bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

AbstractSpongy 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&gt;C; p.Leu329Pro). Pathogenic variants in KCNJ10 were reported previously in humans, mice, and dogs with neurological phenotypes. Therefore, we consider KCNJ10:c.986T&gt;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.
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.
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.
MEMBACA RESISTENSI TERHADAP KOLONIALISME DALAM CERPEN “SAMIN KEMBAR” KARYA TRIYANTO TRIWIKROMO
Authors: Efendi Agik Nur 
Published: February 2017

Abstract This article aims to describe the form of post-colonial resistance from the standpoint of mimicry, hybridity, ambivalence, diaspora, identity is represented on the short story works Triyanto Triwikromo Samin Twins. Samin cePen Twins lift setting colonialism in the area of Sawahlunto, Blora, Grobogan, and Bojonegoro in 1897an. This short story tells the story of Resident Assistant Blora who tried to interrogate the leader who claimed to be Samin. Instead of trying to interrogate, Assistant Resident've got a resistance of interlocutor. Assistant Resident menamkan colonial process in Blora and surrounding communities. The story contains the story of the history of the Dutch colonial times so that the right to be assessed by post-colonial theory. Operationalization of post-colonial theory in the study of literary texts illustrated by efforts to study literary text data that relates to consciousness colonized on the colonizers. Step study conducted dengana, determination of data sources, collection and classification of data, and data analysis. Postcolonial analysis is expected to help in the discovery of awareness of nationalism in order to sustain the unity of the nation.Keywords: post-colonial, resistance, short stories, Samin, Assistant Resident
Detection of Vibrio harveyi using hemolysin primer in tiger shrimp Penaeus monodon
Authors: Suriyani Irma , Kadriah Ince Ayu Khairana , Kuruseng Ilmiah 
Published: February 2017

ABSTRACT This study was aimed to analyze the sensitivity and ability of primer hemolysin in detecting pathogenetic Vibrio on tiger shrimp post-larvae (PL) exposed under different exposure times in media inoculated with Vibrio harveyi. The PL of tiger shrimp were infected with 106 cfu/mL of V. harveyi by immersion method for three, six, 12, 24, 48 and 72 hours. The presence of hemolisin genes was detected by PCR techniques. The electrophoresis detected narrow hemolysin genes after PL were exposed for three and six hours. Clear visible bands of DNA Vibrio were observed for 12 hours of exposure. In contrast, no detected hemolysin gene of Vibrio was observed for PL exposed within 24, 48, and 72 hours. The rapid detection on Vibrio pathogenic for tiger shrimp PL should be conducted within three to 12 hours of exposure. No recommendation in utilizing this rapid detection for tiger shrimp PL exposed beyond 12 hours of V. harveyi. Keywords: specific primer, luminous Vibrio bacteria, pathogenic, PCR method, hemolysin gene ABSTRAK Penelitian ini bertujuan untuk mengetahui kemampuan atau sensitivitas primer hemolisin dalam mendeteksi Vibrio patogen dengan lama pemaparan berbeda. Penelitian ini dilakukan dengan menginfeksikan Vibrio harveyi pada benur udang dengan metode perendaman pada konsentrasi 106 cfu/mL. Pengambilan sampel dilakukan pada waktu tiga, enam, 12, 24, 48, dan 72 jam pascainfeksi. Keberadaan gen hemolisin pada bakteri V. harveyi dideteksi menggunakan teknik polymerase chain reaction (PCR). Hasil elektroforesis memperlihatkan bahwa pada pemaparan tiga dan enam jam keberadaan gen hemolisin dari bakteri Vibrio patogen yang diinfeksikan sudah dapat terdeteksi pada benur walaupun masih terlihat tipis. Pada pemaparan 12 jam terlihat sangat jelas pita-pita DNA dari bakteri patogen. Sedangkan pada pemaparan 24, 48, dan 72 jam sudah tidak terdeteksi lagi gen hemolisin dari bakteri Vibrio. Hal ini diduga disebabkan terjadinya penurunan populasi bakteri Vibrio yang hidup dalam tubuh dan media pemeliharaan udang. Pentingnya deteksi cepat diawal udang terinfeksi bakteri (3–12 jam) karena setelah 12 jam infeksi sudah sulit untuk mendeteksi keberadaan bakteri patogen di dalam tubuh udang. Kata kunci: primer spesifik, bakteri Vibrio berpendar, patogenik, metode PCR, gen hemolisin
GIFT Nile tilapia Oreochromis niloticus fed on diet containing probiotic
Authors: Soedibya Petrus Hari Tjahja 
Published: February 2017

ABSTRACT This research was conducted to evaluate the effect of the diet containing probiotic on Nile tilapia, Oreochromis niloticus. Fish with an initial body weight of 3.62±1.33 g were fed on diet supplemented with either 0%, 10%, 15%, 20% of probiotic. Results showed that fish fed on the diet supplemented with 15% of probiotic had the highest protein retention and specific growth rate, which were16.48±0.49% and 17.65±0.9%/day respectively. Keywords: probiotic, Azola meal, protein retention, specific growth rate ABSTRAK Penelitian ini bertujuan untuk mengevaluasi efek pemberian pakan mengandung probiotik pada ikan nila, Oreochromis niloticus. Ikan dengan bobot awal 3,62±1,33 g diberi pakan mengandung 0%, 10%, 15%, 20% probiotic. Hasil penelitian menunjukkan bahwa ikan yang diberi pakan mengandung 15% probiotik memiliki retensi protein dan laju pertumbuhan tertinggi masing-masing dengan nilai 16,48±0,49% dan 17,65±0,9%/ hari. Kata kunci: probiotik, tepung Azola, retensi protein, laju pertumbuhan harian
Survival and growth of catfish Pangasionodon sp. larvae fed on vitamin C-enriched Artemia
Authors: Setiawati Mia , Putri Darina , Jusadi Dedi 
Published: February 2017

ABSTRACT The research was conducted to evaluate effect of the administration of Artemia enriched with vitamin C on the survival, total body length, and average body weight of Pangasionodon sp. larvae. Artemia were enriched with either 0, 50, 100, or 150 mg/L vitamin C immersed in the culture medium for 13 hours. Two days old larvae were fed on enriched Artemia 12 times/day for seven days. At the end of feeding experiment, it was found that fish fed on Artemia enriched with 100 mg/L culture medium had the highest survival, total length and body weight, respectively 76.17±12.78%, 1.63±0.34 cm, and 20.6±3.8 mg. Keywords: survival, growth, Artemia, vitamin C, catfish, Pangasionodon sp. ABSTRAK Penelitian ini dilakukan untuk mengetahui pengaruh Artemia yang diperkaya dengan vitamin C dosis berbeda terhadap kelangsungan hidup, panjang total, dan bobot tubuh larva ikan patin Pangasionodon sp. Pada penelitian ini, Artemia diperkaya dengan vitamin C dosis 0, 50, 100, atau 150 mg/L media pengayaan. Larva yang berumur dua hari diberi pakan Artemia hasil pengayaan sebanyak 12 kali sehari selama tujuh hari masa pemeliharaan. Pada akhir percobaan, didapatkan bahwa larva ikan yang diberi Artemia diperkaya vitamin C dosis 100 mg/L media pengayaan memberikan kelangsungan hidup 76,17±12,78%, panjang total 1,63±0,34 cm, dan bobot tubuh paling tinggi 20,6±3,8 mg. Kata kunci: kelangsungan hidup, pertumbuhan, Artemia, vitamin C, ikan patin, Pangasionodon sp.