bluuebunny/crossref_metadata_2025 huggingface dataset:
Chromosome Conformation Capture (3C) in Budding Yeast
Authors: Belton Jon-Matthew , Dekker Job
Published: June 2015

Chromosome conformation capture (3C) is a method for studying chromosomal organization that takes advantage of formaldehyde cross-linking to measure the spatial association of two pieces of chromatin. The 3C method begins with whole-cell formaldehyde fixation of chromatin. After cell lysis, solubilized chromatin is digested with a type II restriction endonuclease, and cross-linked DNA fragments are ligated together. Cross-links are reversed by degradation with proteinase K, and chimeric DNA molecules are purified by standard phenol:chloroform extraction. The resulting 3C library represents chromatin fragments that may be separated by large genomic distances or located on different chromosomes, but are close enough in three-dimensional space for cross-linking. Locus-specific oligonucleotide primers are used to detect interactions of interest in the 3C library using end-point polymerase chain reaction (PCR).
Randomized Ligation Control for Chromosome Conformation Capture
Authors: Belton Jon-Matthew , Dekker Job
Published: June 2015

In experiments using chromosome conformation capture followed by PCR (3C-PCR) or chromosome conformation capture carbon copy (5C), it is critical to control for intrinsic biases in the restriction fragments of interest and the probes or primers used for detection. Characteristics such as GC%, annealing temperature, efficiency of 3C primers or 5C probes, and length of restriction fragment can cause variations in primer or probe performance and fragment ligation efficiency. Bias can be measured empirically by production of a random control library, as described here, to be used with the 3C library of interest.
Using the Vital Dye Acridine Orange to Detect Dying Cells in Drosophila
Authors: Denton Donna , Kumar Sharad
Published: June 2015

Acridine orange is a cell-permeable fluorescent dye that binds to nucleic acids, resulting in an altered spectral emission. Acridine orange staining has been shown to be highly selective for apoptotic cells in Drosophila; however, the precise mechanism underlying this effect is not known. Advantages of acridine orange staining include the speed and ease of the staining. But there are disadvantages: It should be performed on unfixed tissue that therefore must be examined immediately, and multiple labeling cannot be performed. Slightly different protocols for the uptake of acridine orange are required for different developmental stages. Here, we present protocols for use of acridine orange to detect apoptosis in Drosophila embryos and in larval tissue. Slight modifications might be required for other Drosophila tissues.
Using the ENCODE Resource for Functional Annotation of Genetic Variants
Authors: Pazin Michael J.
Published: June 2015

This article illustrates the use of the Encyclopedia of DNA Elements (ENCODE) resource to generate or refine hypotheses from genomic data on disease and other phenotypic traits. First, the goals and history of ENCODE and related epigenomics projects are reviewed. Second, the rationale for ENCODE and the major data types used by ENCODE are briefly described, as are some standard heuristics for their interpretation. Third, the use of the ENCODE resource is examined. Standard use cases for ENCODE, accessing the ENCODE resource, and accessing data from related projects are discussed. Although the focus of this article is the use of ENCODE data, some of the same approaches can be used with data from other projects.
Redetermined structure of gossypol (P3 polymorph)
Authors: Honkeldieva Muhabbat , Kunafiev Rishad , Hamidov Hayrullo I.
Published: June 2015

An improved crystal structure of the title compound, C30H30O8(systematic name: 1,1′,6,6′,7,7′-hexahydroxy-5,5′-diisopropyl-3,3′-dimethyl[2,2′-binaphthalene]-8,8′-dicarbaldehyde), was determined based on modern CCD data. Compared to the previous structure [Talipovet al.(1985).Khim. Prirod. Soedin. (Chem. Nat. Prod.),6, 20–24], geometrical precision has been improved (typical C—C bond-distance s.u. = 0.002 Å in the present structure compared to 0.005 Å in the previous structure) and the locations of several H atoms have been corrected. The gossypol molecules are in the aldehyde tautomeric form and the dihedral angle between the naphthyl fragments is 80.42 (4)°. Four intramolecular O—H...O hydrogen bonds are formed. In the crystal, inversion dimers with graph-set motifR22(20) are formed by pairs of O—H...O hydrogen bonds; another pair of O—H...O hydrogen bonds with the same graph-set motif links the dimers into [001] chains. The packing of such chains in the crystal leads to the formation of channels (diameter = 5–8 Å) propagating in the [101] direction. The channels presumably contain highly disordered solvent molecules; their contribution to the scattering was removed with the SQUEEZE [Spek (2015).Acta Cryst. C71, 9–18] routine inPLATONand the stated molecular mass, densityetc., do not take them into account.
Crystal structure of (E)-N′-(5-bromo-2-hydroxybenzylidene)nicotinohydrazide monohydrate
Authors: Sravya S. , Sruthy S. , Aiswarya N. , Sithambaresan M. , Kurup M. R. Prathapachandra
Published: June 2015

In the title compound, C13H10BrN3O2·H2O, the conformation about the azomethine double bond isE. The molecule exists in the amido form with a C=O bond length of 1.229 (2) Å. There is an intramolecular O—H...N hydrogen bond forming anS(6) ring motif. The whole molecule is almost planar, with an r.m.s. deviation of 0.021 Å for all non-H atoms, and the dihedral angle between the planes of the pyridine and benzene rings is 0.74 (12)°. In the crystal, the water molecule of crystallization links the organic moleculesviaOw—H...O, Ow—H...N and N—H...Ow hydrogen bonds and short C—H...Ow contacts, forming sheets lying parallel to (100). Within the sheets there is a weak π–π interaction involving the pyridine and benzene rings [centroid-to-centroid distance = 3.8473 (15) Å]. The sheets are linkedviaC—H...Br interactions, forming a three-dimensional network.
Crystal structure of methyl (S)-2-{(R)-4-[(tert-butoxycarbonyl)amino]-3-oxo-1,2-thiazolidin-2-yl}-3-methylbutanoate: a chemical model for oxidized protein tyrosine phosphatase 1B (PTP1B)
Authors: Ruddraraju Kasi Viswanatharaju , Hillebrand Roman , Barnes Charles L. , Gates Kent S.
Published: June 2015

The asymmetric unit of the title compound, C14H24N2O5S, contains two independent molecules (AandB). In each molecule, the isothiazolidin-3-one ring adopts an envelope conformation with the methylene C atom as the flap. In the crystal, theAmolecules are linked to one another by N—H...O hydrogen bonds, forming columns along [010]. TheBmolecules are also linked to one another by N—H...O hydrogen bonds, forming columns along the same direction,i.e.[010]. Within the individual columns, there are also C—H...S and C—H...O hydrogen bonds present. The columns ofAandBmolecules are linked by C—H...O hydrogen bonds, forming sheets parallel to (10-1). The absolute structure was determined by resonant scattering [Flack parameter = 0.00 (3)].
Chronic cigarette smoke exposure induces microbial and inflammatory shifts and mucin changes in the murine gut
Authors: Allais Liesbeth , Kerckhof Frederiek‐Maarten , Verschuere Stephanie , Bracke Ken R. , De Smet Rebecca , Laukens Debby , Van den Abbeele Pieter , De Vos Martine , Boon Nico , Brusselle Guy G. , Cuvelier Claude A. , Van de Wiele Tom
Published: June 2015

Inflammatory bowel diseases (IBD) are complex multifactorial diseases characterized by an inappropriate host response to an altered commensal microbiome and dysfunctional mucus barrier. Cigarette smoking is the best known environmental risk factor in IBD. Here, we studied the influence of chronic smoke exposure on the gut microbiome, mucus layer composition and immune factors in conventional mice. We compared smoke‐exposed with air‐exposed mice (n = 12) after a smoke exposure of 24 weeks. Both Illumina sequencing (n = 6) and denaturing gradient gel electrophoresis (n = 12) showed that bacterial activity and community structure were significantly altered in the colon due to smoke exposure. Interestingly, an increase of Lachnospiraceae sp. activity in the colon was observed. Also, the mRNA expression of Muc2 and Muc3 increased in the ileum, whereas Muc4 increased in the distal colon of smoke‐exposed mice (n = 6). Furthermore, we observed increased Cxcl2 and decreased Ifn‐γ in the ileum, and increased Il‐6 and decreased Tgf‐β in the proximal colon. Tight junction gene expression remained unchanged. We infer that the modulating role of chronic smoke exposure as a latently present risk factor in the gut may be driven by the altered epithelial mucus profiles and changes in microbiome composition and immune factors.
Effectiveness of physical activity interventions on preventing gestational diabetes mellitus and excessive maternal weight gain: a meta‐analysis
Authors: Sanabria‐Martínez G , García‐Hermoso A , Poyatos‐León R , Álvarez‐Bueno C , Sánchez‐López M , Martínez‐Vizcaíno V
Published: June 2015

Background

It is commonly accepted that pregnancy‐related physiological changes (circulatory, respiratory, and locomotor) negatively influence the daily physical activity of pregnant women.

Objectives

The aim of this study is to conduct a meta‐analysis of randomised controlled trials (RCTs) for assessing the effectiveness of physical exercise interventions during pregnancy to prevent gestational diabetes mellitus and excessive maternal weight gain.

Search strategy

Keywords were used to conduct a computerised search in six databases: Cochrane Library Plus, Science Direct, EMBASE, PubMed, Web of Science, and ClinicalTrials.gov.

Selection criteria

Healthy pregnant women who were sedentary or had low levels of physical activity were selected for RCTs that included an exercise programme.

Data collection and analysis

Two independent reviewers extracted data and assessed the quality of the included studies. Of 4225 articles retrieved, 13 RCTs (2873 pregnant women) met the inclusion criteria. Pooled relative risk (RR) or weighted mean differences (WMDs) (depending on the outcome measure) were calculated using a random‐effects model.

Main results

Overall, physical exercise programmes during pregnancy decreased the risk of gestational diabetes mellitus (RR = 0.69; P = 0.009), particularly when the exercise programme was performed throughout pregnancy (RR = 0.64; P = 0.038). Furthermore, decreases were also observed in maternal weight (WMD = −1.14 kg; 95% CI −1.50 to −0.78; P < 0.001). No serious adverse effects were reported.

Conclusion

Structured moderate physical exercise programmes during pregnancy decrease the risk of gestational diabetes mellitus and diminish maternal weight gain, and seem to be safe for the mother and the neonate; however, further studies are needed to establish recommendations.

Tweetable abstract

Exercise programmes decreased the risk of gestational diabetes mellitus and excessive weight gain.
Social structure and space use of Amur tigers (Panthera tigris altaica) in Southern Russian Far East based on GPS telemetry data
Authors: HERNANDEZ‐BLANCO Jose A. , NAIDENKO Sergei V. , CHISTOPOLOVA Maria D. , LUKAREVSKIY Victor S. , KOSTYRYA Alexey , RYBIN Alexandr , SOROKIN Pavel A. , LITVINOV Mikhail N. , KOTLYAR Andrey K. , MIQUELLE Dale G. , ROZHNOV Viatcheslav V.
Published: June 2015

To better understand the spatial structure of Amur tigers (Panthera tigris altaica) at the southern edge of their range we fitted 14 tigers (6♀♀ and 8♂♂) with 15 GPS‐Argos collars between 2008 and 2011 in 2 study sites: the Ussuriskii Reserve of southern Sikhote‐Alin and the Land of the Leopard National Park in southwest Primorye, Russian Far East. Fixed kernel estimates of male home ranges were larger than those of female home ranges (P < 0.05 [mean 95% fixed kernel♀ = 401 ± 205 km2; mean 95% fixed kernel♂ = 778 ± 267 km2]). The home range size of females varied greatly, but on average was similar to estimates derived from earlier work further north. Low overlap of adjacent home ranges suggested that females retained exclusive territories. Real core areas of females overlapped only slightly, and remained stable over multiple years. The home ranges of adult males were smaller than those of males to the north, and in contrast to previous studies, high overlap among males indicated the absence of territoriality. Nonetheless, real core areas of males did not overlap, suggesting some spatial separation. In comparison to other tiger populations and other areas of the Russian Far East, the sex ratio in our 2 study areas was highly skewed towards males. We believe this skewed sex ratio resulted in the dissolution of territoriality of males due to an inability to defend individual females, with males resorting to scramble competition for mates. Continued monitoring of these sites to determine whether shifts in the sex ratio might result in a return to male territoriality would provide confirmation of our tentative hypothesis.
High genetic diversity in the endangered and narrowly distributed amphibian speciesLeptobrachium leishanense
Authors: ZHANG Wei , LUO Zhenhua , ZHAO Mian , WU Hua
Published: June 2015

Threatened species typically have a small or declining population size, which make them highly susceptible to loss of genetic diversity through genetic drift and inbreeding. Genetic diversity determines the evolutionary potential of a species; therefore, maintaining the genetic diversity of threatened species is essential for their conservation. In this study, we assessed the genetic diversity of the adaptive major histocompatibility complex (MHC) genes in an endangered and narrowly distributed amphibian species,Leptobrachium leishanensein Southwest China. We compared the genetic variation of MHC class I genes with that observed in neutral markers (5 microsatellite loci and cytochromebgene) to elucidate the relative roles of genetic drift and natural selection in shaping the current MHC polymorphism in this species. We found a high level of genetic diversity in this population at both MHC and neutral markers compared with other threatened amphibian species. Historical positive selection was evident in the MHC class I genes. The higher allelic richness in MHC markers compared with that of microsatellite loci suggests that selection rather than genetic drift plays a prominent role in shaping the MHC variation pattern, as drift can affect all the genome in a similar way but selection directly targets MHC genes. Although demographic analysis revealed no recent bottleneck events inL. leishanense, additional population decline will accelerate the dangerous status for this species. We suggest that the conservation management ofL. leishanenseshould concentrate on maximizing the retention of genetic diversity through preventing their continuous population decline. Protecting their living habitats and forbidding illegal hunting are the most important measures for conservation ofL. leishanense.
Visions and Stones: Spirit Matters and the Charm of Small Things in South Korean Shamanic Rock Divination
Authors: Kim David J.
Published: June 2015

This article considers conceptualizations of the sacred via two of the founding members of The College of Sociology (1937–1939), Michel Leiris and Georges Bataille, as they relate to everyday life. Through this sacred lens everyday life in the city is reflexively intertwined with the stories of a Korean shaman, who through rock divination conjures the spirits of nature for her divinations. Her fantastic and uncanny stories are examined in detail, as well as the intricate relationship between the diviner, patron, and materials used in Korean shamanic in‐house divination. Following Atkinson, Taussig, and others, this piece stresses that power in shamanism is a complicated relation of exchanges and activities, readings and writings, of which the shaman is only one component. Not only is it more and more necessary to consider the perspectives of the patrons and the patients, but the materials, social contexts, and spectral machineries that are brought to the discursive table must also bear equal weight—all of which, in turn, constitute the grounds for what might be considered “shamanic” activity. Through divination, physiognomic traces reveal the interior world of things as a waking dream, which takes part in the mysteries of what another member of The College, Roger Caillois, referred to as the “natural fantastic.” The object of divination—ourselves and our fate—is petrified into thing that can be read and critiqued, and subsequently transformed into a medicine or commodity, which is then consumed as the patron returns to the exterior landscape of the city and awaits its effects.
Shifting Ontologies inHuichol Ritual and Art
Authors: Neurath Johannes
Published: June 2015

In regard to anthropology's contemporary ontological turn, it seems to be necessary to raise the question of polyontologies. UsingDescola's terminology, theHuichols (Wixarika) ofWesternMexico seem to be a case combining animistic and analogist tendencies. I avoid declaring analogism to be the dominant ontology of theHuichol, and animism to being a secondary tendency. Rather, my project is to elucidate the ontological implications of ritual complexity.Huichol ontology and cosmology appear to be unstable and based on contradictory schemes of practice. During the Peyote dance people deny the free gifts of the feathered serpent and oblige it to accept “payment.” The cloud serpent's ethos of free gift clashes with the villagers' insistence on reciprocal exchange. The transition from reciprocity to free gift and back to exchange is always a problematic process. There is no easy complementarity between the two. These same tensions are also expressed in theHuichol's peculiar style of art. Contemplating a yarn painting likeThe Vision ofTatutsiXuweriTimaiwemebyJoséBenítezSánchez, the viewer can go back and forth between incompatible forms of knowledge and ways of viewing.
Trends in maternal obesity in a large university hospital 2009–2013
Authors: McKeating Aoife , Maguire Patrick J. , Daly Niamh , Farren Maria , McMahon Léan , Turner Michael J.
Published: June 2015

Introduction

Maternal obesity has been identified as an important clinical priority in contemporary obstetrics. This study aimed to determine the incidence of maternal obesity in early pregnancy and track recent trends in body mass index (BMI) categories over 5 years 2009–2013.

Material and methods

This prospective observational study included all women who delivered an infant weighing ≥500 g during the 5 years 2009–2013 in a large university teaching hospital in Ireland. Body mass index was calculated using early pregnancy weight and height measured at first antenatal visits. Sociodemographic and clinical data were gathered prospectively. Trends in maternal obesity were tracked over 5 years and epidemiological associations with obesity were examined using logistic regression, adjusted for confounding variables.

Results

Of 42 362 women, 99.0% (n = 41 927) were eligible for analysis with a mean BMI of 25.5 kg/m2, mean age of 30.7 years and 40.7% (n = 17054) primigravidas. The absolute number of cases of severe obesity (BMI ≥40.0 kg/m2) increased by 48.5% from 2009 to 2013 (p < 0.001). After multivariate logistic regression analyses, obesity incidence increased with increasing parity, advancing age and socioeconomic disadvantage. The maternal obesity rate among women born in the 13 European Union Accession countries was 8.6%, nearly half that of those born in existing European Union countries (p < 0.001).

Conclusion

It is concerning that while the overall obesity rate remained stable, the number of cases of severe obesity increased over 5 years. We recommend renewed public health efforts addressing obesity rates before pregnancy and reinforcing attempts to optimize a woman's weight after delivery.
Best‐corrected visual acuity and retinal thickness are associated with improved cortical visual processing in treated wet AMD patients
Authors: Vottonen Pasi , Pääkkönen Ari , Tarkka Ina M. , Kaarniranta Kai
Published: June 2015

Purpose

In response to anti‐VEGF treatment for wet AMD retinal anatomy and visual acuity is often remedied. In our previous study, we showed that visual evoked potentials (VEP) improve following successful anti‐VEGF treatment. The aim of this study was to investigate, how visual acuity and retinal thickness changes are reflected in VEP parameters. Moreover, we wanted to assess the feasibility of VEP as a novel monitoring tool for wet AMD patients.

Methods

A total of 16 patients and six control subjects were enrolled in this study. Patients received three bevacizumab intravitreal injections. At the beginning of the study and four to 6 weeks after the last injection, the best‐corrected visual acuity (BCVA) test, full biomicroscope examination, OCT analysis and VEP were performed.

Results

In treated eyes, logMAR visual acuity improved on average 0.18 ± 0.32 units, OCT retinal thickness decreased 170 ± 200 micrometres and VEP amplitude increased 1.0 ± 1.4 microvolts. All changes were significant at p < 0.05. There was a significant correlation between the relative changes of VEP amplitude and retinal thickness r = −0.630 (p < 0.05), and between visual acuity (logMAR) and retinal thickness r = 0.576 (p < 0.05).

Conclusion

We showed that both the increase in VEP amplitude and the improvement in visual acuity are associated with the decrease in retinal thickness in treated wet AMD patients. The results do not indicate additional usefulness of VEP in the diagnosis or monitoring of wet AMD.
Transition between stunted and nonstunted status: both occur from birth to 15 years of age in Malawi children
Authors: Teivaanmäki Tiina , Cheung Yin Bun , Kortekangas Emma , Maleta Kenneth , Ashorn Per
Published: June 2015

Aim

The timing and frequency of stunting and possible catch‐up growth are ambiguous in low‐income settings. This study explored the timing and extent of becoming stunted and nonstunted between birth and 15 years of age in a resource‐poor area of Malawi, south‐east Africa.

Methods

We followed 767 children from the foetal period until 15 years of age and examined the transition between stunted and nonstunted status and the pubertal stage at 15 years of age. We also plotted smoothed curves for the mean absolute deficits in centimetres and height‐for‐age standard deviation scores (HAZ) according to the World Health Organization's 2006 and 2007 references.

Results

Most two‐year olds (80%) were stunted (HAZ < −2 SD), but this had declined to 37% at 15 years of age. During the three five‐year intervals, new stunting cases ranged from 3.9 to 21.3% and the percentage who became nonstunted was 9.1 to 15%. The majority (85%) of the children, who were moderately stunted at two years of age, became nonstunted during the follow‐up period. Only, 9% of boys and 20% of girls had reached advanced puberty by the age of 15.

Conclusion

Becoming stunted and nonstunted status both occurred throughout the period from birth to 15 years of age in Malawi children. The small percentage who had reached advanced puberty by the age of 15 suggests significant further growth potential.
Empirical Bayes Scan Statistics for Detecting Clusters of Disease Risk Variants in Genetic Studies
Authors: McCallum Kenneth J. , Ionita-Laza Iuliana
Published: June 2015

Recent developments of high-throughput genomic technologies offer an unprecedented detailed view of the genetic variation in various human populations, and promise to lead to significant progress in understanding the genetic basis of complex diseases. Despite this tremendous advance in data generation, it remains very challenging to analyze and interpret these data due to their sparse and high-dimensional nature. Here, we propose novel applications and new developments of empirical Bayes scan statistics to identify genomic regions significantly enriched with disease risk variants. We show that the proposed empirical Bayes methodology can be substantially more powerful than existing scan statistics methods especially so in the presence of many non-disease risk variants, and in situations when there is a mixture of risk and protective variants. Furthermore, the empirical Bayes approach has greater flexibility to accommodate covariates such as functional prediction scores and additional biomarkers. As proof-of-concept we apply the proposed methods to a whole-exome sequencing study for autism spectrum disorders and identify several promising candidate genes.
Anatomical variations in epididymal–testicular fusion in stallions and their possible clinical significance
Authors: Pozor M. , Freeman D. , Troedsson M. , Brown M. , Morton A. , Smith A. , McNaughten J.
Published: June 2015

Reasons for performing study

Fusion anomalies of the epididymis with the testis may be clinically relevant in horses. However, anatomical variations in epididymal–testicular fusion have not been classified, and their clinical significance is unknown.

Objectives

To describe anatomical variations and clinical significance of epididymal–testicular fusion in stallions.

Study design

Anatomical study of testes from castrations, and description of 2 clinical cases with atypical epididymal–testicular fusion.

Methods

A total of 104 testes were obtained from equine castrations. Eight patterns of epididymal–testicular fusion were identified. Two clinical cases with epididymal dislocation were also described.

Results

Close attachment of the entire epididymis to the testis was the most common pattern of fusion (40%). Ninety‐five per cent of cryptorchid testes and 34% of scrotal testes in the studied sample had elongated proper ligaments of the testes. Dislocation of the epididymal tail was observed in 2 stallions that had atypically long proper ligaments inserted on the dorsal aspect of the testes.

Conclusions

Patterns of epididymal–testicular fusion can vary in stallions. Elongated proper ligaments of the testes occur mostly in cryptorchid testes but are also found in stallions with scrotal testes. Epididymal dislocation may develop in stallions with long proper ligaments that are inserted dorsally on the testes.
Fungal alteration of the elemental composition of leaf litter affects shredder feeding activity
Authors: Cornut Julien , Ferreira Verónica , Gonçalves Ana Lúcia , Chauvet Eric , Canhoto Cristina
Published: June 2015

Leaf litter from riparian vegetation provides the main source of matter and energy for food webs of small forest streams. Shredding macroinvertebrates mostly feed on this litter when it has been colonised and conditioned by microorganisms, especially by aquatic hyphomycetes. Since shredders feed selectively, they must make foraging decisions based on the physical and chemical characteristics of the food resource, which can change depending on the identity of fungal species.

Here, we addressed the effect of changes in fungal assemblage structure on the elemental composition of oak (Quercus robur) leaf litter and how variation in litter quality affects the feeding of a stream shredder. Leaf discs were incubated in microcosms for 2 weeks, inoculated with various fungal assemblages comprised of three species each, and offered to a shredder (Schizopelex festiva, Trichoptera: Sericostomatidae) as food.

This shredder ate more leaves with a high mycelial biomass, which depended on fungal assemblage composition. Leaf litter conditioned by different fungal assemblages resulted in different litter N and P concentrations. Mycelial biomass was positively related to litter P concentration, with the lowest and highest P concentrations differing by 40% at most, but not to litter N concentration, even though the lowest and highest N concentrations differed by as much as 35%. The caddisfly larvae ate more leaves with a low C/P ratio.

These findings suggest a key role of litter P concentration in eliciting fungal conditioning effects on shredder‐mediated litter decomposition.
Functional role of the C‐terminal tail of the archaeal ribosomal stalk in recruitment of two elongation factors to the sarcin/ricin loop of 23S rRNA
Authors: Imai Hirotatsu , Miyoshi Tomohiro , Murakami Ryo , Ito Kosuke , Ishino Yoshizumi , Uchiumi Toshio
Published: June 2015

Two types of elongation factors alternate in their binding to the factor‐binding center of the ribosome. Both binding events are accompanied by GTP hydrolysis and drive the translation elongation cycle. The multicopy ribosomal protein family, termed the stalk, contributes actively to the elongation process. Recent evidence indicates that the mobile C‐terminal tail of archaeal stalk aP1 directly interacts with both the elongation factors aEF1A and aEF2. To investigate the functional significance of these interactions in recruitment of elongation factors to the factor‐binding center of the ribosome, we substituted the archaeal stalk complex aL10•aP1 for the bL10•bL12 stalk complex in the Escherichia coli 50S subunit. The resultant hybrid ribosome accessed archaeal aEF1A and aEF2 in a manner dependent on the C‐terminal tail containing the hydrophobic residues Leu103, Leu106 and Phe107. Bases G2659 and A2660 in the sarcin/ricin loop (SRL) of 23S rRNA were protected against DMS modification by both factors as was A1067 by aEF2. Mutagenesis indicated that this protection was dependent on the intact C‐terminal tail of aP1. The results suggest a crucial role for the interactions between the stalk C‐terminal tail and elongation factors in their recruitment to the SRL of 23S rRNA within the ribosome.
Assessments of outcome in haemophilia – what is the added value of QoL tools?
Authors: van den Berg H. M. , Feldman B. M. , Fischer K. , Blanchette V. , Poonnoose P. , Srivastava A.
Published: June 2015

Introduction

Access to treatment and especially to long‐term regular replacement treatment with clotting factor concentrates (prophylaxis) have caused dramatic contrasts in the clinical picture between haemophilia populations. An individual patient with severe haemophilia age 20 years can have normal joints or can be severely crippled and unable to work. Assessment of outcome in a standardized way has therefore become essential.

Aim

Discuss the relevance and utility of the different outcome assessment tools in patient groups with different access to treatment.

Methods

In the last decade new outcome assessment tools specific for haemophilia have been developed that measure all aspects of health according to the International Classification of Functioning, Disability and Health (ICF) model. These tools are directed at assessing the clinical and radiological status of joints as well as overall functioning, such as participation and psychosocial aspects, evaluating overall health‐related quality of life (HRQOL). For deciding which tools to use in clinical practice or research, one needs to consider the specific context with regard to disease burden, healthcare environment and socioeconomic background of the patients being evaluated.

Conclusion

Prospective systematic assessment of outcome in haemophilia and related bleeding disorders is important. Based upon recent literature a critical appraisal of outcome tools is described.
Typologies of Deification
Authors: Keating Daniel A.
Published: June 2015

Investigations into the Christian doctrine of deification have multiplied in recent years. Due especially to the emergence of studies on deification from the Western theological tradition, concerns are being raised about what constitutes a genuine doctrine of deification. This article considers three influential efforts to clarify the types of deification – from Norman Russell, Gösta Hallonsten and Paul Gavrilyuk – and offers critical and constructive proposals for identifying the core content of deification and its various types.
DIF Detection Using Multiple‐Group Categorical CFA With Minimum Free Baseline Approach
Authors: Chang Yu‐Wei , Huang Wei‐Kang , Tsai Rung‐Ching
Published: June 2015

The aim of this study is to assess the efficiency of using the multiple‐group categorical confirmatory factor analysis (MCCFA) and the robust chi‐square difference test in differential item functioning (DIF) detection for polytomous items under the minimum free baseline strategy. While testing for DIF items, despite the strong assumption that all but the examined item are set to be DIF‐free, MCCFA with such a constrained baseline approach is commonly used in the literature. The present study relaxes this strong assumption and adopts the minimum free baseline approach where, aside from those parameters constrained for identification purpose, parameters of all but the examined item are allowed to differ among groups. Based on the simulation results, the robust chi‐square difference test statistic with the mean and variance adjustment is shown to be efficient in detecting DIF for polytomous items in terms of the empirical power and Type I error rates. To sum up, MCCFA under the minimum free baseline strategy is useful for DIF detection for polytomous items.
The Impact of Victim Demographics on Case Outcomes in Delinquency Proceedings: An Empirical Test
Authors: McGuire M. Dyan , Fearn Noelle E. , White Norman , Mayo Kenneth , Ondr Megan
Published: June 2015

While the impact of the defendant's sex and race on processing decisions is well researched, less is known about the impact of the victim's sex and race on juvenile court decision making. Using data from the juvenile court in St. Louis, Missouri, this study explores direct and interactive effects of the victim's sex and race on outcome decisions for juvenile offenders. Findings suggest that legal differences account for most of the observed differences in detention, commitment and adjudication among the sample studied.
Juvenile Shackling Reform: The Judicial Role in Ensuring Trauma‐Informed Courts and Why States Are Rethinking Restraints
Authors: Groman Donna Quigley
Published: June 2015

In juvenile courts around the country, youth are routinely shackled, without any evidence that these young people are a danger to anyone or likely to attempt flight. A number of states are moving away from this practice. Shackling reform initiatives are motivated by constitutional issues, emerging science around adolescent development, and a growing recognition of the need for trauma‐informed, evidence‐based courts. Judges are ultimately responsible for safeguarding the rights of the young people who appear in court, and must uphold the dignity of the courtroom. A review of jurisdictions that have adopted limits on juvenile shackling shows that these policies have not resulted in breaches of safety.
Parent‐to‐Child Transition in Managing Cystic Fibrosis: A Research Synthesis
Authors: Leeman Jennifer , Sandelowski Margarete , Havill Nancy L. , Knafl Kathleen
Published: June 2015

Although parents and children must adhere to five primary treatments for cystic fibrosis (CF), and their roles transition over time, the scope of CF studies often has been limited to one treatment regimen or to children within a specified age range. The purpose of this mixed research synthesis study is to integrate findings from qualitative and quantitative studies addressing the transition of CF management from parent to child, as well as factors related to adherence across treatments and over time. An existing grounded theory was used as a framework to synthesize findings in 17 reports from 16 studies. The results confirm the theory and posit 3 additional factors that may influence parent‐to‐child transition of care management.
Decreased glutathione reductase2 leads to early leaf senescence in Arabidopsis
Authors: Ding Shunhua , Wang Liang , Yang Zhipan , Lu Qingtao , Wen Xiaogang , Lu Congming
Published: June 2015

Glutathione reductase (GR) catalyzes the reduction of glutathione disulfide (GSSG) to reduced glutathione (GSH) and participates in the ascorbate‐glutathione cycle, which scavenges H2O2. Here, we report that chloroplastic/mitochondrial GR2 is an important regulator of leaf senescence. Seed development of the homozygous gr2 knockout mutant was blocked at the globular stage. Therefore, to investigate the function of GR2 in leaf senescence, we generated transgenic Arabidopsis plants with decreased GR2 using RNAi. The GR2 RNAi plants displayed early onset of age‐dependent and dark‐ and H2O2‐induced leaf senescence, which was accompanied by the induction of the senescence‐related marker genes SAG12 and SAG13. Furthermore, transcriptome analysis revealed that genes related to leaf senescence, oxidative stress, and phytohormone pathways were upregulated directly before senescence in RNAi plants. In addition, H2O2 accumulated to higher levels in RNAi plants than in wild‐type plants and the levels of H2O2 peaked in RNAi plants directly before the early onset of leaf senescence. RNAi plants showed a greater decrease in GSH/GSSG levels than wild‐type plants during leaf development. Our results suggest that GR2 plays an important role in leaf senescence by modulating H2O2 and glutathione signaling in Arabidopsis.
Agrarian Capitalization without Capitalism? Capitalist Dynamics from Above and Below in China
Authors: Hairong Yan , Yiyuan Chen
Published: June 2015

Cooperatives, family farms and dragon‐head enterprises are emerging as new subjects of agriculture in China and are being promoted by the Chinese government as engines of agricultural development. The current dynamics of increasing capitalization of agriculture in China has been characterized by scholar Philip Huang as ‘Capitalization without Proletarianization’. Through case studies, we examine the dynamics of accumulation in Chinese agriculture, as well as the government's agriculture policy shift. We argue that capitalist dynamics exist in Chinese agricultural production and they come from above and below. We also argue that Chinese government's policy shift towards de‐peasantization began in the early years of the rural reform.
Weight‐Related Behaviors When Children Are in School Versus on Summer Breaks: Does Income Matter?
Authors: Wang Y. Claire , Vine Seanna , Hsiao Amber , Rundle Andrew , Goldsmith Jeff
Published: June 2015

BACKGROUND

Income disparities in US youth in academic achievement appear to widen during the summer because of discontinued learning among children from lower‐income households. Little is known about whether behavioral risk factors for childhood obesity, such as diet and physical activity, also demonstrate a widening difference by income when children are out of school.

METHODS

Data from US children in grades 1‐12 in the National Health and Nutrition Examination Survey 2003‐2008 (N = 6796) were used to estimate screen time, moderate‐to‐vigorous physical activity (MVPA), and consumption of calories, vegetables, and added sugar. Linear regression was used to compare among children of households ≤185% and >185% poverty, as well as during the school year versus on school breaks.

RESULTS

Children surveyed during summer breaks consumed fewer vegetables (−0.2 cups/day) and more added sugar (+2.1 teaspoons/day), were more active (+4.6 MVPA minutes/day) and watched more television (+18 minutes/day). However, the nonsignificant interaction between school breaks and income indicated that lower‐income students were not “less healthy” than higher‐income students during the summer breaks.

CONCLUSION

Obesity‐related risk factors were more prevalent during the summer and among lower‐income youths, but the income disparity in these behaviors was not exacerbated when schools are not in session.
Evaluation of the Health‐Promoting School Supporting Network in Taiwan
Authors: Liao Li‐Ling , Liu Chieh‐Hsing , Chang Fong‐Ching , Cheng Chi‐Chia J. , Niu Yu‐Zhen , Chang Tzu‐Chau
Published: June 2015

BACKGROUND

Taiwan has advocated health‐promoting schools (HPS) since 2001 and established the Health‐Promoting School Supporting Network (HPSSN) in 2005 to offer administrative support and consultation. Respondents' opinions about HPSSN and the relationship between these perceptions and HPS implementation were examined.

METHODS

In 2011, 800 primary and middle schools were selected through stratified random sampling. School staff members (N = 656) in charge of HPS programs reported their impressions of the HPSSN's support.

RESULTS

Respondents were most satisfied with consultants and schools' recognition of responsibilities and rules and their interactions with HPSSN administrators. They were least satisfied with the extent of their HPSSN consultant interaction and believed HPSSN provided insufficient resources to establish HPS. Respondents' consultant partnerships and satisfaction with HPSSN administration significantly predicted HPS implementation. Additionally, the predictive values of healthy policies and school‐community relationships were greater than the other 6 HPS components.

CONCLUSIONS

HPSSN positively influenced HPS implementation; however, consultant/school partnerships and school resource allocations must be improved.
Influence of Simulated Double‐crested Cormorant, Phalacrocorax auritus, Predation on Multiple‐batch Production of Channel Catfish, Ictalurus punctatus
Authors: Dorr Brian S. , Engle Carole R.
Published: June 2015

The double‐crested cormorant, Phalacrocorax auritus, is considered the primary depredating bird species on commercially produced channel catfish, Ictalurus punctatus, in the southeastern USA. We simulated different levels of cormorant predation on losses at harvest and economic effects on channel catfish production in a multiple‐batch cropping system. We observed significant (P < 0.05) declines in catfish production at increasing levels of cormorant predation in this study. This decline was mitigated by increased individual growth of catfish at higher predation rates (i.e., lower catfish densities). This mitigating effect produced a non‐linear relationship with total kg of catfish harvested per pond resulting in a non‐linear incremental increase in breakeven price related to predation. Costs of production ($/kg) increased with increasing predation levels up to very high levels of predation with a cumulative maximum increase in breakeven price of $0.143/kg. These results indicate that losses at harvest due to cormorant predation occur immediately but are mitigated in part by compensatory growth of individual catfish. Losses due to cormorant predation in multi‐batch systems can be considerable, but there is not a 1:1 relationship between losses and kg of catfish harvested due to compensatory factors.
Growth, Survivorship, Air‐bubble Disease, and Attachment of Feeble Juvenile Seahorses, Hippocampus kuda (Bleeker, 1852)
Authors: Zhang Yanhong , Qin Geng , Lin Junda , Lin Qiang
Published: June 2015

Seahorse aquaculture has been a focus for meeting the demand of traditional medicine and aquarium. Feeble (poor quality) juveniles are commonly found in the commercial seahorse culture. In this study, we compared the growth and survival performances of the feeble and healthy common seahorses Hippocampus kuda. The results show that the feeble juveniles had high growth and survival at the temperature of 27–29 C and salinity of 26–28‰ with frequent feeding (≥three times a day) during first 5 wk. Through a 12‐wk investigation, we found that the air‐bubble disease could significantly affect the specific growth rate and survival of the feeble juveniles. There was a positive and significant correlation between the substrate‐attachment rate and survival rate in the feeble juveniles, and substrate‐attachment rate may be used to assess the quality of the feeble populations in the seahorse H. kuda.
Small heterodimer partner (SHP) links hepatitis C and liver fibrosis: a small protein on the big stage
Authors: Weiskirchen Ralf , Tacke Frank
Published: June 2015

See Article on Page 2233
A refractory case of subclinical antibody‐mediated rejection due to anti‐HLA‐DQ antibody in a kidney transplant patient
Authors: Fujimoto Toshinari , Nakada Yasuyuki , Yamamoto Izumi , Kobayashi Akimitsu , Tanno Yudo , Yamada Hiroki , Miki Jun , Ohkido Ichiro , Tsuboi Nobuo , Yamamoto Hiroyasu , Yokoo Takashi
Published: June 2015

We herein report a refractory case of subclinical antibody‐mediated rejection (AMR) due to anti‐HLA‐DQ antibody in a kidney transplant patient. A 45‐year‐old man was admitted for a protocol biopsy; he had a serum creatinine (S‐Cr) level of 1.8 mg/dL 3 years following primary kidney transplantation. Histological examination revealed moderate to severe inflammatory cell infiltration in the peritubular capillaries. Thorough laboratory examination showed that the patient had donor‐specific antibodies (DSAbs) to DR9 and DQ9. Considering both the histological and laboratory findings, we diagnosed acute antibody‐mediated rejection. The patient underwent 3 days of consecutive steroid pulse therapy, intravenous immunoglobulin (IVIG), and plasma exchange. We also administered rituximab (200 mg/body). Six months after the treatment, a second allograft biopsy revealed the progression of interstitial fibrosis and tubular atrophy and persistence of mild peritubular capillaritis. Further analysis showed that the anti‐DR9 antibodies had disappeared, but that the mean fluorescence intensity value of the anti‐DQ9 antibodies had increased. Therefore, we repeated the plasma exchange and IVIG. Allograft function was stable throughout the course of treatment, and the S‐Cr level remained at 1.8 mg/dL. This case report demonstrates the difficulty of treating AMR due to the presence of anti‐DQ DSAbs and the necessity for subsequent therapies in refractory cases.
Recurrence of diabetic kidney disease in a type 1 diabetic patient after kidney transplantation
Authors: Nyumura Izumi , Honda Kazuho , Babazono Tetsuya , Horita Shigeru , Murakami Toru , Fuchinoue Shohei , Uchigata Yasuko
Published: June 2015

Post‐transplant hyperglycaemia of diabetic patients may cause recurrent diabetic kidney disease (DKD) in kidney allografts. We report a patient with slowly progressive DKD with calcineurin inhibitor toxicity (CNI) toxicity after the kidney transplantation. A 28‐year‐old female with type 1 diabetes mellitus underwent successful kidney transplantation from her mother in April 2003, and the kidney graft survived for more than 10 years. She was treated with combined immunosuppressive therapy consisting of cyclosporine and mycophenolate mofetil. After transplantation, she continued to take insulin injection four times per day, but her glycosylated haemoglobin (HbA1c) was above 10%. Protocol allograft kidney biopsies performed 5 and 10 years after transplantation revealed the recurrence of slowly progressive diabetic kidney disease. In addition, arteriolar hyalinosis partly associated with calcineurin inhibitor toxicity (CNI) was detected with progression. Post‐transplant hyperglycaemia causes recurrent diabetic kidney disease (DKD) in kidney allografts, but its progression is usually slow. For long‐term management, it is important to prevent the progression of the calcineurin inhibitor arteriolopathy, as well as maintain favourable glycaemic control.