaowei , Slack Frank J. , Zhao Hongyu 
Published: June 2013

Abstract
Motivation: MicroRNAs (miRNAs) play a crucial role in tumorigenesis and development through their effects on target genes. The characterization of miRNA–gene interactions will lead to a better understanding of cancer mechanisms. Many computational methods have been developed to infer miRNA targets with/without expression data. Because expression datasets are in general limited in size, most existing methods concatenate datasets from multiple studies to form one aggregated dataset to increase sample size and power. However, such simple aggregation analysis results in identifying miRNA–gene interactions that are mostly common across datasets, whereas specific interactions may be missed by these methods. Recent releases of The Cancer Genome Atlas data provide paired expression profiling of miRNAs and genes in multiple tumors with sufficiently large sample size. To study both common and cancer-specific interactions, it is desirable to develop a method that can jointly analyze multiple cancers to study miRNA–gene interactions without combining all the data into one single dataset.
Results: We developed a novel statistical method to jointly analyze expression profiles from multiple cancers to identify miRNA–gene interactions that are both common across cancers and specific to certain cancers. The benefit of this joint analysis approach is demonstrated by both simulation studies and real data analysis of The Cancer Genome Atlas datasets. Compared with simple aggregate analysis or single sample analysis, our method can effectively use the shared information among different but related cancers to improve the identification of miRNA–gene interactions. Another useful property of our method is that it can estimate similarity among cancers through their shared miRNA–gene interactions.
Availability and implementation: The program, MCMG, implemented in R is available at http://bioinformatics.med.yale.edu/group/.
Contact: hongyu.zhao@yale.edu
The response of plant diversity to grazing varies along an elevational gradient
Authors: Speed James D. M. , Austrheim Gunnar , Mysterud Atle 
Published: June 2013

Summary

Species richness of plants generally decreases along elevational gradients or peaks at intermediate elevations. Land use including grazing by wild and domestic herbivores also affects plant communities and diversity, but how grazing affects plant diversity along elevational gradients is less clear.

Using a field experiment along an elevational gradient in Norway, we tested whether the impact of grazing on plant diversity interacts with elevation. Vascular plant communities were sampled following 10 years of experimental sheep grazing (decreased/ceased, maintained and increased densities of 0, 25 and 80 sheep km−2) and compared with pre‐experimental baseline data.

The impact of grazing on species richness (alpha diversity) was investigated at the species level, and temporal community variance was used to investigate community stability (temporal beta diversity). Spatial community variance (spatial beta diversity) at the enclosure level was used to test whether community homogenization differed between treatments.

Species richness and temporal stability varied between treatments and along the elevational gradient. Where grazing was ceased, species richness declined by up 3.7 species at low elevations and increased by up to 3.5 species at high elevations, whilst where grazing was maintained or increased, changes were less extreme along the elevational gradient.

Temporal stability of plant communities was highest at low elevations and lowest at high elevations where grazing was reduced. There were no clear differences in spatial homogenization between grazing treatments, although spatial species turnover increased in heathlands where grazing decreased.

Synthesis. This study shows that the effect of grazing on plant diversity varies with elevation, and grazing herbivores can thus directly affect elevational patterns of plant diversity. Grazing can buffer changes in plant communities and species richness, even in the face of other environmental drivers such as climatic warming.
Effects of nutrient enrichment on seagrass population dynamics: evidence and synthesis from the biomass–density relationships
Authors: Cabaço Susana , Apostolaki Eugenia T. , García‐Marín Patricia , Gruber Renee , Hernández Ignacio , Martínez‐Crego Begoña , Mascaró Oriol , Pérez Marta , Prathep Anchana , Robinson Cliff , Romero Javier , Schmidt Allison L. , Short Fred T. , van Tussenbroek Brigitta I. , Santos Rui 
Published: June 2013

Summary

The available data from experimental and descriptive studies on seagrass biomass and density responses to nutrient enrichment were analysed to assess the intraspecific mechanisms operating within seagrass populations and whether biomass–density relationships can provide relevant metrics for monitoring seagrasses.

The response of shoot biomass and density to nutrient enrichment was dependent on the type of study; the short‐term positive response of biomass and density in experimental studies reveals context‐specific nutrient limitation of seagrasses. The long‐term negative response of descriptive studies probably results from ecosystem‐scale events related to nutrient enrichment such as increased turbidity, algal blooms, epiphyte loads and anoxia.

Most seagrass species analysed lie in the nonthinning part of the theoretical biomass–density curves. A simultaneous increase in biomass and decrease in density, evidence of self‐thinning, were only observed in 4 of 28 studies. The analysis of both the static and the dynamic biomass–density relationships revealed that the slopes increase under nutrient enrichment. Surprisingly, the species‐specific slopes (log B‐log D) were higher than one, revealing that the B/D ratio, that is, the average shoot biomass, increases with density in all seagrass species analysed. Nutrient enrichment further enhanced this effect as biomass–density slopes increased to even higher values. The main drivers behind the increasing biomass–density slopes under nutrient enrichment were the increase in shoot biomass at densities above a species‐specific threshold and/or its decrease below that threshold.

Synthesis. Contrasting short‐ and long‐term responses of both biomass and density of seagrasses to nutrient enrichment suggest that the former, positive ones result from nutrient limitation, whereas the later, negative ones are mediated by whole ecosystem responses. In general, shoot biomass of seagrasses increases with density, and nutrient enrichment enhances this effect. Experimental testing of facilitation processes related to clonal integration in seagrasses needs to be done to reveal whether they determine the low incidence of self‐thinning and the intriguing biomass–density relationships of seagrass species. The increasing slopes and decreasing intercepts of the species‐specific dynamic biomass–density relationships of seagrasses and the decreasing coefficients of variation of both biomass and density constitute relevant, easy‐to‐collect metrics that may be used in environmental monitoring.
Microbial survey of the mummies from the Capuchin Catacombs of Palermo, Italy: biodeterioration risk and contamination of the indoor air
Authors: Piñar Guadalupe , Piombino-Mascali Dario , Maixner Frank , Zink Albert , Sterflinger Katja 
Published: June 2013

Abstract
The Capuchin Catacombs of Palermo contain over 1800 preserved bodies dating from the 16th to 20th centuries AD and showing evidence of biodeterioration. An extensive microbiological and molecular investigation was recently performed. Samples were taken from skin, muscle, hair, bone, stuffing materials, clothes, and surrounding walls as well as from the indoor air. In this study, we witnessed that the different degradation phenomena observed on the variety of materials located at the Capuchin Catacombs of Palermo are biological in origin. Molecular techniques showed the dominance of halophilic species of the domains Bacteria and Archaea on the walls and – as a result of salt emanating from the walls – on the mummies themselves. Nevertheless, specialized microorganisms belonging to taxa well-known for their cellulolytic and proteolytic activities were detected on clothes and stuffing material, and on skin, muscle, hair, and bone, respectively. This specialized microbiota is threatening the conservation of the mummies themselves. Additionally, sequences related to the human skin microbiome and to some pathogenic Bacteria (order Clostridiales) and fungi (genus Phialosimplex) were identified on samples derived from the mummies. Furthermore, a phosphate-reducing fungus, Penicillium radicum, was detected on bone. Finally, the high concentration of airborne fungal spores is not conducive to the conservation of the human remains and is posing a potential health risk for visitors.
Iron status and developmental scores in 6‐year‐olds highlights ongoing need to tackle iron deficiency in infants
Authors: Thorisdottir Asa Vala , Gunnarsdottir Ingibjorg , Palsson Gestur I. , Gretarsson Sigurdur J. , Thorsdottir Inga 
Published: June 2013

AbstractAimTo investigate iron status and developmental scores at 6 years of age in a population with decreased prevalence of iron deficiency in infancy. Iron status at 6 years and tracking from 12 months were also studied.MethodsChildren (n = 143) born in Iceland in 2005 were followed up at the age of six. Motor and verbal development was assessed by a parental questionnaire, and iron status was assessed by Hb, MCV and serum ferritin (SF). Iron depletion was defined as SF <15 μg/L and deficiency as MCV <76 fL and SF <15 μg/L.ResultsIron depletion was observed in 5.6% of 6‐year‐olds, and 1.4% were iron deficient. Self‐help (subset in motor development) differed by −4.14 (95% CI = −7.61, −0.67), between those iron depleted at 12 months (n = 6) and those nondepleted (n = 102), adjusted for maternal education. The combined motor developmental score seemed lower in iron depleted infants, although of borderline significance (p = 0.066). MCV concentration tracked from 12 months to 6 years (r = 0.31, p < 0.002), but Hb and SF did not.ConclusionImproved iron status at 12 months and 6 years has diminished the public health threat associated with iron depletion in the population studied, but iron depletion and development still associate weakly. Action to prevent iron depletion in infancy remains important.
Genetics of steroid‐resistant nephrotic syndrome: a review of mutation spectrum and suggested approach for genetic testing
Authors: Joshi S , Andersen R , Jespersen B , Rittig S 
Published: June 2013

AbstractIdentification of genes, associated mutations and genotype–phenotype correlations in steroid‐resistant nephrotic syndrome (SRNS) is being translated to clinical practice through genetic testing. This review provides an update on the genes and mutations associated with SRNS along with a suggested approach for genetic testing in patients with SRNS.ConclusionThe number of indentified genes associated with SRNS is increasing along with our understanding of their impact on treatment response and risk of recurrence. A systematic approach to genetic testing in patients with SRNS might aid the physician in selecting appropriate treatment.
Central nervous system involvement with multiple myeloma: long term survival can be achieved with radiation, intrathecal chemotherapy, and immunomodulatory agents
Authors: Chen Christine I. , Masih‐Khan Esther , Jiang Haiyan , Rabea Ahmed , Cserti‐Gazdewich Christine , Jimenez‐Zepeda Victor H. , Chu Chia‐Min , Kukreti Vishal , Trudel Suzanne , Tiedemann Rodger , Tsang Richard , Reece Donna E. 
Published: June 2013

SummaryInvolvement of the central nervous system (CNS) in multiple myeloma (MM) is a rare complication, with reported survival of <6 months. This report describes 37 MM patients with leptomeningeal and/or parenchymal brain involvement treated at our institution and identifies factors associated with long‐term survival. From January 1999 to December 2010, 37 patients with CNS MM were evaluated at our institution. Clinical characteristics, treatment and survival were retrospectively collected. CNS disease was present at MM diagnosis in 24% and at relapse in 76%. Plasma cell leukemia (40%) and skull plasmacytomas (65%) were common, suggesting haematological and contiguous spread. Intrathecal (IT) chemotherapy was used in 81%, cranial and/or spinal irradiation in 78%, and various systemic therapies [immunomodulatory agents (IMiDs) (51%), cisplatin‐based (DPACE; cisplatin, doxorubicin, cyclophosphamide, etoposide) (27%), bortezomib (19%), alkylators (11%), dexamethasone alone (8%), auto‐transplant (5%)]. Median survival from CNS disease was only 4·6 months [95% confidence interval (CI): 2·8–6·7]; however, nine patients had prolonged survival (median: 17·1 months, 95% CI: 13·2–67·4). In general, these long‐term survivors were treated with radiotherapy, multi‐dosing IT chemotherapy, and IMiD‐containing therapy. CNS MM is a highly aggressive disease but in our experience, long‐term survival can be achieved with the combination of multi‐dosing IT chemotherapy, radiation and IMiD‐based therapy.
Microbiological screening for earlier detection of central venous catheter–related bloodstream infections
Authors: Wagner Jasmin , Schilcher Gernot , Zollner‐Schwetz Ines , Hoenigl Martin , Valentin Thomas , Ribitsch Werner , Horina Joerg , Rosenkranz Alexander R. , Grisold Andrea , Unteregger Matthias , Troppan Katharina , Valentin Angelika , Neumeister Peter , Krause Robert 
Published: June 2013

AbstractBackgroundCatheter‐related bloodstream infections (CRBSIs) are currently detected with a reactive diagnostic policy, that is, application of tests to patients with clinically suspected CRBSI. The aim of our study was to evaluate whether CRBSIs could be anticipated in an earlier stage by microbiological screening using peptide nucleic acid fluorescence in situ hybridization (PNA FISH) with universal hybridization probes or acridine‐orange leucocyte cytospin (AOLC) tests in haemodialysis and haematological patients with CVCs in situ compared with routine test.Materials and methodsPeptide nucleic acid fluorescence in situ hybridization (PNA FISH) and AOLC tests using blood samples from both CVC lines in patients undergoing haemodialysis were performed three times a week and from one CVC line in haematological patients were performed daily. Results were compared with those obtained from routinely performed CRBSI diagnostic tests.ResultsOne hundred fifteen patients with 139 catheter periods were investigated. The mean observation time per catheter period was 25 days (IQR 13·5–43·5), resulting in 5615 CVC days with a total of 4839 tested blood samples. Five CRBSI cases were detected by routine measures resulting in a CRBSI rate of 0·9/1000 catheter days. Four of five CRBSIs could be anticipated by positive PNA FISH and AOLC tests 2–8 days before the diagnosis was established with routine measures.ConclusionsThe proactive anticipative strategy using microscopic examination of CVC blood samples to anticipate CRBSI in an earlier stage compared with routine measures is a new diagnostic approach in patients with CVCs and a high risk of developing CRBSI.
A novel RT‐qPCR assay for quantification of the MLL‐MLLT3 fusion transcript in acute myeloid leukaemia
Authors: Abildgaard Lotte , Ommen Hans Beier , Lausen Birgitte , Hasle Henrik , Nyvold Charlotte Guldborg 
Published: June 2013

AbstractObjectivesPatients with acute myeloid leukaemia (AML) of the monocytic lineage often lack molecular markers for minimal residual disease (MRD) monitoring. The MLL‐MLLT3 fusion transcript found in patients with AML harbouring t(9;11) is amenable to RT‐qPCR quantification but because of the heterogeneity of translocation break points, the MLL‐MLLT3 fusion gene is a challenging target. We hypothesised that MRD monitoring using MLL‐MLLT3 as a RT‐qPCR marker is feasible in the majority of patients with t(9;11)‐positive AML.MethodsUsing a locked nucleic acid probe, we developed a sensitive RT‐qPCR assay for quantification of the most common break point region of the MLL‐MLLT3 fusion gene. Five paediatric patients with t(9;11)‐positive AML were monitored using the MLL‐MLLT3 assay.ResultsA total of 43 bone marrow (BM) and 52 Peripheral blood (PB) samples were collected from diagnosis until follow‐up. Two patients relapsed, and both were MRD positive in BM after first induction course. A total of three relapses occurred, and they were detected by RT‐qPCR 3 wks before haematological relapse was diagnosed.ConclusionThis MLL‐MLLT3 RT‐qPCR assay could be useful in MRD monitoring of a group of patients with AML who often lack reliable MRD markers.
The kinetic, mechanistic and cytomorphological effects of palytoxin in human intestinal cells (Caco‐2) explain its lower‐than‐parenteral oral toxicity
Authors: Fernández Diego A. , Louzao M. Carmen , Vilariño Natalia , Espiña Begoña , Fraga María , Vieytes Mercedes R. , Román Albina , Poli Mark , Botana Luis M. 
Published: June 2013

Palytoxin is one of the most toxic marine toxins known. Distributed worldwide, it poses a potential human health risk linked to the consumption of contaminated seafood. Despite its high parenteral toxicity, the lethal oral dose of palytoxin is several times higher than the intraperitoneal lethal dose. In the present study, we investigated the passage of palytoxin through the human intestinal barrier by employing a well‐characterized and accepted in vitro model of intestinal permeability that uses differentiated Caco‐2 cell monolayers. Trans‐epithelial electric resistance measurements showed that palytoxin disrupts the integrity of Caco‐2 monolayers at concentrations > 0.135 nm. However, confocal microscopy imaging showed that the tight‐junction protein occludin was not affected by palytoxin in the nanomolar range. This finding was supported by transmission electron microscopy imaging, where tight‐junctions appeared to be unaffected by palytoxin treatment. In addition, the nuclear envelope does not appear to be altered by high concentrations of palytoxin. However, palytoxin‐treated cells showed electron‐dense and damaged mitochondria. Toxin exposure also induced the disappearance of the differentiated Caco‐2 microvilli and organelles, as well as chromatin de‐condensation. Permeability assays showed that palytoxin could not significantly pass the Caco‐2 monolayer, despite the lack of epithelium integrity, suggesting that palytoxins would be poorly transported to blood, which may explain its lower oral toxicity. These data can help to achieve a better understanding of palytoxin poisoning. However, more studies regarding its repeated administration and chronic effects are needed.
Adiponectin protects Leydig cells against proinflammatory cytokines by suppressing the nuclear factor‐κB signaling pathway
Authors: Wu Ling , Xu Bufang , Fan Weimin , Zhu Xiaobin , Wang Guangyan , Zhang Aijun 
Published: June 2013

Adiponectin is an adipocyte hormone that is predominantly secreted by adipocytes, and has important roles in glucose and lipid homeostasis. Recent studies have shown that adiponectin is also involved in the regulation of many endocrine organs, such as the ovary, adrenal gland, and pituitary. However, its biological role in male testes is largely unexplored. The present findings demonstrate the presence of adeponectin receptors (adiponectin receptor 1 and adiponectin receptor 2) in TM3 cells derived from mouse Leydig cells. Proinflammatory cytokine treatment significantly downregulated mRNA and protein levels of adiponectin receptor 1 and adiponectin receptor 2. However, adiponectin pretreatment successfully inhibited the signaling pathway mediated by proinflammatory cytokines. At the molecular level, we provide compelling evidence that adeponectin achieves this by suppressing nuclear factor‐κB activation through promotion of AMP‐activated protein kinase phosphorylation. Thus, our data clearly indicate that adiponectin plays a protective role in Leydig cells through its anti‐inflammatory actions.
Low‐temperature atmospheric pressure plasma enhanced tooth whitening: the next‐generation technology
Authors: Claiborne D , McCombs G , Lemaster M , Akman MA , Laroussi M 
Published: June 2013

AbstractObjectivesTo evaluate the safety and effectiveness of the plasma pencil (PP) device in conjunction with H2O2 gel. The purpose of this study was to determine whether LTAPP delivered using the PP would enhance the tooth‐whitening process while causing no thermal threat.MethodsThe study consisted of thirty extracted human teeth that were randomized into two groups: Group I received LTAPP plus 36% H2O2 gel at 10, 15 and 20 min and Group II received 36% H2O2 gel only at the same time intervals. Tooth surface temperature was measured periodically throughout the experiment using a non‐contact thermometer. Digital photographs were taken pre‐ and post‐treatment and transferred to Adobe Photoshop for comparison, using the CIELAB Color Value System. Only L* (lightness) values were evaluated in this study. Data were analysed using descriptive statistics and t‐test at the 0.05 level.ResultsThe results revealed a statistically significant difference in mean CIE L* values after exposure to LTAPP plus 36% H2O2 gel, compared with 36% H2O2 only, in the 10‐ and 20‐min groups (P = 0.0003 and 0.0103, respectively). The temperature in both treatment groups remained under 80°F throughout the study, which is below the thermal threat for vital tooth bleaching.ConclusionUtilizing PP device in conjunction with 36% H2O2 safely accelerates and enhances the tooth‐whitening process.
NaOH treatment reduces capsaicin content and pungency of ‘Makedoniko’ pepper (Capsicum annuum L.)
Authors: Kosmidou Elisavet , Kefalas Panagiotis , Gerasopoulos Dimitrios 
Published: June 2013

SummaryPickled peppers are preferred by certain consumer groups at reduced pungency. To investigate the reduction in pepper pungency and capsaicin content, fresh ‘Makedoniko’ hot peppers were treated with 0, 0.5 or 1% NaOH before preserved in acid brine for 60 days. Pepper physicochemical traits were monitored following NaOH treatment and during preservation. Capsaicin content was measured in the beginning and at the end of preservation, and the peppers were also tested organoleptically. Preservation in acid brine induced the typical green–yellow product colour, increased firmness and decreased the dry mass in all treatments. NaOH‐treated pepper increased phenolics, chlorophyll and antioxidant content in dry mass during preservation faster than the control. Capsaicin content was reduced by 25 or 50% following 0.5 or 1% NaOH treatment, respectively. Pepper organoleptic pungency was also decreased following 1% NaOH treatment. NaOH reduces capsaicin content and pungency of ‘Makedoniko’ pepper, with minor effects on its processed product quality.