bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single-cell genomics reveals complex carbohydrate degradation patterns in poribacterial symbionts of marine sponges
Authors: Kamke Janine , Sczyrba Alexander , Ivanova Natalia , Schwientek Patrick , Rinke Christian , Mavromatis Kostas , Woyke Tanja , Hentschel Ute 
Published: July 2013

Abstract
Many marine sponges are hosts to dense and phylogenetically diverse microbial communities that are located in the extracellular matrix of the animal. The candidate phylum Poribacteria is a predominant member of the sponge microbiome and its representatives are nearly exclusively found in sponges. Here we used single-cell genomics to obtain comprehensive insights into the metabolic potential of individual poribacterial cells representing three distinct phylogenetic groups within Poribacteria. Genome sizes were up to 5.4 Mbp and genome coverage was as high as 98.5%. Common features of the poribacterial genomes indicated that heterotrophy is likely to be of importance for this bacterial candidate phylum. Carbohydrate-active enzyme database screening and further detailed analysis of carbohydrate metabolism suggested the ability to degrade diverse carbohydrate sources likely originating from seawater and from the host itself. The presence of uronic acid degradation pathways as well as several specific sulfatases provides strong support that Poribacteria degrade glycosaminoglycan chains of proteoglycans, which are important components of the sponge host matrix. Dominant glycoside hydrolase families further suggest degradation of other glycoproteins in the host matrix. We therefore propose that Poribacteria are well adapted to an existence in the sponge extracellular matrix. Poribacteria may be viewed as efficient scavengers and recyclers of a particular suite of carbon compounds that are unique to sponges as microbial ecosystems.
Measurement Error in Fish Lengths: Evaluation and Management Implications
Authors: Bunch Aaron J , Walters Carl J , Coggins Lewis G 
Published: July 2013

ABSTRACT
A fundamental aspect of fisheries science is measuring body length. Humans are inherently prone to error despite systems and provisions made to reduce it. We evaluated length measurement error (herein, referred to as “error”) and digit preference from fish studies conducted on the Colorado River and Little Colorado River in Arizona. Empirical error estimates varied among fish species and generally increased with fish size. We identified a digit preference for numbers ending in zero and five, which was exacerbated with larger sizes. Error effects on growth estimates were largest for fish recaptured after a short time, and we suggest guarding against the error phenomenon by removing data from fish captured and recaptured within a minimum of 30 days. Human, situation, and specimen induced error factors are described. Fisheries professionals should be cognizant of error factors, especially in situations when high precision and accuracy are required and results have important management implications.
RESUMEN
un aspecto fundamental en las ciencias pesqueras es la medición de la talla corporal. Los humanos somos inherentemente propensos a cometer errores pese a los sistemas y medidas preventivas que se utilizan para reducirlos. En este trabajo se evalúa el error asociado a la medición de la talla (en lo sucesivo se le llamará “error”) y la preferencia en el número de dígitos en los estudios ícticos llevados a cabo en el Río Colorado y el Río Coloradito, Arizona. Los estimados empíricos del error variaron entre especies de peces y en general se incrementaron conforme la aumenta la talla de los peces. Se identificaron preferencias en cuanto al número de dígitos para los números con terminación cero y cinco, lo cual se amplificó en los peces más grandes. Los efectos del error en las estimaciones de crecimiento fueron más grandes en el caso de los peces recién recapturados. Se sugiere tratar el fenómeno del error mediante la remoción de los datos provenientes de peces recapturados en los primeros 30 días después de su liberación. Se describen los factores de error humano, de medición y asociado al espécimen. Los profesionales de las pesquerías deben ser conscientes de los factores de error, especialmente en situaciones en las que se requieren precisión y exactitud y cuando hay implicaciones importantes para el manejo.
Physiological Stress Response of Yellow Perch Subjected to Repeated Handlings and Salt Treatments at Different Temperatures
Authors: Eissa Nour , Wang Han-Ping 
Published: July 2013

Abstract
Yellow Perch Perca flavescens were subjected to handling stress and salt treatments at different temperatures to determine their physiological changes. Yellow Perch, held at 8–10°C, were divided into three groups with four replicates and subjected to water temperatures of 14, 20, and 26°C to acclimate. Then they were subjected to acute handling twice within separate intervals, in addition to a salt treatment at a salinity of 5‰ for each of the fish groups. Plasma cortisol was used as a stress indicator, and blood samples were taken periodically for plasma cortisol concentration analysis. An increase in plasma cortisol after handling occurred in all groups, but the lowest level of plasma cortisol was in fish subjected to 20°C. We concluded that the optimum water temperature for handling Yellow Perch that results in minimal stress may be 20°C. Salt treatment after handling further stimulated the stress response and increased plasma cortisol levels. Research is needed to identify the optimal salinity to use for Yellow Perch and other fish species when handling fish during common aquaculture practices.
Antimicrobial Activity of Honey Bee Venom against Select Infectious Fish Pathogens
Authors: Han Sang Mi , Lee Kwang Gill , Park Kwan Kyu , Pak Sok Cheon 
Published: July 2013

Abstract
In this study, bee venom (BV) isolated from honey bees Apis mellifera was assessed for its potential use as an antimicrobial agent against fish pathogenic bacteria. We used three bacterial isolates (Edwardsiella tarda, Vibrio ichthyoenteri, and Streptococcus iniae) that were originally obtained from the gastrointestinal tracts of moribund Olive Flounder Paralichthys olivaceus. Bee venom exhibited antibacterial activity against all three infectious fish pathogens. The minimum inhibitory concentration and minimum bactericidal concentration (mean ± SE) of BV were 17.6 ± 2.6 and 34.9 ± 3.4 μg/mL, respectively, against E. tarda; 1.76 ± 0.3 and 6.8 ± 2.6 μg/mL against V. ichthyoenteri; and 3.49 ± 0.9 and 11 ± 1.6 μg/mL against S. iniae. The postantibiotic effect of BV was 5 ± 0.6 h for E. tarda, 6 ± 0.3 h for V. ichthyoenteri, and 7 ± 0.6 h for S. iniae. In addition, the antimicrobial activity of BV was not pH dependent, as inhibition zones were identical at pH levels ranging from 2 to 11. These results indicate that BV inhibits the growth and survival of bacterial strains and that BV may be a useful complementary antimicrobial agent against fish pathogenic bacteria.
nhmmer: DNA homology search with profile HMMs
Authors: Wheeler Travis J. , Eddy Sean R. 
Published: July 2013

Abstract
Summary: Sequence database searches are an essential part of molecular biology, providing information about the function and evolutionary history of proteins, RNA molecules and DNA sequence elements. We present a tool for DNA/DNA sequence comparison that is built on the HMMER framework, which applies probabilistic inference methods based on hidden Markov models to the problem of homology search. This tool, called nhmmer, enables improved detection of remote DNA homologs, and has been used in combination with Dfam and RepeatMasker to improve annotation of transposable elements in the human genome.
Availability: nhmmer is a part of the new HMMER3.1 release. Source code and documentation can be downloaded from http://hmmer.org. HMMER3.1 is freely licensed under the GNU GPLv3 and should be portable to any POSIX-compliant operating system, including Linux and Mac OS/X.
Contact: wheelert@janelia.hhmi.org
Fingolimod Therapy and Macular Hemorrhage
Authors: Bhatti M. Tariq , Freedman S. Mitchell , Mahmoud Tamer H. 
Published: July 2013

Abstract:
A 54-year-old woman with relapsing-remitting multiple sclerosis (MS) developed visual loss in her left eye due to a macular hemorrhage 11 months after starting fingolimod. Visual acuity was 20/80 in the left eye, with a dense retinal hemorrhage involving the fovea with adjacent hard exudate and macular thickening confirmed by spectral domain optical coherence tomography. Three months after stopping fingolimod, vision in the left eye improved to 20/30 with resolution of the macular hemorrhage and exudates. Fingolimod has been associated with macular edema, but prior to this report, the authors are unaware of it causing a macular hemorrhage in a MS patient. The authors speculate that the macular hemorrhage may be due to a disruption of cellular adhesions between vascular endothelial cells that maintain the inner blood–retinal barrier.
Comparative Transcriptome Profiling of Maize Coleoptilar Nodes during Shoot-Borne Root Initiation
Authors: Muthreich Nils , Majer Christine , Beatty Mary , Paschold Anja , Schützenmeister André , Fu Yan , Malik Waqas Ahmed , Schnable Patrick S. , Piepho Hans-Peter , Sakai Hajime , Hochholdinger Frank 
Published: July 2013

Abstract
Maize (Zea mays) develops an extensive shoot-borne root system to secure water and nutrient uptake and to provide anchorage in the soil. In this study, early coleoptilar node (first shoot node) development was subjected to a detailed morphological and histological analysis. Subsequently, microarray profiling via hybridization of oligonucleotide microarrays representing transcripts of 31,355 unique maize genes at three early stages of coleoptilar node development was performed. These pairwise comparisons of wild-type versus mutant rootless concerning crown and seminal roots (rtcs) coleoptilar nodes that do not initiate shoot-borne roots revealed 828 unique transcripts that displayed RTCS-dependent expression. A stage-specific functional analysis revealed overrepresentation of “cell wall,” “stress,” and “development”-related transcripts among the differentially expressed genes. Differential expression of a subset of 15 of 828 genes identified by these microarray experiments was independently confirmed by quantitative real-time-polymerase chain reaction. In silico promoter analyses revealed that 100 differentially expressed genes contained at least one LATERAL ORGAN BOUNDARIES domain (LBD) motif within 1 kb upstream of the ATG start codon. Electrophoretic mobility shift assay experiments demonstrated RTCS binding for four of these promoter sequences, supporting the notion that differentially accumulated genes containing LBD motifs are likely direct downstream targets of RTCS.
Inhibitory effect of oral contraceptives on CYP2C19 activity is not significant in carriers of the CYP2C19*17 allele
Authors: Pedersen Rasmus S. , Noehr‐Jensen Lene , Brosen Kim 
Published: July 2013

Summary

The purpose of the present study was to examine whether cytochrome P450 2C19 (CYP2C19) in carriers of the CYP2C19*17 allele is inhibited in vivo by oral contraceptives (OC).

Retrospective CYP2C19 phenotyping according to omeprazole : 5‐OH‐omeprazole molar 3 h plasma metabolic ratios (MR) from a population (n = 222) genotyped as CYP2C19*1/*1, CYP2C19*1/*17 and CYP2C19*17/*17 was analysed. Furthermore, 30 women genotyped as CYP2C19*1/*1 (n = 11), CYP2C19*1/*17 (n = 11) and CYP2C19*17/*17 (n = 8) were prospectively CYP2C19 phenotyped during the administration of OC and again after a minimum 5 days break from OC.

We found a significantly higher MR in the CYP2C19*1/*1 genotype group that took OC (n = 48) compared with women who did not take OC (n = 31; geometric mean 1.37 vs 0.83, respectively; P < 0.05). However, in the CYP2C19*1/*17 genotype group, the geometric means of the MR in the 37 women taking OC and the 20 women not taking OC were 0.67 and 0.46, respectively (P > 0.05). In the CYP2C19*1/*1 panel of the prospective cross‐over study, we found a significantly higher MR while women were taking the OC compared with the MR during the OC break (geometric mean 1.21 vs 0.91, respectively; P = 0.0123). However, in the CYP2C19*1/*17 group, the geometric means of the MR with and without OC were 0.77 and 0.65, respectively, compared with 1.05 and 0.79, respectively, in the CYP2C19*17/*17 group (P = 0.20 and 0.17, respectively).

In conclusion, we have shown that OC intake inhibits CYP2C19 in homozygous carriers of the CYP2C19 wild type but that the inhibition is not significant in heterozygous and homozygous carriers of the CYP2C19*17 allele.
Use of eye‐pointing by children with cerebral palsy: what are we looking at?
Authors: Sargent Jenefer , Clarke Michael , Price Katie , Griffiths Tom , Swettenham John 
Published: July 2013

AbstractBackgroundChildren with cerebral palsy often show significant communication impairment due to limited or absent speech. Further, motor impairment can restrict the use of movement, including pointing, to signal interest and intent. For some children, controlled gaze can be an effective ‘point‐substitute’: such ‘eye‐pointing’ can be used to request items, establish mutual interest in an event, or select vocabulary within an alternative or augmentative communication (ACC) system. However, in clinical practice there is a lack of clarity about how the term ‘eye‐pointing’ is used, how ‘eye‐pointing’ is recognized or how it relates to social development.AimsTo present a clinical description of the term ‘eye‐pointing’ with reference to children with severe cerebral palsy who cannot speak or finger‐point. To consider this description within a wider discussion of the importance of gaze in communication development.Methods & ProceduresCumulative clinical observations during assessment of children referred to a specialist multidisciplinary communication clinic have provoked discussion between the authors on what factors precipitate use of the term ‘eye‐pointing’ in young children with severe cerebral palsy. In particular, discussion has centred on whether use of the term is appropriate in individual cases and whether guidance is available about how gaze should be observed in this developmentally vulnerable group of children. A literature search was also conducted in order to explore whether the use and meaning of the term is established.Conclusions & ImplicationsIn interactions with non‐speaking children, determining whether a child is using eye‐gaze communicatively requires observation and interpretation of several factors. These processes will be informed by reflection on what is known about other aspects of the child's communication and interaction skills. Within the literature, the term ‘eye‐pointing’ is sometimes used when describing the communication functions of individuals using augmentative and alternative communication (AAC) systems, and is occasionally qualified by a definition. No papers have been found that set out a clinical description universally applicable to children with severe motor impairment. Moreover, guidance is lacking on how possible episodes of ‘eye‐pointing’ might be confidently distinguished from other episodes of directed gaze in young, developing communicators. The discussion of the term makes reference to the importance of gaze in early communication development, and explores factors that might influence gaze and its interpretation in young children with cerebral palsy. A description of eye‐pointing for this group is offered. The authors suggest that this will bring practical benefits to those supporting the communication development of children with severe cerebral palsy.
How (Not) to Reform the Euro Area's Economic Governance
Authors: Collignon Stefan 
Published: July 2013

AbstractEuropean monetary union presents a paradox. On the one hand, despite three years of continuous battering and pounding, the euro still exists. On the other, the crisis has revealed serious flaws in the governance of the Euro Area and it has become clear that the old system of managing the euro macroeconomy is not sustainable. This article attempts to explain this apparent contradiction and how to resolve it.
Institutions for Crisis Prevention: the Case of Switzerland
Authors: Baur Martin , Bruchez Pierre‐Alain , Schlaffer Barbara 
Published: July 2013

AbstractThe Swiss economy's comparatively robust performance in the current economic crisis is partly the result of its characteristics, but public institutions also made Switzerland resilient. We focus here on institutions that foster sound public finances. The Swiss federal debt brake played a key role in keeping the federal debt in check; along with fiscal rules, institutions such as direct democracy and federalism counteract the biases that tend to make elected representatives less fiscally conservative than citizens. This leads to more well‐targeted public expenditure and greater public efficiency and helps to avoid excessively high taxes. These features are beneficial in ordinary times, and they increase the scope of action in times of crisis.
A Model for a Fiscal Union? What Europe Can Learn from the German Experience
Authors: Höhn Alfred , Schramm Thorsten , Straubhaar Thomas 
Published: July 2013

AbstractThe euro has strengthened the economic differences between a more affluent north and a struggling south, which is the core problem of the current crisis in the euro zone. A potential solution to this problem could be to transform the monetary union into a fiscal union. This article sketches two different models for fiscal unions: a federal structure like that of Germany, where federal revenues and expenditures are controlled in significant part by federals laws, which has an extensive bailout system built in; and a confederal system like that of Switzerland, where Cantons are autonomous in their fiscal policies but clear bankruptcy rules are implemented. The article describes the reasons for which the German arrangement, one that strongly relies on income equalisation, have not proven successful in harmonising the financial position of the Länder and municipalities and why bailouts have become rather the rule than the exception. In consequence Germany has introduced a debt brake that does not allow expenditures to be structurally higher than revenues. Although it is too early to evaluate the sustainability of such a mechanism yet, the debt brake seems to be a promising means for preventing an unsustainable built‐up of debt under normal economic conditions. This article concludes that as long as debt brakes are not fully implemented and further fiscal harmonisation cannot be expected, the European Union will still have to rely on market‐based regulatory instruments and the disciplinary function of interest rates, possibly culminating in a bankruptcy procedure.
What Governments Can Do to Support their Economies: The Case for a Strategic Econsystem
Authors: Meyer Henning , Klasen Andreas 
Published: July 2013

AbstractMore than half a decade after the outbreak of the greatest economic crisis since the Great Depression, the world economy is still facing serious difficulties. Much more than during a ‘normal’ recession, the Great Recession of recent years has uncovered serious structural problems in the world economy and has brought about levels of unemployment unprecedented in modern times (Elsby et al. ). It first became clear that the financial sector had become in effect self‐referential and too much removed from its traditional role of allocating finance throughout the whole economy (Menkhoff and Meyer, ). Following this, the structural weaknesses of the Euro were exposed leading to serious questions about the long‐term sustainability of the most ambitious currency union ever attempted.
Effects of animal liver and bile extracts on biochemical values of rat ethanol‐induced fatty liver
Authors: Wan Tien‐Chun , Liu Yu‐Tse , Duann Lan‐Tyi , Yu Kuo‐Hui , Chen Chih‐Ming , Lin Liang‐Chuan , Sakata Ryoichi 
Published: July 2013

AbstractThe purposes of this study were to assess the improvement of fatty liver induced by ethanol with animal liver and bile extracts. This research aimed to increase the economic values of animal liver and bile extracts and used these to reduce damage of ethanol‐induced fatty liver. Extracts came from animal liver and bile, including pig bile powder, pig liver extract, a mixture of pig bile powder and pig liver extract, chicken bile powder, chicken liver extract, and a mixture of chicken bile powder and chicken liver extract, and these were fed to Long‐Evans rats. The results showed that rats fed ethanol for long terms could increase values of aspartate transaminase, cholesterol, γ‐glutamy‐transferase and alkaline phosphatase. Pig bile powder could decrease the values of aspartate transaminase, cholesterol and γ‐glutamy‐transferase. The significances also decreased on aspartate transaminase, γ‐glutamy‐transferase and aspartate transaminase, which were carried out with the pig liver extract treatment. These results suggest pig bile and liver extracts have high potential to improve rats' ethanol‐induced fatty liver with serum biochemical parameters.
Latent factor regression models for grouped outcomes
Authors: Woodard D. B. , Love T. M. T. , Thurston S. W. , Ruppert D. , Sathyanarayana S. , Swan S. H. 
Published: July 2013

SummaryWe consider regression models for multiple correlated outcomes, where the outcomes are nested in domains. We show that random effect models for this nested situation fit into a standard factor model framework, which leads us to view the modeling options as a spectrum between parsimonious random effect multiple outcomes models and more general continuous latent factor models. We introduce a set of identifiable models along this spectrum that extend an existing random effect model for multiple outcomes nested in domains. We characterize the tradeoffs between parsimony and flexibility in this set of models, applying them to both simulated data and data relating sexually dimorphic traits in male infants to explanatory variables.
Diffuse large B‐cell lymphoma (Richter syndrome) in patients with chronic lymphocytic leukaemia (CLL): a cohort study of newly diagnosed patients
Authors: Parikh Sameer A. , Rabe Kari G. , Call Timothy G. , Zent Clive S. , Habermann Thomas M. , Ding Wei , Leis Jose F. , Schwager Susan M. , Hanson Curtis A. , Macon William R. , Kay Neil E. , Slager Susan L. , Shanafelt Tait D. 
Published: July 2013

SummaryNearly all information about patients with chronic lymphocytic leukaemia (CLL) who develop diffuse large B‐cell lymphoma [Richter syndrome (RS)] is derived from retrospective case series or patients treated on clinical trials. We used the Mayo Clinic CLL Database to identify patients with newly diagnosed CLL between January 2000 and July 2011. Individuals who developed biopsy‐proven RS during follow‐up were identified. After a median follow‐up of 4 years, 37/1641 (2·3%) CLL patients developed RS. The rate of RS was approximately 0·5%/year. Risk of RS was associated with advanced Rai stage at diagnosis (P < 0·001), high‐risk genetic abnormalitites on fluorescence in situ hybridization (P < 0·0001), unmutated IGHV (P = 0·003), and expression of ZAP70 (P = 0·02) and CD38 (P = 0·001). The rate of RS doubled in patients after treatment for CLL (1%/year). Stereotyped B‐cell receptors (odds‐ratio = 4·2; P = 0·01) but not IGHV4‐39 family usage was associated with increased risk of RS. Treatment with combination of purine analogues and alkylating agents increased the risk of RS three‐fold (odds‐ratio = 3·26, P = 0·0003). Median survival after RS diagnosis was 2·1 years. The RS prognosis score stratified patients into three risk groups with median survivals of 0·5 years, 2·1 years and not reached. Both underlying characteristics of the CLL clone and subsequent CLL therapy influence the risk of RS. Survival after RS remains poor and new therapies are needed.