bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single-molecule optical genome mapping of a human HapMap and a colorectal cancer cell line
Authors: Teo Audrey S. M. , Verzotto Davide , Yao Fei , Nagarajan Niranjan , Hillmer Axel M. 
Published: December 2015

Abstract

Background:
Next-generation sequencing (NGS) technologies have changed our understanding of the variability of the human genome. However, the identification of genome structural variations based on NGS approaches with read lengths of 35–300 bases remains a challenge. Single-molecule optical mapping technologies allow the analysis of DNA molecules of up to 2 Mb and as such are suitable for the identification of large-scale genome structural variations, and for de novo genome assemblies when combined with short-read NGS data. Here we present optical mapping data for two human genomes: the HapMap cell line GM12878 and the colorectal cancer cell line HCT116.

Findings:
High molecular weight DNA was obtained by embedding GM12878 and HCT116 cells, respectively, in agarose plugs, followed by DNA extraction under mild conditions. Genomic DNA was digested with KpnI and 310,000 and 296,000 DNA molecules (≥150 kb and 10 restriction fragments), respectively, were analyzed per cell line using the Argus optical mapping system. Maps were aligned to the human reference by OPTIMA, a new glocal alignment method. Genome coverage of 6.8× and 5.7× was obtained, respectively; 2.9× and 1.7× more than the coverage obtained with previously available software.

Conclusions:
Optical mapping allows the resolution of large-scale structural variations of the genome, and the scaffold extension of NGS-based de novo assemblies. OPTIMA is an efficient new alignment method; our optical mapping data provide a resource for genome structure analyses of the human HapMap reference cell line GM12878, and the colorectal cancer cell line HCT116.
On the robustness of minimum wage effects: geographically-disparate trends and job growth equations
Authors: Addison John T. , Blackburn McKinley L. , Cotti Chad D. 
Published: December 2015

Abstract
Recent attempts to incorporate spatial heterogeneity in minimum-wage employment models have been targeted for using overly simplistic trend controls and for neglecting the potential impact of wage minima on employment growth. This paper investigates whether such considerations call into question findings of statistically insignificant employment effects reported in the literature for an archetypal low-wage sector in the United States: restaurants and bars. Understanding this relationship goes to the heart of the policy debate surrounding minimum wages and, hence, is critical to investigate carefully. Our results conclude that a focus on employment levels is appropriate for this sector and, further, that the deployment of nonlinear trend controls does not dislodge prior research which finds weak support for the existence of adverse minimum-wage employment effects on employment.

JEL Classification: J23, J38
Monitoring, endogenous comparative advantage, and immigration
Authors: Qirjo Dhimitri 
Published: December 2015

Abstract
We propose a theory of free movement of goods and labor between two economies in the presence of moral hazard. Each country produces two final goods where the productive efforts of workers cannot be perfectly observed, or verified only in the complex industry. We show that national institutional quality and the system of the early childhood care and education determine the pattern of international trade. However, individuals’ decisions to emigrate depend only on the national institutional quality, where the country with more developed institutions serves as the host country of immigrants. We conclude that international labor movement promotes international trade.
JEL classification: B52, I21, F10, F16, F22, J24.
Technique modifications for septodermoplasty: An illustrative case
Authors: Bastianelli Mark , Kilty Shaun J. 
Published: December 2015

Background Hereditary hemorrhagic telangiectasia (HHT) is an autosomal dominant disease that results in telangiectasia of the sinonasal tract, gastro-intestinal tract as well as possible arteriovenous malformations of the lung, liver and brain. One of the most common disease manifestations of HHT is epistaxis. Severe recurrent epistaxis necessitating iron therapy and blood transfusion is often managed with septodermoplasty. Its initial description was as an open surgical technique requiring nasal packing. Case presentation We describe a modified approach to septodermoplasty done completely endoscopically and without nasal packing for a patient with severe epistaxis due to HHT. Conclusion The described technique modifications for the presented case allowed for same day discharge following surgery, complete take of the skin graft and resultant epistaxis control that ended thepatient's transfusion dependency. The merits of these modifications should be further evaluated in a clinical trial.
Rituximab Maintenance for a Maximum of 5 Years After Single-Agent Rituximab Induction in Follicular Lymphoma: Results of the Randomized Controlled Phase III Trial SAKK 35/03
Authors: Taverna Christian , Martinelli Giovanni , Hitz Felicitas , Mingrone Walter , Pabst Thomas , Cevreska Lidija , del Giglio Auro , Vanazzi Anna , Laszlo Daniele , Raats Johann , Rauch Daniel , Vorobiof Daniel A. , Lohri Andreas , Biaggi Rudolf Christine , Rondeau Stéphanie , Rusterholz Corinne , Heijnen Ingmar A.F.M. , Zucca Emanuele , Ghielmini Michele 
Published: December 2015

Purpose Rituximab maintenance therapy has been shown to improve progression-free survival in patients with follicular lymphoma; however, the optimal duration of maintenance treatment remains unknown. Patients and Methods Two hundred seventy patients with untreated, relapsed, stable, or chemotherapy-resistant follicular lymphoma were treated with four doses of rituximab monotherapy in weekly intervals (375 mg/m2). Patients achieving at least a partial response were randomly assigned to receive maintenance therapy with one infusion of rituximab every 2 months, either on a short-term schedule (four administrations) or a long-term schedule (maximum of 5 years or until disease progression or unacceptable toxicity). The primary end point was event-free survival (EFS). Progression-free survival, overall survival (OS), and toxicity were secondary end points. Comparisons between the two arms were performed using the log-rank test for survival end points. Results One hundred sixty-five patients were randomly assigned to the short-term (n = 82) or long-term (n = 83) maintenance arms. Because of the low event rate, the final analysis was performed after 95 events had occurred, which was before the targeted event number of 99 had been reached. At a median follow-up period of 6.4 years, the median EFS was 3.4 years (95% CI, 2.1 to 5.3) in the short-term arm and 5.3 years (95% CI, 3.5 to not available) in the long-term arm (P = .14). Patients in the long-term arm experienced more adverse effects than did those in the short-term arm, with 76% v 50% of patients with at least one adverse event (P < .001), five versus one patient with grade 3 and 4 infections, and three versus zero patients discontinuing treatment because of unacceptable toxicity, respectively. There was no difference in OS between the two groups. Conclusion Long-term rituximab maintenance therapy does not improve EFS, which was the primary end point of this trial, or OS, and was associated with increased toxicity.
Prospective Study of 68Ga-DOTATATE Positron Emission Tomography/Computed Tomography for Detecting Gastro-Entero-Pancreatic Neuroendocrine Tumors and Unknown Primary Sites
Authors: Sadowski Samira M. , Neychev Vladimir , Millo Corina , Shih Joanna , Nilubol Naris , Herscovitch Peter , Pacak Karel , Marx Stephen J. , Kebebew Electron 
Published: December 2015

Purpose Gastro-entero-pancreatic neuroendocrine tumors (GEPNETs) are increasing in incidence, and accurate staging is important for selecting the appropriate treatment. 68Ga-DOTATATE imaging is a promising approach for detecting GEPNETs and could help in selecting optimal therapeutic strategies. The aim of this study was to prospectively determine the clinical utility of 68Ga-DOTATATE positron emission tomography (PET)/computed tomography (CT) in detecting unknown primary and metastatic GEPNETs. Patients and Methods One hundred thirty-one patients were enrolled in a prospective study of patients undergoing 68Ga-DOTATATE PET/CT, 111In-pentetreotide single-photon emission computed tomography (SPECT)/CT and multiphasic CT scan, and/or magnetic resonance imaging in a blinded fashion with comprehensive biochemical testing. The primary outcome measure was the detection of lesions by each imaging study. Results 68Ga-DOTATATE PET/CT imaging detected 95.1% of lesions (95% CI, 92.4% to 96.8%) with an average maximum standardized uptake value of 65.4 ± 47 (range, 6.9 to 244), anatomic imaging detected 45.3% of lesions (95% CI, 37.9% to 52.9%), and 111In-pentetreotide SPECT/CT detected 30.9% of lesions (95% CI, 25.0% to 37.5%), with a significant difference between imaging modalities (P < .001). In four of 14 patients (28.6%), 68Ga-DOTATATE PET/CT found a previously unknown primary tumor, and detected primary GEPNET, lymph node, and distant metastases correctly in 72 of 113 lesions (63.7%) when compared with histopathology, with 22.1% and 38.9% detected by using 111In-pentetreotide SPECT/CT and anatomic imaging, respectively. On the basis of findings with 68Ga-DOTATATE PET/CT, 43 of 131 patients (32.8%) had a change in management recommendation. In patients with carcinoid symptoms but negative biochemical testing, 68Ga-DOTATATE PET/CT detected lesions in 65.2% of patients, 40% of which were detected neither by anatomic imaging nor by 111In-pentetreotide SPECT/CT. Conclusion 68Ga-DOTATATE PET/CT imaging provides important information for accurate staging of GEPNETs and selection of appropriate treatment interventions even in the absence of biochemical evidence of disease in symptomatic patients.
Activin Decoy Receptor ActRIIB:Fc Lowers FSH and Therapeutically Restores Oocyte Yield, Prevents Oocyte Chromosome Misalignments and Spindle Aberrations, and Increases Fertility in Midlife Female SAMP8 Mice
Authors: Bernstein Lori R. , Mackenzie Amelia C. L. , Lee Se-Jin , Chaffin Charles L. , Merchenthaler István 
Published: December 2015

AbstractWomen of advanced maternal age (AMA) (age ≥ 35) have increased rates of infertility, miscarriages, and trisomic pregnancies. Collectively these conditions are called “egg infertility.” A root cause of egg infertility is increased rates of oocyte aneuploidy with age. AMA women often have elevated endogenous FSH. Female senescence-accelerated mouse-prone-8 (SAMP8) has increased rates of oocyte spindle aberrations, diminished fertility, and rising endogenous FSH with age. We hypothesize that elevated FSH during the oocyte's FSH-responsive growth period is a cause of abnormalities in the meiotic spindle. We report that eggs from SAMP8 mice treated with equine chorionic gonadotropin (eCG) for the period of oocyte growth have increased chromosome and spindle misalignments. Activin is a molecule that raises FSH, and ActRIIB:Fc is an activin decoy receptor that binds and sequesters activin. We report that ActRIIB:Fc treatment of midlife SAMP8 mice for the duration of oocyte growth lowers FSH, prevents egg chromosome and spindle misalignments, and increases litter sizes. AMA patients can also have poor responsiveness to FSH stimulation. We report that although eCG lowers yields of viable oocytes, ActRIIB:Fc increases yields of viable oocytes. ActRIIB:Fc and eCG cotreatment markedly reduces yields of viable oocytes. These data are consistent with the hypothesis that elevated FSH contributes to egg aneuploidy, declining fertility, and poor ovarian response and that ActRIIB:Fc can prevent egg aneuploidy, increase fertility, and improve ovarian response. Future studies will continue to examine whether ActRIIB:Fc works via FSH and/or other pathways and whether ActRIIB:Fc can prevent aneuploidy, increase fertility, and improve stimulation responsiveness in AMA women.
Identification of Males with Cryptic Fragile X Alleles by Methylation-Specific Quantitative Melt Analysis
Authors: Aliaga Solange M , Slater Howard R , Francis David , Du Sart Desiree , Li Xin , Amor David J , Alliende Angelica M , Santa Maria Lorena , Faundes Víctor , Morales Paulina , Trigo Cesar , Salas Isabel , Curotto Bianca , Godler David E 
Published: December 2015

Abstract

BACKGROUND
FMR1 full mutations (FMs) (CGG expansion &gt;200) in males mosaic for a normal (&lt;45 CGG) or gray-zone (GZ) (45–54 CGG) allele can be missed with the standard 2-step fragile X syndrome (FXS) testing protocols, largely because the first-line PCR tests showing a normal or GZ allele are not reflexed to the second-line test that can detect FM.

METHODS
We used methylation-specific quantitative melt analysis (MS-QMA) to determine the prevalence of cryptic FM alleles in 2 independent cohorts of male patients (994 from Chile and 2392 from Australia) referred for FXS testing from 2006 to 2013. All MS-QMA–positive cases were retested with commercial triplet primed PCR, methylation-sensitive Southern blot, and a methylation-specific EpiTYPER-based test.

RESULTS
All 38 FMs detected with the standard 2-step protocol were detected with MS-QMA. However, MS-QMA identified methylation mosaicism in an additional 15% and 11% of patients in the Chilean and Australian cohorts, respectively, suggesting the presence of a cryptic FM. Of these additional patients, 57% were confirmed to carry cryptic expanded alleles in blood, buccal mucosa, or saliva samples. Further confirmation was provided by identifying premutation (CGG 55–199) alleles in mothers of probands with methylation-sensitive Southern blot. Neurocognitive assessments showed that low-level mosaicism for cryptic FM alleles was associated with cognitive impairment or autism.

CONCLUSIONS
A substantial number of mosaic FM males who have cognitive impairment or autism are not diagnosed with the currently recommended 2-step testing protocol and can be identified with MS-QMA as a first-line test.
Chilean 12th graders’ Attitudes towards English as a Foreign Language
Authors: Gómez Burgos Eric , Pérez Pérez Sandra 
Published: December 2015

<p>This article aims to provide the results of a research focusing on 12<sup>th</sup> graders’ attitudes towards English as a Foreign Language in two secondary schools in Puerto Montt, Chile. Attitude towards a language has been considered as an important factor that influences the process of learning a foreign language (Shams, 2008); for this reason, it is fundamental to identify students’ attitudes since positive attitudes towards English allow the students to have favourable orientation towards learning it (Karahan, 2007). Under this premise, this study corresponds to a case study that includes a quantitative method of data analysis. A survey of five dimensions was conducted amongst 154 students in order to measure their attitudes towards the target language. The results show that their attitudes towards English as a foreign language are favourable; however, the dimensions related to learning English, and English as a subject at school obtained unfavourable attitudes. </p>
Tejiendo memoria
Authors: Suarez Bautista Leidy Fernanda , Vargas Caro Andrea Carolina , Rayo Montealegre Carolina 
Published: December 2015

<p>El siguiente trabajo presenta los resultados de una investigación realizada en la ciudad de Bogotá sobre el desplazamiento forzado desde la reconstrucción narrativa de una víctima del conflicto armado en nuestro país teniendo en cuenta la importancia de la memoria en un escenario de posconflicto; dentro de la cual se tendrá como base el contexto geográfico en el que se desarrollan los hechos relatados por la señora Claudia Estrada,<strong> </strong>así como los referentes teóricos que dan cuenta de los conceptos de desplazamiento forzado, narración y memoria histórica. Esta investigación se realiza en el marco de la asignatura Narraciones y Testimonios de Conflicto de la Licenciatura en Educación Básica con Énfasis en Humanidades y Lengua Castellana a la que pertenecemos.</p><div> </div>
Changing Trends in Asthma Prevalence Among Children
Authors: Akinbami Lara J. , Simon Alan E. , Rossen Lauren M. 
Published: December 2015

BACKGROUND:
Childhood asthma prevalence doubled from 1980 to 1995 and then increased more slowly from 2001 to 2010. During this second period, racial disparities increased. More recent trends remain to be described.

METHODS:
We analyzed current asthma prevalence using 2001–2013 National Health Interview Survey data for children ages 0 to 17 years. Logistic regression with quadratic terms was used to test for nonlinear patterns in trends. Differences between demographic subgroups were further assessed with multivariate models controlling for gender, age, poverty status, race/ethnicity, urbanicity, and geographic region.

RESULTS:
Overall, childhood asthma prevalence increased from 2001 to 2009 followed by a plateau then a decline in 2013. From 2001 to 2013, multivariate logistic regression showed no change in prevalence among non-Hispanic white and Puerto Rican children and those in the Northeast and West; increasing prevalence among 10- to 17-year-olds, poor children, and those living in the South; increasing then plateauing prevalence among 5- to 9-year-olds, near-poor children, and non-Hispanic black children; and increasing then decreasing prevalence among 0- to 4-year-olds, nonpoor, and Mexican children and those in the Midwest. Non-Hispanic black-white disparities stopped increasing, and Puerto Rican children remained with the highest prevalence.

CONCLUSIONS:
Current asthma prevalence ceased to increase among children in recent years and the non-Hispanic black-white disparity stopped increasing due mainly to plateauing prevalence among non-Hispanic black children.
Perkawinan Islam Wetu Telu Masyarakat Bayan Lombok Utara
Authors: Rachmadhani Arnis 
Published: December 2015

<p>This article examines the doctrine of marriage in Wetu Telu society in<br />Bayan, North Lombok. According to the community marriage is carried out<br />by three steps: perondongan, mepadik lamar, and selarian which is finished<br />with some rituals, such as menjojok, memulang, sejati, pemuput selabar,<br />akad nikah, sorong serah, nyongkolan, and balik onos nae. The marriage<br />ritual is led in accordance with Islamic teachings by the Head of Office of<br />Religious Affairs. <br />In spite of referring to Islamic sharia, the Wetu Telu also strongly holds<br />the teaching of their ancestors which is more identical with Siva-Buddhist<br />teaching. After a long process of acculturation with Hinduism, the later<br />takes a part in marriage process within the Wetu Telu. Therefore, the mar-<br />riage concept carried out by the Wetu Telu is a combination of Siva-Budhist <br />(as the religion of indigenous people) and Balinese Hinduism carried out by<br />Balinese kingdom which had been mixed with Islamic teachings that later<br />become local tradition. This local tradition then does create social stratification, <br />marriage procedures and marriage procession. The local wisdom of marriage among the Wetu Telu has a potential role to strengthen religious<br />harmony in multicultural society.</p><p> </p>
Ahmadiyah di Kabupaten Kudus
Authors: Rosyid Moh 
Published: December 2015

This research was picturing the society of Ahmadiyah (which consists<br />of only ten families) in Kudus, Central Java. On one hand this community <br />can be so adaptive to outers (non-Ahmadiyah people) such as joining their yasiinan or manaqiban groups and attending neighborhood meetings and can be so exclusive on the other hand. By exclusive here means that the Ahmadiyah people in Kudus will recite the quran and perform daily prayers together with themselves in their own mosque (Ahmadi mosque). The acceptance of Ahmadiyah in Kudus began when in 1989 some people in Kudus looked for physical and spiritual tranquility to Ahmadi people in Gabus, Pati, Central Java. The Ahmadi people of Gabus then taught them sesorah (Ahmadi teachings) which was suitable with them so that the Ahmadi teaching then well received. Kinship and patron client (employer-employee) relationship are two significant factors for the Ahmadiyah recruitment. The Ahmadiyah in Kudus could exist for the “center” (Bogor) sends them religious teachers who teach and lead their daily prayers in their own masjid. This masjid is built on a piece of land given by Ahmadi people. In order for their existence among local people not to be regarded such as creating “water and oil” relationship, Ahmadi people perform some social events which more outers are involved in, such as inviting them to halal bihalal forum and blood donor.<br /><br />
Pelaksanaan Kurikulum Tingkat Satuan Pendidikan Pada MTs Negeri Yogyakarta II
Authors: Khudrin Ali 
Published: December 2015

The purpose of this research is to investigate the implementation of Kurikulum <br />Tingkat Satuan Pendidikan (School-Based Curriculum) in MTsN Yogyakarta <br />II. Using descriptive qualitative method, the research successfully reveals that the MTsN II Yogyakrta provides some steps for implementing the School-Based Curriculum: preparation, implementation, and evaluation. The first step, preparation, is started from making rules, regulations, technical guidelines and socialization, continued with organizing documents I and II of the curriculum. The second stage is the implementation of the School-Based Curriculum itself. The result of the research shows that MTsN II Yogyakarta performs the curriculum according to the document I and document II. The last step is evaluation. Some supporting factors for the implementation of the curriculum are facilities and infrastructures, instructional media, teaching materials, learning resources, and qualified human resources. While the only inhibiting factor is the fact that some teachers find difficulties in applying multi learning media.<br /><br />
Kompetensi Guru Pendidikan Agama Islam
Authors: Taruna Mulyani Mudis 
Published: December 2015

Kajian dampak sertifikasi guru terhadap kompetensi perlu terus dilakukan, termasuk kajian terhadap guru mata pelajaran PAI (Pendidikan Agama Islam) di<br /> Madrasah Tsanawiah. Salah satu tujuan dari penelitian ini adalah untuk mengetahui perbedaan kompetensi guru PAI MTs yang berstatus tersertifikasi dan guru PAI MTs yang belum tersertifikasi. Metode penelitian ini menggunakan pendekatan kuantitatif dengan analisis Anova dua jalur. Populasi dalam penelitian ini adalah seluruh guru PAI MTs negeri dan swasta di Kabupaten Banjar Kalimantan Selatan. Sampel dalam penelitian ini dipilih secara random dengan teknik strata berjumlah 60 orang guru PAI dan untuk sampel siswa sebanyak 120. Salah satu hasil enelitian adalah diketahui terdapat perbedaan kompetensi guru PAI yang tersertifikasi dan kompetensi guru PAI yang belum tersertifikasi. Hasil analisis lanjut diketahui bahwa kompetensi guru PAI yang belum tersertifikasi lebih baik daripada kompetensi guru PAI yang sudah tersertifikasi <br /><br />