bluuebunny/crossref_metadata_2025 huggingface dataset:
Cushing’s syndrome in children and adolescents: a Danish nationwide population-based cohort study
Authors: Holst Johanne Marie , Horváth-Puhó Erzsébet , Jensen Rikke Beck , Rix Mariane , Kristensen Kurt , Hertel Niels Thomas , Dekkers Olaf M , Sørensen Henrik Toft , Juul Anders , Jørgensen Jens Otto L
Published: February 2017

Objective

Cushing’s syndrome (CS) affects all age groups, but epidemiologic data in young patients are very limited. We therefore examined the incidence, prevalence and hospital morbidity of CS in children and adolescents.

Design

In a nationwide cohort study, we included all Danish citizens aged 0–20 years from 1977 to 2012. Data were obtained from the Danish National Patient Registry using the International Classification of Diseases (ICD) codes and the Danish Civil Registration System. The diagnosis and treatment were validated by means of individual patient charts. Incidence rate of CS patients aged 0–20 years at diagnosis were computed (standardized to the age and sex distribution of the Danish population). The patients were followed for a maximum of 36 years. Standardized incidence ratios (SIRs) of different hospital-recorded outcomes based on the ICD codes in patients with CS compared to the general population were assessed.

Results

We identified a total of 40 pediatric patients with CS, yielding an annual incidence of 0.89 cases/106 population (95% confidence interval (CI) = 0.63–1.16). The median age at the time of diagnosis was 13.8 years (interquartile range: 10.5–18.2 years), 58% were female and 70% had adrenocorticotropic hormone-producing pituitary adenomas. During follow-up, CS patients (excluding three malignant cases) were at increased risk of being diagnosed with infections (SIR: 3.24, 95% CI: 1.05–7.54) and infertility (SIR: 4.56, 95% CI: 1.48–10.63). The three patients with an adrenocortical carcinoma died shortly after diagnosis, but mortality was not increased in the remaining patients.

Conclusions

CS is rare in the pediatric population. The risk of morbidity related to infections and infertility is elevated and merits further attention.
The IGF system in patients with type 2 diabetes: associations with markers of cardiovascular target organ damage
Authors: Hjortebjerg Rikke , Laugesen Esben , Høyem Pernille , Oxvig Claus , Stausbøl-Grøn Brian , Knudsen Søren T , Kim Won Y , Poulsen Per L , Hansen Troels K , Bjerre Mette , Frystyk Jan
Published: February 2017

Objective

Perturbations in the insulin-like growth factor (IGF) system may contribute to the accelerated cardiovascular disease (CVD) that occurs in patients with type 2 diabetes (T2D). However, it remains unknown whether the IGF system is also involved in the development of early, subclinical CVD. We characterised the IGF system in T2D patients and matched controls and examined the associations with markers of subclinical target organ damage.

Methods

The study included 99 patients with recently diagnosed T2D and 99 age- and sex-matched controls. IGF-1 and IGFBP-1 to -4 were measured by immunoassays, as were pregnancy-associated plasma protein-A (PAPP-A) and the PAPP-A-generated N-terminal (NT) and C-terminal (CT) IGFBP-4 fragments, which are novel CVD risk markers. Arterial stiffness was evaluated by carotid-femoral pulse wave velocity (PWV). Cerebral white matter lesions (WMLs) and carotid artery remodelling were determined by MRI.

Results

After multivariate adjustments, patients with T2D had lower concentrations of IGFBP-2, IGFBP-4, NT- and CT-IGFBP-4, when compared with controls. IGFBP-2 was inversely correlated to PWV in all subjects in multivariate analysis (P < 0.05), and IGFBP-3 was inversely associated with severity of WMLs (P < 0.05). The NT-IGFBP-4 fragment was associated with the degree of carotid artery remodelling among all subjects (regression coefficient (95% CI): 2.95 (0.70, 5.16), P = 0.011). Levels of NT- and CT-IGFBP-4 were reduced in T2D patients receiving metformin compared to those in controls and patients not receiving metformin.

Conclusions

Even in recently diagnosed and well-controlled T2D patients, IGF protein levels are altered and associated with CVD risk factors.
DIAGNOSIS OF ENDOCRINE DISEASE: Differentiation of pathologic/neoplastic hypercortisolism (Cushing’s syndrome) from physiologic/non-neoplastic hypercortisolism (formerly known as pseudo-Cushing’s syndrome)
Authors: Findling James W , Raff Hershel
Published: February 2017

Endogenous hypercortisolism (Cushing’s syndrome) usually implies the presence of a pathologic condition caused by either an ACTH-secreting neoplasm or autonomous cortisol secretion from a benign or malignant adrenal neoplasm. However, sustained or intermittent hypercortisolism may also accompany many medical disorders that stimulate physiologic/non-neoplastic activation of the HPA axis (formerly known as pseudo-Cushing’s syndrome); these two entities may share indistinguishable clinical and biochemical features. A thorough history and physical examination is often the best (and sometimes only) way to exclude pathologic/neoplastic hypercortisolism. The presence of alcoholism, renal failure, poorly controlled diabetes and severe neuropsychiatric disorders should always raise suspicion that the presence of hypercortisolism may be related to physiologic/non-neoplastic Cushing’s syndrome. As late-night salivary cortisol and low-dose dexamethasone suppression have good sensitivity and negative predictive value, normal studies exclude Cushing’s syndrome of any form. However, these tests have imperfect specificity and additional testing over time with clinical follow-up is often needed. When there is persistent diagnostic uncertainty, secondary tests such as the DDAVP stimulation test and the dexamethasone-CRH test may provide evidence for the presence or absence of an ACTH-secreting tumor. This review will define and characterize the numerous causes of physiologic/non-neoplastic hypercortisolism and provide a rational clinical and biochemical approach to distinguish it from pathologic/neoplastic hypercortisolism (true Cushing’s syndrome).
Isolation of luteal endothelial cells and functional interactions with T lymphocytes
Authors: Walusimbi S S , Wetzel L M , Townson D H , Pate J L
Published: February 2017

The objectives of this study were to optimize the isolation of luteal endothelial cells (LEC) and examine their functional interactions with autologous T lymphocytes. Analysis by flow cytometry showed that the purity of LEC isolated by filtration was nearly 90% as indicated byBandeiraea simplicifolia(BS)-1 lectin binding. LEC expressed mRNA for progesterone receptor (PGR), prostaglandin receptors (PTGFR, PTGER2 and 4, and PTGIR), tumor necrosis factor receptors (TNFRSF1A&B) and interleukin (IL) 1B receptors (IL1R1&2). LEC were pretreated with either vehicle, progesterone (P4; 0–20 µM), prostaglandin (PG) E2or PGF2α(0–0.2 µM), and further treated with or without TNF and IL1B (50 ng/mL each). LEC were then incubated with autologous T lymphocytes in an adhesion assay. Fewer lymphocytes adhered to LEC after exposure to high compared to low P4concentrations (cubic response;P < 0.05). In contrast, 0.2 µM PGE2and PGF2αeach increased T lymphocyte adhesion in the absence of cytokines (P < 0.05). LEC induced IL2 receptor alpha (CD25) expression and proliferation of T lymphocytes. In conclusion, filtration is an effective way of isolating large numbers of viable LEC. It is proposed that PGs and P4modulate the ability of endothelial cells to bind T lymphocytes, potentially regulating extravasation, and that LEC activate T lymphocytes migrating into or resident in the CL.
Comparative Analysis Highlights Variable Genome Content of Wheat Rusts and Divergence of the Mating Loci
Authors: Cuomo Christina A , Bakkeren Guus , Khalil Hala Badr , Panwar Vinay , Joly David , Linning Rob , Sakthikumar Sharadha , Song Xiao , Adiconis Xian , Fan Lin , Goldberg Jonathan M , Levin Joshua Z , Young Sarah , Zeng Qiandong , Anikster Yehoshua , Bruce Myron , Wang Meinan , Yin Chuntao , McCallum Brent , Szabo Les J , Hulbert Scot , Chen Xianming , Fellers John P
Published: February 2017

Three members of the Puccinia genus, Pucciniatriticina (Pt), P. striiformis f.sp. tritici (Pst), and P. graminis f.sp. tritici (Pgt), cause the most common and often most significant foliar diseases of wheat. While similar in biology and life cycle, each species is uniquely adapted and specialized. The genomes of Pt and Pst were sequenced and compared to that of Pgt to identify common and distinguishing gene content, to determine gene variation among wheat rust pathogens, other rust fungi, and basidiomycetes, and to identify genes of significance for infection. Pt had the largest genome of the three, estimated at 135 Mb with expansion due to mobile elements and repeats encompassing 50.9% of contig bases; in comparison, repeats occupy 31.5% for Pst and 36.5% for Pgt. We find all three genomes are highly heterozygous, with Pst [5.97 single nucleotide polymorphisms (SNPs)/kb] nearly twice the level detected in Pt (2.57 SNPs/kb) and that previously reported for Pgt. Of 1358 predicted effectors in Pt, 784 were found expressed across diverse life cycle stages including the sexual stage. Comparison to related fungi highlighted the expansion of gene families involved in transcriptional regulation and nucleotide binding, protein modification, and carbohydrate degradation enzymes. Two allelic homeodomain pairs, HD1 and HD2, were identified in each dikaryotic Puccinia species along with three pheromone receptor (STE3) mating-type genes, two of which are likely representing allelic specificities. The HD proteins were active in a heterologous Ustilago maydis mating assay and host-induced gene silencing (HIGS) of the HD and STE3 alleles reduced wheat host infection.
Screening and Analysis of Janelia FlyLight Project Enhancer-Gal4 Strains Identifies Multiple Gene Enhancers Active During Hematopoiesis in Normal and Wasp-ChallengedDrosophilaLarvae
Authors: Tokusumi Tsuyoshi , Tokusumi Yumiko , Brahier Mark S , Lam Victoria , Stoller-Conrad Jessica R , Kroeger Paul T , Schulz Robert A
Published: February 2017

A GFP expression screen has been conducted on >1000 Janelia FlyLight Project enhancer-Gal4 lines to identify transcriptional enhancers active in the larval hematopoietic system. A total of 190 enhancers associated with 87 distinct genes showed activity in cells of the third instar larval lymph gland and hemolymph. That is, gene enhancers were active in cells of the lymph gland posterior signaling center (PSC), medullary zone (MZ), and/or cortical zone (CZ), while certain of the transcriptional control regions were active in circulating hemocytes. Phenotypic analyses were undertaken on 81 of these hematopoietic-expressed genes, with nine genes characterized in detail as to gain- and loss-of-function phenotypes in larval hematopoietic tissues and blood cells. These studies demonstrated the functional requirement of the cut gene for proper PSC niche formation, the hairy, Btk29A, and E2F1 genes for blood cell progenitor production in the MZ domain, and the longitudinals lacking, dFOXO, kayak, cap-n-collar, and delilah genes for lamellocyte induction and/or differentiation in response to parasitic wasp challenge and infestation of larvae. Together, these findings contribute substantial information to our knowledge of genes expressed during the larval stage of Drosophila hematopoiesis and newly identify multiple genes required for this developmental process.
A High Copy Suppressor Screen for Autophagy Defects inSaccharomyces arl1Δ andypt6Δ Strains
Authors: Yang Shu , Rosenwald Anne
Published: February 2017

In Saccharomyces cerevisiae, Arl1 and Ypt6, two small GTP-binding proteins that regulate membrane traffic in the secretory and endocytic pathways, are also necessary for autophagy. To gain information about potential partners of Arl1 and Ypt6 specifically in autophagy, we carried out a high copy number suppressor screen to identify genes that when overexpressed suppress the rapamycin sensitivity phenotype of arl1Δ and ypt6Δ strains at 37°. From the screen results, we selected COG4, SNX4, TAX4, IVY1, PEP3, SLT2, and ATG5, either membrane traffic or autophagy regulators, to further test whether they can suppress the specific autophagy defects of arl1Δ and ypt6Δ strains. As a result, we identified COG4, SNX4, and TAX4 to be specific suppressors for the arl1Δ strain, and IVY1 and ATG5 for the ypt6Δ strain. Through this screen, we were able to confirm several membrane traffic and autophagy regulators that have novel relationships with Arl1 and Ypt6 during autophagy.
Exon-Enriched Libraries Reveal Large Genic Differences Between Aedes aegypti from Senegal, West Africa, and Populations Outside Africa
Authors: Dickson Laura B , Campbell Corey L , Juneja Punita , Jiggins Francis M , Sylla Massamba , Black William C
Published: February 2017

Aedes aegypti is one of the most studied mosquito species, and the principal vector of several arboviruses pathogenic to humans. Recently failure to oviposit, low fecundity, and poor egg-to-adult survival were observed when Ae. aegypti from Senegal (SenAae) West Africa were crossed with Ae. aegypti (Aaa) from outside of Africa, and in SenAae intercrosses. Fluorescent in situ hybridization analyses indicated rearrangements on chromosome 1, and pericentric inversions on chromosomes 2 and 3. Herein, high throughput sequencing (HTS) of exon-enriched libraries was used to compare chromosome-wide genetic diversity among Aaa collections from rural Thailand and Mexico, a sylvatic collection from southeastern Senegal (PK10), and an urban collection from western Senegal (Kaolack). Sex-specific polymorphisms were analyzed in Thailand and PK10 to assess genetic differences between sexes. Expected heterozygosity was greatest in SenAae. FST distributions of 15,735 genes among all six pairwise comparisons of the four collections indicated that Mexican and Thailand collections are genetically similar, while FST distributions between PK10 and Kaolack were distinct. All four comparisons of SenAae with Aaa indicated extreme differentiation. FST was uniform between sexes across all chromosomes in Thailand, but were different, especially on the sex autosome 1, in PK10. These patterns correlate with the reproductive isolation noted earlier. We hypothesize that cryptic Ae. aegypti taxa may exist in West Africa, and the large genic differences between Aaa and SenAae detected in the present study have accumulated over a long period following the evolution of chromosome rearrangements in allopatric populations that subsequently cause reproductive isolation when these populations became sympatric.
The Impact of Open Pollination on the Structural Evolutionary Dynamics, Meiotic Behavior, and Fertility of Resynthesized AllotetraploidBrassica napusL.
Authors: Rousseau-Gueutin Mathieu , Morice Jérôme , Coriton Olivier , Huteau Virginie , Trotoux Gwenn , Nègre Sylvie , Falentin Cyril , Deniot Gwennaëlle , Gilet Marie , Eber Frédérique , Pelé Alexandre , Vautrin Sonia , Fourment Joëlle , Lodé Maryse , Bergès Hélène , Chèvre Anne-Marie
Published: February 2017

Allopolyploidy, which results from the merger and duplication of two divergent genomes, has played a major role in the evolution and diversification of flowering plants. The genomic changes that occur in resynthesized or natural neopolyploids have been extensively studied, but little is known about the effects of the reproductive mode in the initial generations that may precede its successful establishment. To truly reflect the early generations of a nascent polyploid, two resynthesized allotetraploid Brassica napus populations were obtained for the first time by open pollination. In these populations, we detected a much lower level of aneuploidy (third generation) compared with those previously published populations obtained by controlled successive selfing. We specifically studied 33 resynthesized B. napus individuals from our two open pollinated populations, and showed that meiosis was affected in both populations. Their genomes were deeply shuffled after allopolyploidization: up to 8.5 and 3.5% of the C and A subgenomes were deleted in only two generations. The identified deletions occurred mainly at the distal part of the chromosome, and to a significantly greater extent on the C rather than the A subgenome. Using Fluorescent In Situ Hybridization (BAC-FISH), we demonstrated that four of these deletions corresponded to fixed translocations (via homeologous exchanges). We were able to evaluate the size of the structural variations and their impact on the whole genome size, gene content, and allelic diversity. In addition, the evolution of fertility was assessed, to better understand the difficulty encountered by novel polyploid individuals before the putative formation of a novel stable species.
Genome Report: Identification and Validation of Antigenic Proteins from Pajaroellobacter abortibovis Using De Novo Genome Sequence Assembly and Reverse Vaccinology
Authors: Welly Bryan T , Miller Michael R , Stott Jeffrey L , Blanchard Myra T , Islas-Trejo Alma D , O’Rourke Sean M , Young Amy E , Medrano Juan F , Van Eenennaam Alison L
Published: February 2017

Epizootic bovine abortion (EBA), or “foothill abortion,” is the leading cause of beef cattle abortion in California and has also been reported in Nevada and Oregon. In the 1970s, the soft-shelled tick Ornithodoros coriaceus, or “pajaroello tick,” was confirmed as the disease-transmitting vector. In 2005, a novel Deltaproteobacterium was discovered as the etiologic agent of EBA (aoEBA), recently named Pajaroellobacter abortibovis. This organism cannot be grown in culture using traditional microbiological techniques; it can only be grown in experimentally-infected severe combined immunodeficient (SCID) mice. The objectives of this study were to perform a de novo genome assembly for P. abortibovis and identify and validate potential antigenic proteins as candidates for future recombinant vaccine development. DNA and RNA were extracted from spleen tissue collected from experimentally-infected SCID mice following exposure to P. abortibovis. This combination of mouse and bacterial DNA was sequenced and aligned to the mouse genome. Mouse sequences were subtracted from the sequence pool and the remaining sequences were de novo assembled at 50x coverage into a 1.82 Mbp complete closed circular Deltaproteobacterial genome containing 2250 putative protein-coding sequences. Phylogenetic analysis of P. abortibovis predicts that this bacterium is most closely related to the organisms of the order Myxococcales, referred to as Myxobacteria. In silico prediction of vaccine candidates was performed using a reverse vaccinology approach resulting in the identification and ranking of the top 10 candidate proteins that are likely to be antigenic. Immunologic testing of these candidate proteins confirmed antigenicity of seven of the nine expressed protein candidates using serum from P. abortibovis immunized mice.
Expression Patterns of Atlantic Sturgeon (Acipenser oxyrinchus) During Embryonic Development
Authors: Kaitetzidou Elisavet , Ludwig Arne , Gessner Jörn , Sarropoulou Elena
Published: February 2017

During teleost ontogeny the larval and embryonic stages are key stages, since failure during this period of tissue differentiation may cause malformations, developmental delays, poor growth, and massive mortalities. Despite the rapid advances in sequencing technologies, the molecular backgrounds of the development of economically important but endangered fish species like the Atlantic sturgeon (Acipenser oxyrinchus) have not yet been thoroughly investigated. The current study examines the differential expression of transcripts involved in embryonic development of the Atlantic sturgeon. Addressing this goal, a reference transcriptome comprising eight stages was generated using an Illumina HiSequation 2500 platform. The constructed de novo assembly counted to 441,092 unfiltered and 179,564 filtered transcripts. Subsequently, the expression profile of four developmental stages ranging from early (gastrula) to late stages of prelarval development [2 d posthatching (dph)] were investigated applying an Illumina MiSeq platform. Differential expression analysis revealed distinct expression patterns among stages, especially between the two early and the two later stages. Transcripts upregulated at the two early stages were mainly enriched in transcripts linked to developmental processes, while transcripts expressed at the last two stages were mainly enriched in transcripts important to muscle contraction. Furthermore, important stage-specific expression has been detected for the hatching stage with transcripts enriched in molecule transport, and for the 2 dph stage with transcripts enriched in visual perception and lipid digestion. Our investigation represents a significant contribution to the understanding of Atlantic sturgeon embryonic development, and transcript characterization along with the differential expression results will significantly contribute to sturgeon research and aquaculture.
An Unbiased Estimator of Gene Diversity with Improved Variance for Samples Containing Related and Inbred Individuals of any Ploidy
Authors: Harris Alexandre M , DeGiorgio Michael
Published: February 2017

Gene diversity, or expected heterozygosity (H), is a common statistic for assessing genetic variation within populations. Estimation of this statistic decreases in accuracy and precision when individuals are related or inbred, due to increased dependence among allele copies in the sample. The original unbiased estimator of expected heterozygosity underestimates true population diversity in samples containing relatives, as it only accounts for sample size. More recently, a general unbiased estimator of expected heterozygosity was developed that explicitly accounts for related and inbred individuals in samples. Though unbiased, this estimator’s variance is greater than that of the original estimator. To address this issue, we introduce a general unbiased estimator of gene diversity for samples containing related or inbred individuals, which employs the best linear unbiased estimator of allele frequencies, rather than the commonly used sample proportion. We examine the properties of this estimator, H∼BLUE, relative to alternative estimators using simulations and theoretical predictions, and show that it predominantly has the smallest mean squared error relative to others. Further, we empirically assess the performance of H∼BLUE on a global human microsatellite dataset of 5795 individuals, from 267 populations, genotyped at 645 loci. Additionally, we show that the improved variance of H∼BLUE leads to improved estimates of the population differentiation statistic, FST, which employs measures of gene diversity within its calculation. Finally, we provide an R script, BestHet, to compute this estimator from genomic and pedigree data.
Genetic and Targeted eQTL Mapping Reveals Strong Candidate Genes Modulating the Stress Response During Chicken Domestication
Authors: Fallahsharoudi Amir , de Kock Neil , Johnsson Martin , Bektic Lejla , Ubhayasekera S J Kumari A , Bergquist Jonas , Wright Dominic , Jensen Per
Published: February 2017

The stress response has been largely modified in all domesticated animals, offering a strong tool for genetic mapping. In chickens, ancestral Red Junglefowl react stronger both in terms of physiology and behavior to a brief restraint stress than domesticated White Leghorn, demonstrating modified functions of the hypothalamic–pituitary–adrenal (HPA) axis. We mapped quantitative trait loci (QTL) underlying variations in stress-induced hormone levels using 232 birds from the 12th generation of an advanced intercross between White Leghorn and Red Junglefowl, genotyped for 739 genetic markers. Plasma levels of corticosterone, dehydroepiandrosterone (DHEA), and pregnenolone (PREG) were measured using LC-MS/MS in all genotyped birds. Transcription levels of the candidate genes were measured in the adrenal glands or hypothalamus of 88 out of the 232 birds used for hormone assessment. Genes were targeted for expression analysis when they were located in a hormone QTL region and were differentially expressed in the pure breed birds. One genome-wide significant QTL on chromosome 5 and two suggestive QTL together explained 20% of the variance in corticosterone response. Two significant QTL for aldosterone on chromosome 2 and 5 (explaining 19% of the variance), and one QTL for DHEA on chromosome 4 (explaining 5% of the variance), were detected. Orthologous DNA regions to the significant corticosterone QTL have been previously associated with the physiological stress response in other species but, to our knowledge, the underlying gene(s) have not been identified. SERPINA10 had an expression QTL (eQTL) colocalized with the corticosterone QTL on chromosome 5 and PDE1C had an eQTL colocalized with the aldosterone QTL on chromosome 2. Furthermore, in both cases, the expression levels of the genes were correlated with the plasma levels of the hormones. Hence, both these genes are strong putative candidates for the domestication-induced modifications of the stress response in chickens. Improved understanding of the genes associated with HPA-axis reactivity can provide insights into the pathways and mechanisms causing stress-related pathologies.
Polygenic Control of Carotid Atherosclerosis in a BALB/cJ × SM/J Intercross and a Combined Cross Involving Multiple Mouse Strains
Authors: Grainger Andrew T , Jones Michael B , Chen Mei-Hua , Shi Weibin
Published: February 2017

Atherosclerosis in the carotid arteries is a major cause of ischemic stroke, which accounts for 85% of all stroke cases. Genetic factors contributing to carotid atherosclerosis remain poorly understood. The aim of this study was to identify chromosomal regions harboring genes contributing to carotid atherosclerosis in mice. From an intercross between BALB/cJ (BALB) and SM/J (SM) apolipoprotein E-deficient (Apoe−/−) mice, 228 female F2 mice were generated and fed a “Western” diet for 12 wk. Atherosclerotic lesion sizes in the left carotid artery were quantified. Across the entire genome, 149 genetic markers were genotyped. Quantitative trait locus (QTL) analysis revealed eight loci for carotid lesion sizes, located on chromosomes 1, 5, 12, 13, 15, 16, and 18. Combined cross-linkage analysis using data from this cross, and two previous F2 crosses derived from BALB, C57BL/6J and C3H/HeJ strains, identified five significant QTL on chromosomes 5, 9, 12, and 13, and nine suggestive QTL for carotid atherosclerosis. Of them, the QTL on chromosome 12 had a high LOD score of 9.95. Bioinformatic analysis prioritized Arhgap5, Akap6, Mipol1, Clec14a, Fancm, Nin, Dact1, Rtn1, and Slc38a6 as probable candidate genes for this QTL. Atherosclerotic lesion sizes were significantly correlated with non-HDL cholesterol levels (r = 0.254; p = 0.00016) but inversely correlated with HDL cholesterol levels (r = −0.134; p = 0.049) in the current cross. Thus, we demonstrated the polygenic control of carotid atherosclerosis in mice. The correlations of carotid lesion sizes with non-HDL and HDL suggest that genetic factors exert effects on carotid atherosclerosis partially through modulation of lipoprotein homeostasis.
Highly Efficient Cpf1-Mediated Gene Targeting in Mice Following High Concentration Pronuclear Injection
Authors: Watkins-Chow Dawn E , Varshney Gaurav K , Garrett Lisa J , Chen Zelin , Jimenez Erin A , Rivas Cecilia , Bishop Kevin S , Sood Raman , Harper Ursula L , Pavan William J , Burgess Shawn M
Published: February 2017

Cpf1 has emerged as an alternative to the Cas9 RNA-guided nuclease. Here we show that gene targeting rates in mice using Cpf1 can meet, or even surpass, Cas9 targeting rates (approaching 100% targeting), but require higher concentrations of mRNA and guide. We also demonstrate that coinjecting two guides with close targeting sites can result in synergistic genomic cutting, even if one of the guides has minimal cutting activity.
A Missense Variant inKCNJ10in Belgian Shepherd Dogs Affected by Spongy Degeneration with Cerebellar Ataxia (SDCA1)
Authors: Mauri Nico , Kleiter Miriam , Leschnik Michael , Högler Sandra , Dietschi Elisabeth , Wiedmer Michaela , Dietrich Joëlle , Henke Diana , Steffen Frank , Schuller Simone , Gurtner Corinne , Stokar-Regenscheit Nadine , O’Toole Donal , Bilzer Thomas , Herden Christiane , Oevermann Anna , Jagannathan Vidhya , Leeb Tosso
Published: February 2017

Spongy degeneration with cerebellar ataxia (SDCA) is a severe neurodegenerative disease with monogenic autosomal recessive inheritance in Malinois dogs, one of the four varieties of the Belgian Shepherd breed. We performed a genetic investigation in six families and seven isolated cases of Malinois dogs with signs of cerebellar dysfunction. Linkage analysis revealed an unexpected genetic heterogeneity within the studied cases. The affected dogs from four families and one isolated case shared a ∼1.4 Mb common homozygous haplotype segment on chromosome 38. Whole genome sequence analysis of three affected and 140 control dogs revealed a missense variant in the KCNJ10 gene encoding a potassium channel (c.986T>C; p.Leu329Pro). Pathogenic variants in KCNJ10 were reported previously in humans, mice, and dogs with neurological phenotypes. Therefore, we consider KCNJ10:c.986T>C the most likely candidate causative variant for one subtype of SDCA in Malinois dogs, which we propose to term spongy degeneration with cerebellar ataxia 1 (SDCA1). However, our study also comprised samples from 12 Malinois dogs with cerebellar dysfunction which were not homozygous for this variant, suggesting a different genetic basis in these dogs. A retrospective detailed clinical and histopathological analysis revealed subtle neuropathological differences with respect to SDCA1-affected dogs. Thus, our study highlights the genetic and phenotypic complexity underlying cerebellar dysfunction in Malinois dogs and provides the basis for a genetic test to eradicate one specific neurodegenerative disease from the breeding population. These dogs represent an animal model for the human EAST syndrome.
URBANIZACIÓN, GLOBALIZACIÓN Y EXCLUSIÓN SOCIAL: REFLEXIONES A PARTIR DE CASO BRASILEÑO
Authors: Nascimento Ederson
Published: February 2017

El artículo presenta un análisis histórico y geográfico de la evolución del proceso de urbanización en Brasil, centrándose en su relación con la globalización y en las características de los procesos más importantes de exclusión social originados en él. La urbanización es asimilada a partir de las influencias de la economía globalizada, a través de la acción de las empresas transnacionales y del Estado, de la aceleración de la industrialización y de la modernización agrícola en el país, que ha impulsado el éxodo rural y la redistribución territorial de la población. La correlación entre las innovaciones tecnológicas en los sectores productivos y la flexibilidad/precariedad del mercado de trabajo, el mantenimiento de las estructuras sociales antiguas y la fragilidad de las políticas públicas para promover la ciudadanía, empeoraron la situación de desigualdad y exclusión social, con su concentración en centros urbanos. Se destaca la importancia de la acción del Estado para promover políticas que puedan reducir o incluso revertir el cuadro social de exclusión en el país.
Sobrecarga y calidad de vida del cuidador principal del adulto mayor
Authors: Fhon Jack Roberto Silva , Gonzales Janampa Judyth Tereza , Mas Huaman Teresa , Marques Sueli , Rodrigues Rosalina Aparecida Partezani
Published: February 2017

Objetivo: Determinar la sobrecarga de trabajo y la calidad de vida del cuidador principal del adulto mayor atendido en un consultorio de geriatría.Metodología: Estudio cuantitativo, descriptivo, de corte transversal, realizado con 183 adultos mayores y sus respectivos cuidadores atendidos en un consultorio degeriatría. Para la recolección de los datos, fueron utilizados los instrumentos de perfil demográfico para el adulto mayor y su cuidador Escala de Zarit y The Medical Outcomes Study 36-item (sf-36). El análisis se realizó por medio de la estadísticadescriptiva y de la prueba de correlación de Spearman, con un nivel de significancia de p ≤ 0,05.Resultados: En los adultos mayores, hubo predominio del sexo masculino; la edad promedio fue de 74,8 años y estaban casados/as. En los cuidadores, predominó el sexo femenino; la edad promedio fue de 44,3 años. El total de cuidadorestenían estudios superiores, estaban casados/as y eran hijos/asde los adultos mayores. Según la evaluación con la Escala de Zarit, el 18,1% presentó algún tipo de sobrecarga; en cuanto a la calidad de vida, las dimensiones con menor puntuación fueron Salud general, Salud mental y Vitalidad. Se obtuvo una correlación inversa entre la puntuación total de la Escala deZarit y todas las dimensiones de la calidad de vida.Conclusión: Se observó que el desgaste de la calidad de vida sedebe a la sobrecarga en el cuidado del adulto mayor. Por lo tanto, se hace necesario acompañar el estado de salud de los cuidadores con la finalidad de prevenir alteraciones físicas y mentales.
Islamic Education Values in Minangkabau Wedding Ceremony (Study of Traditional Mariage in Pauh, Padang, West Sumatera)
Authors: Furqan Al
Published: February 2017

The aim of the research is to describe the processions of wedding ceremony that done by Pauh society. It also aims to find out whether the values of Islamic education are still carried out by the society in the wedding processions. The research was descriptive qualitative method using naturalistic approach where the data were obtained through observation and interview. The subjects of the research were the head of KAN Kerapatan Adat Nagari in Pauh, ninik mamak, cerdik pandai, the head of KUA, and religious leaders. Snowballing sampling technique was used and the head of the KAN of Pauh was decided to be the first key informant. Based on the information gathered from the key informants, it was found that Islamic education values were reflected in the procession of wedding ceremony. It is recommended that wedding ceremony in West Sumatra should be held properly based on the Isamic teaching.
The Effectiveness of Premarital Counseling Service on the Harmony of Marriage in Family Resilience
Authors: Samad Duski , Remiswal Remiswal , Kenedi Gusril , Mustqim Mujahidil
Published: February 2017

The hypothesis of preliminary research stated that the high rate of divorcement in West Sumatera was caused by the weakness of the role and function of Badan Penasihatan Pembinaan dan Pelestarian Perkawinan (Board of Marriage Advisory and Preservation) or BP4 in every district in providing premarital counseling service, thus prospective couples have not enough marital knowledge to work on their households. The aim of the research is to reveal the effectiveness of premarital counseling service on the harmony of marriage in realizing family resilience in West Sumatera.The research applied the mixed research method by using sequential explanatory design model. The research object included first, the prospective husbands/wives who had been provided premarital counseling service by the BP4 in West Sumatera, and second, the coaches and counselors of the BP4 premarital counseling service in West Sumatera.The results showed that, first, the effectiveness of premarital counseling service on the harmony of marriage reached as high as 3% in Pariaman, and as low as 0.1% in Pesisir Selatan; second, the effectiveness of premarital counseling service on family resilience had as high as 4.5% in Lima Puluh Kota district, and as low as 0.1 % in Pesisir Selatan; and third, the role of the BP4 in West Sumatera was, in fact, very low.
UPAYA, LAJU TANGKAP, DAN ANALISIS USAHA PENANGKAPAN UDANG PEPEH (Metapenaeus ensis) DENGAN TUGUK BARIS (FILTERING DIVICE) DI PERAIRAN ESTUARIA SUNGAI BANYUASIN, SUMATERA SELATAN
Authors: Rupawan Rupawan , Dharyati Emmy
Published: February 2017

Perairan estuaria merupakan daerah pertemuan air tawar dan laut. Secara ekologi, mempunyai karakteristik yang khas dan dinamis. Estuaria sebagai daerah perangkap unsur hara yang menjadikan perairan ini relatif lebih subur. Di pantai timur Sumatera Selatan yang menghadap Selat Bangka, perairan estuaria dibentuk oleh muara Sungai Upang, Sungai Musi, Sungai Banyuasin, dan Sungai Sembilang. Di perairan ini aktivitas penangkapan ikan sangat berkembang. Tuguk baris merupakan salah satu alat tangkap yang sangat berkembang dari 13 jenis alat tangkap yang ada diperairan ini. Penelitian ini untuk mengetahui laju tangkap dan analisis usaha penangkapan udang pepeh (Metapenaeus ensis) dengan alat tangkap tuguk baris (filtering divice) telah dilakukan pada tahun2006 di perairan estuaria Sungai Banyuasin. Data diperoleh dengan cara pengamatan dan wawancara. Hasil penelitian menunjukan bahwa upaya penangkapan berdasarkan pada jumlah hari operasi berkisar antara 8-19 hari per bulan atau 160 hari per tahun. Laju tangkap udang pepeh rata-rata 4,84±2,49 kg per unit jaring tuguk atau upaya, setara dengan 774,40 kg per jaring per tahun. Komposisi bobot hasil tangkapan adalah udang 90,46% dan ikan 9,54%. Analisis operasional terhadap 34 buah jaring tuguk selama 1 tahun sebagai berikut biaya investasi awal Rp.80.240.000, total biaya tetap dan biaya operasional Rp.53.780.000, pendapatan bersih antara Rp.10.140.000-145.596.000, atau ratarata Rp.77.868.000 atau Rp.1.622.000 per kepala keluarga per bulan. B/C ratio 2,44. Ditinjau dari analisis usaha, penangkapan udang pepeh dengan alat tangkap tuguk baris menguntungkan.
KEBIASAAN MAKAN DAN HUBUNGAN PANJANG BOBOT IKAN GULAMO KEKEN (Johnius belangerii) DI ESTUARI SUNGAI MUSI
Authors: Prianto Eko , Suryati Ni Komang
Published: February 2017

Penelitian ini dilaksanakan pada tahun 2007 dan 2008 dengan lokasi estuari Sungai Musi, Sumatera Selatan. Penelitian ini bertujuan untuk mengetahui kebiasaan makan dan hubunganpanjang bobot ikan gulamo keken (Johnius belangerii) di estuari Sungai Musi yang berfungsi sebagai data dasar dalam pengelolaan sumber daya perikanan. Pengambilan ikan contoh dilakukan pada bulan Juli 2007 dan Januari 2008 dengan menggunakan alat tangkap jaring kantong dan trawl. Analisis data meliputi hubungan panjang bobot, faktor kondisi, luas relung makanan, dan indeks preponderance. Frekuensi ikan gulamo keken yang diamati selama penelitian berjumlah 81 ekor dengan panjang total berkisar antara 7,2-23,8 cm. Berdasarkan pada analisis hubungan panjang bobot Ikan gulamo keken diperoleh nilai b 2,8266 dengan nilai koefisien korelasi (r) sebesar 0,93. Hasil uji t menunjukkan pola pertumbuhan ikan gulamo keken yaitu allometrik negatif dan faktor kondisi memiliki kisaran nilai antara 0,58-1,44 dengan rata-rata 1,01. Ikan gulamo keken merupakan jenis ikan karnivora dengan nilai perbandingan panjang usus dengan panjang tubuh berkisar antara 0,22-0,73 (<1). Makanan yang ditemukan di dalam saluran pencernaan ikan gulamo keken adalah udang (89,39%), ikan (6,56%), kepiting (4,03%), dan serangga (0,02%). Sedangkan luas relung makanan tergolong kecil yaitu sebesar 1,24.
THE EFFECT OF ATTRACTOR MATERIAL ON PELAGIC FISH CAPTURED USING PAYANG BUGIS IN PASAURAN WATERS, PROVINCE OF BANTEN
Authors: Yusfiandayani Roza
Published: February 2017

Rumpon (fish aggregating device) as an auxiliary gear operated in Pasauran waters, Sunda Strait was longer and more widely used in Indonesia to catch pelagic fish. The characteristic speciescomposition, size, and gonado somato index (GSI) pelagic fish around 3 kinds of rumpon attractor materials, i.e. Cocos nucifera, Nypa fructican, and Areca catechu leaves will determine the effects of attractor materials will affect the sustainability of pelagic fish associated. Identification and composition length, weight and gonado somato index pelagic fish were identified in this research with different attractor material in all seasons. Experimental fishing carried out by using payang Bugis. The result show that the Cocos nucifera leaves are the best attractor material based on the number of fish species and durability in all seasons. Further, the gonado somato index of small pelagic fish were caught around rumpon are gonado somato index I 4%, gonado somato index II 33%, gonado somato index III 35%, gonado somato index IV 25%, and gonado somato index V 3%. Pelagic fish around attractor materials have gonado somato index I-III 72%. This result indicated that the small pelagic fish caught around rumpon are immature fish.
SELEKTIVITAS KISI-KISI JUVENILE AND TRASH EXCLUDER DEVICES PADAALAT TANGKAP TRAWL MINI DI PERAIRAN UTARA JAWA
Authors: Hufiadi Hufiadi , Mahiswara Mahiswara , Nurdin Erfind
Published: February 2017

Perikanan trawl mini dasar yang berkembang merupakan alat tangkap yang efektif dalam memanfaatkan sumber daya ikan demersal. Permasalahan utama pada perikanan ini banyak jumlah hasil tangkap sampingan berukuran kecil yang belum layak tangkap. Penelitian observasi dan uji coba operasi penangkapan untuk mengetahui tipe perikanan trawl mini dan upaya untuk mengurangi tangkapan ikan muda telah dilakukan di perairan utara Jawa. Uji coba operasi penangkapan dilakukan melalui penggunaan perangkat juvenile and trash excluder devices pada alat tangkap trawl mini. Perangkat juvenile and trash excluder devices yang digunakan dibedakan pada ukuran jarak antar kisi-kisi 10,0; 17,5; dan 25,4 mm. Analisis selektivitas kisi menggunakan model kurva logistik dengan bantuan solver pada microsoft excel. Hasil penelitian menunjukkan penggunaan juvenile and trash excluder devices pada trawl mini dapat meloloskan ikan muda atau ukuran kecil berkisar 2,42 sampai dengan 63,45%. Juvenile and trash excluder devices dengan ukuran kisi-kisi 17,5 mm memiliki tingkat pelolosan ikan-ikan muda atau rucah paling efektif pada tingkat seleksi 50% (FL50%). Mini bottom trawls are effective fishing gear to exploit demersal fish resources. However, the gears operation have serious problem on amount of bycatch caught especially for juvenile and trash fish. Observation and experimental fishing were conducted to know type of mini bottom trawls in northern Java waters and to reduce catches of juvenile and trash fish. Juvenile and trash excluder devices are a selective device that equipped on mini trawl in the experimental fishing with different space bar of the juvenile and trash excluder devices (i.e.10.0; 17.5; and 25.4 mm). The selectivity analysis of logistic curve by using solver on microsoft excel was applied. The results show that juvenile and trash excluder devices could reduced catches of juvenile and trash fish about 2.42 to 63.45%. Juvenile and trash excluder devices with 17.5 mm of the space bar was better for juvenile selection length of 50% (FL50%) selection level.
KOMPOSISI JENIS, DISTRIBUSI, DAN KEPADATAN STOK IKAN EKOR TIKUS (MACROURIDAE) DI PERAIRAN LAUT DALAM ZONA EKONOMI EKSKLUSIF INDONESIA SAMUDERA HINDIA
Authors: Suprapto Suprapto
Published: February 2017

Penelitian ini bertujuan untuk mengkaji, komposisi jenis, penyebaran, dan kepadatan stok ikan ekor tikus (Macrouridae) di perairan laut dalam zona ekonomi eksklusif Indonesia Samudera Hindia meliputi selatan Jawa dan barat Sumatera. Data yang dianalisis merupakan sebagian hasil survei yang dilakukan bulan Juni sampai dengan Agustus 2005 dengan menggunakan K. R. Baruna Jaya (1.219 GT). Estimasi kepadatan stok dilakukan dengan menggunakan metode sapuan dengan pengambilan contoh acak bertingkat. Hasil penelitian menunjukkan bahwa, ikan ekor tikus (Macrouridae) yang tertangkap terdiri atas 35 spesies, mewakili 11 genera. Komposisi hasil tangkapan didominansi oleh spesies Caelorinchus divergens dan Caelorinchus smithi, (19,2 sampai dengan 77,2%). Penyebaran laju tangkap secara horisontal, paling tinggi ditemukan di perairan selatan Jawa, sebaliknya semakin ke arah perairan barat Sumatera, cenderung rendah. Sedangkan secara vertikal, laju tangkap cenderung meningkat seiring dengan bertambah kedalaman. Laju tangkap paling tinggi pada umumnya berada pada kedalaman mulai dari 500 sampai dengan 1.200 m. Jumlah spesies yang tertangkap pada kedalaman lebih dangkal (200 sampai dengan 300 m) relatif sedikit, selanjutnya semakin bertambah kedalaman, jumlah spesies tersebut cenderung meningkat. Spesies yang memperlihatkan penyebaran paling luas terdiri atas Coryphaenoides sp.1 dan Macrouridae sp.1. Kelimpahan stok ikan ekor tikus (Macrouridae) tertinggi ditemukan pada kisaran kedalaman 800 sampai dengan 900 m dan terendah pada kedalaman 200 sampai dengan 300 m. Kepadatan stok di perairan sebelah selatan Jawa, berkisar antara 4 sampai dengan 1.221 kg km-2, rata-rata sekitar 336,53 kg km-2. Sedangkan di perairan barat Sumatera berkisar antara 0,85 sampai dengan 478,4 kg km-2, rata-rata sekitar 167,30 kg km-2. The objective of this research is to study species composition, distribution, and stock density of rattail fish (Macrouridae) in the waters of southern Java and western Sumatera of the Indian Ocean Indonesian ekslusive economic zone. The study was done based on the data collected from the survey conducted between June and August 2005 using R. V. Baruna Jaya IV (1,219 GT). The study was basically conducted by applying swept area method with stratified random sampling. The results show that the species composition of rattail fish in the of the waters Indian Ocean consisted of 35 spesies and 11 genera. The catch of Macrouridae was dominated by Caelorinchus divergens and Caelorinchus smithi about 19.2 to 77.2%. The widest species distribution of this resources was Coryphaenoides sp.1 and Macrouridae sp.1. The highest abundance of rattail fish resources was caught at the depth of 800 to 900 m and the lowest at the depth of 200 to 300 m. Stock density in southern off Java waters ranging from 4 to 1.221 kg km-2 and about 0,85 to 478,4 kg km-2 in western off Sumatera waters.
How language shapes psychiatric case formulation
Authors: Walsh John , Cominos Nayia , Jureidini Jon
Published: February 2017

The aim of this paper is to describe, analyse, and discuss the process of formulation in the specific context of mental health (MH). Formulation is a fundamental element of the work of psychiatrists and other MH clinicians that is expected to be mastered during training. The literature, however, shows that formulation is rarely explicitly addressed in the psychiatric curriculum; rather, it is implicitly developed through modelling, and/or clinical practice. This paper focuses on case formulation in one MH context in Australia. It tracks the iterative formulation of one patient in a hospital emergency department. The analysis uses resources from systemic functional linguistics (SFL) situated within a broader framework of discourse analysis. It highlights patterns of lexical relations and nominalisation as well as the range of conjunctions. These make explicit how the clinicians talk about the patient's illness and shape their developing understanding into a logical formulation. We see applications of this work for the training of mental health professionals. These data make explicit the ways in which the participating clinicians use language in the process of formulation. By bringing this process to the level of consciousness, it can be discussed and evaluated and become a pedagogic resource.