bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data
Authors: Shen Xing-Xing , Zhou Xiaofan , Kominek Jacek , Kurtzman Cletus P , Hittinger Chris Todd , Rokas Antonis 
Published: October 2016

AbstractUnderstanding the phylogenetic relationships among the yeasts of the subphylum Saccharomycotina is a prerequisite for understanding the evolution of their metabolisms and ecological lifestyles. In the last two decades, the use of rDNA and multilocus data sets has greatly advanced our understanding of the yeast phylogeny, but many deep relationships remain unsupported. In contrast, phylogenomic analyses have involved relatively few taxa and lineages that were often selected with limited considerations for covering the breadth of yeast biodiversity. Here we used genome sequence data from 86 publicly available yeast genomes representing nine of the 11 known major lineages and 10 nonyeast fungal outgroups to generate a 1233-gene, 96-taxon data matrix. Species phylogenies reconstructed using two different methods (concatenation and coalescence) and two data matrices (amino acids or the first two codon positions) yielded identical and highly supported relationships between the nine major lineages. Aside from the lineage comprised by the family Pichiaceae, all other lineages were monophyletic. Most interrelationships among yeast species were robust across the two methods and data matrices. However, eight of the 93 internodes conflicted between analyses or data sets, including the placements of: the clade defined by species that have reassigned the CUG codon to encode serine, instead of leucine; the clade defined by a whole genome duplication; and the species Ascoidea rubescens. These phylogenomic analyses provide a robust roadmap for future comparative work across the yeast subphylum in the disciplines of taxonomy, molecular genetics, evolutionary biology, ecology, and biotechnology. To further this end, we have also provided a BLAST server to query the 86 Saccharomycotina genomes, which can be found at http://y1000plus.org/blast.
Genomic Prediction of Resistance to Pasteurellosis in Gilthead Sea Bream (Sparus aurata) Using 2b-RAD Sequencing
Authors: Palaiokostas Christos , Ferraresso Serena , Franch Rafaella , Houston Ross D , Bargelloni Luca 
Published: October 2016

Abstract
Gilthead sea bream (Sparus aurata) is a species of paramount importance to the Mediterranean aquaculture industry, with an annual production exceeding 140,000 metric tons. Pasteurellosis due to the Gram-negative bacterium Photobacterium damselae subsp. piscicida (Phdp) causes significant mortality, especially during larval and juvenile stages, and poses a serious threat to bream production. Selective breeding for improved resistance to pasteurellosis is a promising avenue for disease control, and the use of genetic markers to predict breeding values can improve the accuracy of selection, and allow accurate calculation of estimated breeding values of nonchallenged animals. In the current study, a population of 825 sea bream juveniles, originating from a factorial cross between 67 broodfish (32 sires, 35 dams), were challenged by 30 min immersion with 1 × 105 CFU virulent Phdp. Mortalities and survivors were recorded and sampled for genotyping by sequencing. The restriction-site associated DNA sequencing approach, 2b-RAD, was used to generate genome-wide single nucleotide polymorphism (SNP) genotypes for all samples. A high-density linkage map containing 12,085 SNPs grouped into 24 linkage groups (consistent with the karyotype) was constructed. The heritability of surviving days (censored data) was 0.22 (95% highest density interval: 0.11–0.36) and 0.28 (95% highest density interval: 0.17–0.4) using the pedigree and the genomic relationship matrix respectively. A genome-wide association study did not reveal individual SNPs significantly associated with resistance at a genome-wide significance level. Genomic prediction approaches were tested to investigate the potential of the SNPs obtained by 2b-RAD for estimating breeding values for resistance. The accuracy of the genomic prediction models (r = 0.38–0.46) outperformed the traditional BLUP approach based on pedigree records (r = 0.30). Overall results suggest that major quantitative trait loci affecting resistance to pasteurellosis were not present in this population, but highlight the effectiveness of 2b-RAD genotyping by sequencing for genomic selection in a mass spawning fish species.
A Simplified Strategy for Introducing Genetic Variants intoDrosophilaCompound Autosome Stocks
Authors: Gilliland William D , May Dennis P , Colwell Eileen M , Kennison James A 
Published: October 2016

AbstractDrosophila stocks bearing compound chromosomes, single molecules of DNA that carry the genomic complement of two chromosomes, are useful tools for studying meiosis and mitosis. However, these stocks cannot easily be crossed to stocks with regular chromosomes, due to the lethality of the resulting whole-chromosome aneuploidy. This prevents the examination of interesting genetic variants in a compound chromosome background. Methods to circumvent this difficulty have included the use of triploid females or nondisjunction (caused by either cold-induced microtubule depolymerization or meiotic mutants). Here, we present a new approach for crossing compound chromosomes that takes advantage of the nonhomologous segregations that result when multiple chromosomes in the same genome are prevented from meiotic crossing over by heterozygosity for balancer chromosomes. This approach gives higher yields of the desired progeny in fewer generations of crossing. Using this technique, we have created and validated stocks carrying both a compound-X and compound-2, as well as compound-2 stocks carrying the meiotic mutant nod.
Fiqh Issues in the Border Areas of West Kalimantan
Authors: Siregar Hamka 
Published: October 2016

The less prosperous condition of the community in the Indonesia-Malaysia border area in the province of West Kalimantan has resulted in several problems including those related to fiqh, such as the sale and purchase of illegal goods from Malaysia, the phenomena of illegal migrant workers from Indonesia, human trafficking, transnational marriages, double identity cards, etc. In the perspective of fiqh, there is no ban on trading between people of different nationalities. In the legislative provisions, all citizens are bound not to commit illegal trade. On the other hand, the cases of double identity cards, transnational marriages, and the issue of migrant workers, in fact, are against the fiqh. However, in the context of citizenship, people should follow the provisions of the prevailing legislation. These fiqh issues have motivated the author to analyze them from the perspective of fiqh. Hopefully, we can get a picture of the fiqh problems in the Indonesia-Malaysia border area and find solutions to them.DOI: 10.15408/sdi.v23i2.2654
Pasang Surut Hubungan Aceh dan Turki Usmani: Perspektif Sejarah
Authors: Burhanudin Jajat 
Published: October 2016

A. C. S. Peacock and Annabel Teh Gallop, eds. 2015. From Anatolia to Aceh: Ottomans, Turks, and Southeast Asia. Oxford: The British Academy by Oxford University Press.This book comprises of some articles with the major contribution to investigating further the relation between the Ottoman in Istanbul and Muslim kingdoms in Southeast Asia. Using the archival sources from the Ottoman period, those articles highlight new information on the Ottoman-Southeast Asia network, which has been rather neglected from any scholarly studies. Especially in relation with the Acehnese kingdom, the discussions of this book demonstrate that Aceh was the only Southeast Asian Islamic kingdom which made serious efforts to make relation with the Ottoman. Issues related to politics, commerce, and military aids constituted the main substance in the relation they established in the sixteenth century, which then continued in the seventeenth century in the form of intellectual and religious network. The period of the nineteenth century witnessed the re-emergence of the political issue in Aceh-Ottoman relation, as Aceh looked for Ottoman protection to face the Dutch military invasion.DOI: 10.15408/sdi.v23i2.3259
Al-Islām wa al-Madd wa al-Jazr fī al-‘Alāqāt bayn al-Dīn wa al-Dawlah fī Indonesia
Authors: Ropi Ismatu 
Published: October 2016

This article reviews the complex contestation between religion and state in terms of the Muslims role in the formation of nation state since Indonesia’s independence. The article’s first part discusses the emergence of new middle-class Muslims that played a key role in the Islamization process and contribute to the emergence of Islamist attitudes and behavior. These attitudes tend to be strengthened and lead the potential latent extremism endangering multiculturalism and multireligious life in Indonesia. The article’s second part focuses on the long history of the Muslims role as majority groups in the formation of the constitution’s nomenclature relating to the position of religion in the state system. The new middle-class Muslims also have a desire to achieve their dreams exposing the greater portion of religion in public sphere. It can be seen from the strengthening of those Muslims activists in the parliament to transform the comprehensive meaning of the concept of God.DOI: 10.15408/sdi.v23i2.3715
Efficacy of septoplasty with endoscopic osteomeatal clearance in the management of headaches due to chronic sinusitis secondary to Deviated nasal septum
Authors: Babu Binu , Reynolds Anjana Mary , N. Gopinathan Pillai 
Published: October 2016

<p class="abstract"><strong>Background:</strong> Deviated nasal septum (DNS) is a common condition which affects most children and adults. Several surgical procedures are available for DNS. Endoscopic septoplasty is a minimally invasive surgical technique which can minimise trauma to the nasal septum and decrease post-operative morbidity. The present study was aimed to study the efficacy of septoplasty with endoscopic osteomeatal clearance, on headache due to sinusitis secondary to DNS<span lang="EN-IN">. </span></p><p class="abstract"><strong>Methods:</strong> The study was longitudinal in nature and involved patients undergoing septoplasty with endoscopic osteomeatal clearance at Government Medical College Hospital, Kottayam, Kerala, India. Patients with significant nasal obstruction due to DNS, and having recurrent sinusitis causing headache, were included into the study. Patients were discharged after 3 days and were called up for review at 2 weeks, 6 weeks, 3 months, 6 months, and 1 year and evaluated for change in headache as assessed by visual analogue score (VAS). </p><p class="abstract"><strong>Results:</strong> A total of 50 participants were enrolled into the study over a period of 2 years. Maxillary sinus was involved in almost 96% of the cases while frontal sinus was affected in 46% and ethmoid sinus in 50% of participants. Seventy four percent participants had subjective symptomatic improvement at 2 weeks after surgery. The mean (SD) VAS score pre-operatively was 6.54 (1.5) and it improved to 4.18 (1.8) at 2 weeks following surgery (p &lt;0.05)<span lang="EN-IN">. </span></p><p class="abstract"><strong>Conclusions:</strong> Septoplasty with endoscopic osteomeatal clearance is a procedure which is highly efficacious and well tolerated in treating headache due to sinusitis secondary to DNS<span lang="EN-IN">.</span></p>
Excesivo rastreo de osteoporosis en mujeres menores de 65 años: estudio de corte transversal
Authors: Ganiele María de las Nieves , Terrasa Sergio Adrián , Kopitowski Karin Silvana 
Published: October 2016

<p>El rastreo de osteoporosis en mujeres con bajo riesgo de fractura (sobreuso) puede conducir a sobrediagnóstico, tratamiento inapropiado y medicalización. El objetivo de este trabajo fue determinar la proporción de mujeres de 45 a 64 años afiliadas a un plan de medicina prepaga de Buenos Aires, Argentina, que realizaron al menos una densitometría ósea de cadera durante 2011 y no cumplían criterios para el rastreo. Se realizó un estudio observacional de corte transversal. Se identificaron 4.310 mujeres de este rango etario que se realizaron una densitometría ósea, entre las que se seleccionó una muestra aleatorizada de 401 mujeres y se obtuvieron datos completos para 178 mujeres. Para determinar si el rastreo era apropiado se utilizaron dos criterios: 1) tener un riesgo de fractura a 10 años mayor que una mujer de 65 años (regla FRAX®); 2) presentar al menos un factor de riesgo de fractura. Un 86,5% de las densitometrías óseas fueron realizadas en mujeres cuyo riesgo estimado por FRAX® no superaba el umbral mínimo recomendado, constatándose osteoporosis en el 5,8% y osteopenia en el 61,0%. En relación con el segundo criterio, el 49,4% no presentaba siquiera un factor de riesgo, documentándose osteoporosis en el 3,4%, y osteopenia en el 62,5%. Los resultados muestran que al menos la mitad de las mujeres no cumplía con los criterios de rastreo. </p>
1.2% Rosuvastatin and 1.2% Atorvastatin Gel Local Drug Delivery and Redelivery in the Treatment of Class II Furcation Defects: A Randomized Controlled Clinical Trial
Authors: Garg Shruti , Pradeep A.R. 
Published: October 2016

Background: Statins are one of the lipid‐lowering drugs that help in reducing cholesterol levels in the body by specifically inhibiting 3‐hydroxy‐3‐methylglutaryl coenzyme A reductase, which is a rate‐limiting enzyme for cholesterol synthesis. Rosuvastatin (RSV) and atorvastatin (ATV) have shown bone stimulatory and anti‐inflammatory effects. The present study aims to explore efficacy of 1.2% RSV and 1.2% ATV gels as a local drug delivery and redelivery system adjunct to scaling and root planing (SRP) for treatment of Class II furcation defects.Methods: Ninety patients with mandibular buccal Class II furcation defects were randomly allocated to three treatment groups: 1) SRP with placebo gel (group 1); 2) SRP with 1.2% RSV gel (group 2); and 3) SRP with 1.2% ATV gel (group 3). Clinical and radiographic parameters were recorded at baseline and after 6 months. Gels were redelivered at the respective sites at a 6‐month recall appointment. All clinical and radiographic parameters were recorded again after 3 months (i.e., 9 months from baseline).Results: Greater mean probing depth (PD) reduction and greater mean gain in relative vertical clinical attachment level (CAL) and relative horizontal CAL were seen in the RSV group than in the ATV group at 6 and 9 months. Significantly greater mean percentage of defect depth reduction (DDR) was found in the RSV group (30.80% ± 8.35%, 41.86% ± 6.76%) than in the ATV group (25.54% ± 8.89%, 34.31% ± 8.04%) at 6 and 9 months, respectively.Conclusion: The RSV group shows significant improvement in all clinical parameters and significantly greater DDR compared with the ATV group in treatment of mandibular Class II furcation defects as an adjunct to SRP.
Working on a Standard Joint Unit: A pilot test
Authors: Casajuana Cristina , López-Pelayo Hugo , Mercedes Balcells María , Miquel Laia , Teixidó Lídia , Colom Joan , Gual Antoni 
Published: October 2016

Introduction. Assessing cannabis consumption remains complex due to no reliable registration systems. We tested the likelihood of establishing a Standard Joint Unit (SJU) which considers the main cannabinoids with implication on health through a naturalistic approach.
Methodology. Pilot study with current cannabis users of four areas of Barcelona: universities, nightclubs, out-patient mental health service, and cannabis associations. We designed and administered a questionnaire on cannabis use-patterns and determined the willingness to donate a joint for analysis. Descriptive statistics were used to analyze the data.
Results. Forty volunteers answered the questionnaire (response rate 95%); most of them were men (72.5%) and young adults (median age 24.5 years; IQR 8.75 years) who consume daily or nearly daily (70%). Most participants consume marihuana (85%) and roll their joints with a median of 0.25 gr of marihuana. Two out of three (67.5%) stated they were willing to donate a joint.
Conclusion. Obtaining an SJU with the planned methodology has proved to be feasible. Pre-testing resulted in an improvement of the questionnaire and retribution to incentivize donations. Establishing an SJU is essential to improve our knowledge on cannabis-related outcomes.
Terapia de rehabilitación cognitiva en pacientes con trastorno por consumo de alcohol y trastorno neurocognitivo. Estudio piloto.
Authors: Frías-Torres Cindy , Moreno-España José , Ortega Lluisa , Barrio Pablo , Gual Antoni , Teixidor López Lídia 
Published: October 2016

El deterioro cognitivo es común en los pacientes alcohólicos. Éste se manifiesta por alteraciones en la memoria anterógrada y retrógrada, el procesamiento visual-espacial, y en las habilidades cognitivas y la atención, siendo algunas reversibles. Las terapias de rehabilitación cognitiva podrían mejorar el rendimiento de los pacientes, siendo una alternativa terapéutica de interés. El objetivo de este estudio piloto fue evaluar la implementación, viabilidad y efectividad de la terapia de rehabilitación cognitiva en pacientes con dependencia al alcohol y deterioro cognitivo asociado. Se trata de un estudio piloto con 16 pacientes (63% hombres, edad media de 59 años) seguidos en la Unidad de Conductas Adictivas de un hospital de tercer nivel. Siendo la abstinencia un requisito para la inclusión, durante 6 meses una enfermera realizó sesiones semanales de una hora (24 sesiones), realizándose ejercicios de psico-estimulación para la mejora del rendimiento cognitivo, funcional y social. Se evaluó a los pacientes al inicio, al final y pasados 6 meses, mediante las escalas MMSE (test Mini-mental de Lobo) y T@M (test de Alteración de Memoria). Sus puntuaciones medias respectivas fueron 26.4 (DE 3,16), 29 (DE 1,67) y 27 (DE 3,1) para MMSE y 38,7 (DE 6,81), 45,7 (DE 5,6) y 41,1 (DE 7,86) para T@M. Los datos se analizaron mediante la prueba de Friedman y se comparon los distintos periodos temporales mediante la prueba de rangos con signo de Wilcoxon, siendo la mayoría de comparaciones significativas (p < 0,05). La asistencia y la satisfacción fueron elevadas. Así pues, la terapia fue viable, ampliamente aceptada y mostró ser efectiva.
Socio Economic Factors of Contract Farming: A Logistic Analysis
Authors: Pandey A. P. 
Published: October 2016

<p><em>According to studies from Lajili et al. (1997), Rehber (2000), Sartwelle et al. (2000) and Key (2003), a farmer’s discrete choice to join contract farming scheme or not it is influenced by the household’s characteristics, operational features, socio-economic characteristics, market attributes of product and underlying agreement condition. Zhu found in a study of contract arrangement in China, that farmers’ decisions to enter into contract with their sponsors were influenced by Economic influence, distance from the target market, specialization and commercialization of the production. In a study of contract farming in transitional economies of Eastern Europe, Swinnen (2005), found that the most important factors which is more influenced farmers to enter into contracts or not, in order of importance were; guaranteed product sales, avoidance of price uncertainty, higher price offers, profitability, pre-payment offer input supply and technical assistance and some form of credit.</em></p><p><em> </em></p><p><em>In a detailed study of contract farming in poultry, chilly, Potato, banana, Wheat, Rice, maize, fruits and vegetables in Bali ,south Africa, India, America and Lombok province of Indonesia, it was revealed that factors that the important considerations and motivating factors for farmers were the increasing the productivity of crops, and getting better Income &amp; Price and less uncertainty; past experience in working with Contracting firm and agribusiness; education levels credit constraints and strong borrowing histories. The contracts were more appealing to less well-capitalization smallholders who were well educated, were credit constrained but who had strong borrowing histories (Patrick, 2004)<a title="" href="file:///E:/July%202016%20Back%20up/IRA%20June%202016%20Issues/IRAJMSS/IRAJMSS31.doc#_ftn1">[1]</a>.</em></p><p><em> </em></p><p><em>The main objective of this paper is to analyze the main socio-economic factors that motivate smallholder farmers to engage in contract farming mechanism or not.</em></p><div><br clear="all" /><hr align="left" size="1" width="33%" /><div><p><em><a title="" href="file:///E:/July%202016%20Back%20up/IRA%20June%202016%20Issues/IRAJMSS/IRAJMSS31.doc#_ftnref1">[1]</a> Patrick I. (2003). Contract farming in Indonesia: Smallholders and agribusiness working together.</em></p></div></div>
Analisis Sistem Informasi yang Sedang Berjalan dan Rencana Proyek E-Procurement dengan Pendekatan Metode New Information Economics
Authors: So Idris Gautama , Saputri Devy Listisari 
Published: October 2016

PT PLN (Persero) is a state owned which manages the biggest electricity businesses that cover the entire territory of Indonesia. His position is very potential for the Indonesian public life requires that PLN is able to manage the investment means the supply of electricity to customers. This is done with the information systems that support business processes in the body of PLN. PT PLN (Persero) has some application systems, infrastructure, service, and management used to increase the ability of the company. In PLN, there is an application that is capable of supporting PLN to conduct the procurement process is procurement information system (e-procurement). PSI Sub-party service providers as e-procurement to see investment information system (SI) and Information Technology (IT) which is proportional to the amount issued benefits and bottom-line impact for companies and can find out the level of funds / investment budgets and alignment of Information Technology there is a project in accordance with company requirements. Those needs based on business needs and applications currently running in the intersection so as to project better. Based on this, the author proposes to analyze the benefits of information technology investments by using the method of New Information Economics (NIE) that combines the two approaches both financial and non-financial. In the method NIE (New Information Economics) will be used four of the five practices that NIE Strategic Demand / Supply Planning, Innovation, Prioritization, and Alignment. The results are expected to help the company to allocate investments SI / IT is more appropriate and supports the company's performance, especially in providing added value to the parties concerned.
Perancangan E-Learning Berbasis Internet pada Sekolah SMK Negeri 13 Jakarta
Authors: So Idris Gautama , Kurniawan Fajar 
Published: October 2016

Technology advances in education is very influential for educators to solve problems such as lack of adequate study time, and lack of auxiliary equipment to support learning. Therefore, it is required to know how far SMKN 13 Jakarta will need e-Learning and the extent of readiness of existing infrastructure on students to support the implementation of e-Learning. The research method is direct survey by distributing questionnaires to students and interviews with teachers. The method of analysis used by researchers is to use SWOT analysis,Porter, and the Cost and Benefit. The results showed that the school does require an e-Learning to improve its services to the community and the students have sufficient infrastructure to support the implementation of e-Learning.