bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNA Methylome Analyses Implicate Fallopian Tube Epithelia as the Origin for High-Grade Serous Ovarian Cancer
Authors: Klinkebiel David , Zhang Wa , Akers Stacey N. , Odunsi Kunle , Karpf Adam R. 
Published: June 2016

Abstract
High-grade serous ovarian cancer (HGSC) is the most common and lethal form of epithelial ovarian cancer (EOC). Two distinct tissues have been suggested as the tissue of origin: ovarian surface epithelia (OSE) and fallopian tube epithelia (FTE). We hypothesized that the DNA methylome of HGSC should more closely resemble the methylome of its tissue of origin. To this end, we profiled HGSC (n = 10), and patient-matched OSE and FTE (n = 5) primary fresh-frozen tissues, and analyzed the DNA methylome using Illumina 450K arrays (n = 20) and Agilent Sure Select methyl-seq (n = 7). Methylomes were compared using statistical analyses of differentially methylated CpG sites (DMC) and differentially methylated regions (DMR). In addition, methylation was evaluated within a variety of different genomic contexts, including CpG island shores and Homeobox (HOX) genes, due to their roles in tissue specification. Publicly available HGSC methylome data (n = 628) were interrogated to provide additional comparisons with FTE and OSE for validation. These analyses revealed that HGSC and FTE methylomes are significantly and consistently more highly conserved than are HGSC and OSE. Pearson correlations and hierarchal clustering of genes, promoters, CpG islands, CpG island shores, and HOX genes all revealed increased relatedness of HGSC and FTE methylomes. Thus, these findings reveal that the landscape of FTE more closely resembles HGSC, the most common and deadly EOC subtype.
Implications: DNA methylome analyses support the hypothesis that HGSC arise from the fallopian tube and that due to its tissue-specificity and biochemical stability, interrogation of the methylome may be a valuable approach to examine cell/tissue lineage in cancer. Mol Cancer Res; 14(9); 787–94. ©2016 AACR.
Genomic Copy Number Dictates a Gene-Independent Cell Response to CRISPR/Cas9 Targeting
Authors: Aguirre Andrew J. , Meyers Robin M. , Weir Barbara A. , Vazquez Francisca , Zhang Cheng-Zhong , Ben-David Uri , Cook April , Ha Gavin , Harrington William F. , Doshi Mihir B. , Kost-Alimova Maria , Gill Stanley , Xu Han , Ali Levi D. , Jiang Guozhi , Pantel Sasha , Lee Yenarae , Goodale Amy , Cherniack Andrew D. , Oh Coyin , Kryukov Gregory , Cowley Glenn S. , Garraway Levi A. , Stegmaier Kimberly , Roberts Charles W. , Golub Todd R. , Meyerson Matthew , Root David E. , Tsherniak Aviad , Hahn William C. 
Published: June 2016

Abstract
The CRISPR/Cas9 system enables genome editing and somatic cell genetic screens in mammalian cells. We performed genome-scale loss-of-function screens in 33 cancer cell lines to identify genes essential for proliferation/survival and found a strong correlation between increased gene copy number and decreased cell viability after genome editing. Within regions of copy-number gain, CRISPR/Cas9 targeting of both expressed and unexpressed genes, as well as intergenic loci, led to significantly decreased cell proliferation through induction of a G2 cell-cycle arrest. By examining single-guide RNAs that map to multiple genomic sites, we found that this cell response to CRISPR/Cas9 editing correlated strongly with the number of target loci. These observations indicate that genome targeting by CRISPR/Cas9 elicits a gene-independent antiproliferative cell response. This effect has important practical implications for the interpretation of CRISPR/Cas9 screening data and confounds the use of this technology for the identification of essential genes in amplified regions.
Significance: We found that the number of CRISPR/Cas9-induced DNA breaks dictates a gene-independent antiproliferative response in cells. These observations have practical implications for using CRISPR/Cas9 to interrogate cancer gene function and illustrate that cancer cells are highly sensitive to site-specific DNA damage, which may provide a path to novel therapeutic strategies. Cancer Discov; 6(8); 914–29. ©2016 AACR.
See related commentary by Sheel and Xue, p. 824.
See related article by Munoz et al., p. 900.
This article is highlighted in the In This Issue feature, p. 803
CRISPR Screens Provide a Comprehensive Assessment of Cancer Vulnerabilities but Generate False-Positive Hits for Highly Amplified Genomic Regions
Authors: Munoz Diana M. , Cassiani Pamela J. , Li Li , Billy Eric , Korn Joshua M. , Jones Michael D. , Golji Javad , Ruddy David A. , Yu Kristine , McAllister Gregory , DeWeck Antoine , Abramowski Dorothee , Wan Jessica , Shirley Matthew D. , Neshat Sarah Y. , Rakiec Daniel , de Beaumont Rosalie , Weber Odile , Kauffmann Audrey , McDonald E. Robert , Keen Nicholas , Hofmann Francesco , Sellers William R. , Schmelzle Tobias , Stegmeier Frank , Schlabach Michael R. 
Published: June 2016

Abstract
CRISPR/Cas9 has emerged as a powerful new tool to systematically probe gene function. We compared the performance of CRISPR to RNAi-based loss-of-function screens for the identification of cancer dependencies across multiple cancer cell lines. CRISPR dropout screens consistently identified more lethal genes than RNAi, implying that the identification of many cellular dependencies may require full gene inactivation. However, in two aneuploid cancer models, we found that all genes within highly amplified regions, including nonexpressed genes, scored as lethal by CRISPR, revealing an unanticipated class of false-positive hits. In addition, using a CRISPR tiling screen, we found that sgRNAs targeting essential domains generate the strongest lethality phenotypes and thus provide a strategy to rapidly define the protein domains required for cancer dependence. Collectively, these findings not only demonstrate the utility of CRISPR screens in the identification of cancer-essential genes, but also reveal the need to carefully control for false-positive results in chromosomally unstable cancer lines.
Significance: We show in this study that CRISPR-based screens have a significantly lower false-negative rate compared with RNAi-based screens, but have specific liabilities particularly in the interrogation of regions of genome amplification. Therefore, this study provides critical insights for applying CRISPR-based screens toward the systematic identification of new cancer targets. Cancer Discov; 6(8); 900–13. ©2016 AACR.
See related commentary by Sheel and Xue, p. 824.
See related article by Aguirre et al., p. 914.
This article is highlighted in the In This Issue feature, p. 803
Synchronverter Control for Parallel Operation of Cascaded H-Bridge Inverter
Authors: Hamza Amar , Altahir Sara , Yan Xiangwu 
Published: June 2016

<p>A 21-levels cascaded H-bridge multilevel inverter topology based on three-phase voltage source inverter has been proposed as a superior replacement for conventional two-level in high voltage applications. In this work we have presented the usage of the new technique called virtual synchronous generator based synchronverter model to operate the multilevel inverter as synchronous generator, and to share active and reactive power automatically in case of parallel operated inverters of the same type. Carrier-based PWM is used to control each phase leg of the cascaded H-bridge multilevel inverter. This carrier-based PWM scheme is derived from the carrier phase disposition pulse width modulation strategy. By aid of MATLAB/Simulink package a simulation experiment is established to verify the performance of the proposed technique.</p><p> </p>
Background Modeling to Detect Foreground Objects Based on ANN and Spatio-Temporal Analysis
Authors: Kumar N. Satish , G Shobha 
Published: June 2016

<p>This paper presented an approach to building background model for moving object detection using unsupervised Artificial Neural Network (ANN) without any prior knowledge about foreground objects. First, using Local Binary Pattern (LBP) which is texture feature, builds a statistical Background Model using ANN, then, comparing the behavior of next incoming frame with model and decide each pixel whether is deviating from a model or not. And based on if method detects foreground objects then background model is updated to make this model adaptive. Also, spatial-temporal information has been exploited in this method to suppress sudden illumination variation and to suppress false foreground pixels. It was demonstrated and proved, by qualitative and quantitative metrics that the newly presented approach is adaptive, generic and can address all issues and challenges for background subtraction. To evaluate the performance of the presented approach this paper compared with recent approaches by using standard metrics and proved that presented method outperforms many existing recent approaches.</p>
Challenges Over Two Semantic Repositories - OWLIM and AllegroGraph
Authors: Tajabor Paria , Raafat Tara 
Published: June 2016

<p>The purpose of this research study is exploring two kind of semantic repositories with regards to various factors to find the best approaches that an artificial manager can use to produce ontology in a system based on their interaction, association and research. To this end, as the best way to evaluate each system and comparing with others is analysis, several benchmarking over these two repositories were examined. These two semantic repositories: OWLIM and AllegroGraph will be the main core of this study. The general objective of this study is to be able to create an efficient and cost-effective manner reports which is required to support decision making in any large enterprise.</p>
Information Retrieval: Textual Indexing Using an Oriented Object Database
Authors: Erritali Mohammed 
Published: June 2016

The growth in the volume of text data such as books and articles in libraries for centuries has imposed to establish effective mechanisms to locate them. Early techniques such as abstraction, indexing and the use of classification categories have marked the birth of a new field of research called "Information Retrieval". Information Retrieval (IR) can be defined as the task of defining models and systems whose purpose is to facilitate access to a set of documents in electronic form (corpus) to allow a user to find the relevant ones for him, that is to say, the contents which matches with the information needs of the user. Most of the models of information retrieval use a specific data structure to index a corpus which is called "inverted file" or "reverse index". This inverted file collects information on all terms over the corpus documents specifying the identifiers of documents that contain the term in question, the frequency of each term in the documents of the corpus, the positions of the occurrences of the word. In this paper we use an oriented object database (db4o) instead of the inverted file, that is to say, instead to search a term in the inverted file, we will search it in the db4o database. The purpose of this work is to make a comparative study to see if the oriented object databases may be competing for the inverse index in terms of access speed and resource consumption using a large volume of data.
Single Phase Variable Sampling Phase Locked Loop using Composite Observer
Authors: Arun K , Selvajyothi K 
Published: June 2016

<p>An observer based variable sampling period phase locked loop is introduced for grid connected systems. The composite observer acts as an efficient estimator of the fundamental components from a periodic input signal rich in DC and harmonics. The observer gains are designed using pole placement technique, which inherently ensures the stability of this estimator. Even under drift frequency, a constant number of samples (512) per cycle are maintained with the help of the numerically controlled oscillator. This makes the oscillator gain elements in the observer a constant and eliminates the trigonometric computation. This phase locked loop is found to be working in a wide range of frequency 40 – 70Hz. The performance of the proposed scheme is studied with a synthetic harmonic rich signal as well as validated by implementing the PLL in Cyclone IV FPGA with a real time grid voltage.</p>
Bridgeless Isolated Cuk PFC Implementation using PID and Neural Controller
Authors: Pireethi R. , Balamurugan R. 
Published: June 2016

<p> The comparision of Bridgeless Isolated Cuk converter using Proportional Integral Derivative (PID) and Neural controller (NC) is presented in this paper. Due to Diode Bridge Rectifier (DBR) conventional converters suffer from high conduction loss. Bridgeless Cuk converter is used to eliminate the issues. Bridgeless Isolated (BLI) Cuk converter is used to withstand high voltage. Compare to Continuous Conduction Mode (CCM) Discontinuous Conduction Mode (DCM) utilize less number of sensors. To obtain unity power factor it is used to work in DCM mode. BLI Cuk Converter is implemented in two controller PID and Neural controller to observe power factor. Performance of BLDC motor is simulated by using MATLAB/SIMULINK software. </p>
The mental health of sexually trafficked female survivors in Nepal
Authors: Rimal Retina , Papadopoulos Chris 
Published: June 2016

Background: Despite further recent research into the consequences associated with human sex trafficking, scant evidence associated with the mental health outcomes among victims of sex trafficking remains, including within Nepal where trafficking continues to be a growing problem. Aim: To investigate the prevalence and explanatory factors of depression, anxiety and post-traumatic stress disorder (PTSD) symptoms among female survivors being housed and supported by two non-governmental organisations (NGOs) in Nepal. Methods: A total of 66 female sex trafficking survivors being housed by two NGOs were purposively sampled. Anxiety and depression symptomatology were measured using the Hopkins Symptoms Checklist–25 instrument and PTSD symptomatology was measured using the PTSD Checklist–Civilian Version. Results: In all, 87%, 85.5% and 29.7% of the sample scored above anxiety, depression and PTSD thresholds, respectively. HIV-positive status and length of workday during trafficking period significantly associated with at least one outcome measure. Conclusion: The results contribute further evidence of how damaging sex trafficking can be to victims, particularly in terms of being at risk of clinical depression and/or anxiety. Continued efforts to prevent trafficking from occurring as well as effective, timely intervention for survivors are needed.
Oil and the Chávez Legacy
Authors: Hellinger Daniel 
Published: June 2016

In the final 15 years of the Punto Fijo era (1958–1998), as state institutions and socioeconomic conditions deteriorated, the executive class of Petróleos de Venezuela S.A. broke free from state control. In his 15 years as president of Venezuela, Hugo Chávez reasserted the state’s control over the company and reestablished a fiscal regime that brought the country enormous financial benefits. It is a legacy, however, that has an uncertain future. En los últimos 15 años de la era del Punto Fijo (1958–1998), mientras las instituciones estatales y las condiciones socioeconómicas se deterioraban, los ejecutivos de Petróleos de Venezuela S.A. se independizaron del control estatal. Durante sus 15 años como presidente de Venezuela, Hugo Chávez reafirmó el control del estado sobre esta compañía y reestableció un régimen fiscal que le rindió grandes beneficios económicos al país. Se trata, sin embargo, de un legado que tiene un futuro incierto.
Results of a Pilates exercise program in patients with chronic non-specific low back pain: a randomized controlled trial
Authors: Valenza MC , Rodríguez-Torres J , Cabrera-Martos I , Díaz-Pelegrina A , Aguilar-Ferrándiz ME , Castellote-Caballero Y 
Published: June 2016

Objective: To investigate the effects of a Pilates exercise program on disability, pain, lumbar mobility, flexibility and balance in patients with chronic non-specific low back pain. Design: Randomized controlled trial. Setting: University laboratory. Participants: A total of 54 patients with chronic non-specific low back pain. Intervention: Patients were randomly allocated to an experimental group ( n=27) included in a Pilates exercise program or to a control group ( n=27) receiving information in a form of a leaflet. Main outcome measures: Disability (Roland-Morris Disability Questionnaire and Oswestry Disability Index), current, average and pain at it least and at its worst (Visual Analogue Scales), lumbar mobility (modified Shober test), flexibility (finger-to-floor test) and balance (single limb stance test) were measured at baseline and after the intervention. Results: A between-group analysis showed significant differences in the intervention group compared to the control group for both disability scores, the Rolland-Morris questionnaire (mean change±standard deviation of 5.31±3.37 and 2.40±6.78 respectively and between-groups mean difference of 3.2 ± 4.12, p=0.003) and the Oswestry Disability Index ( p<0.001), current pain ( p=0.002) and pain at it least ( p=0.033), flexibility (0.032) and balance (0.043). Conclusions: An 8-week Pilates exercise program is effective in improving disability, pain, flexibility and balance in patients with chronic non-specific low back pain.
Femoral Neck Stress Fracture
Authors: Ramey Lindsay N. , McInnis Kelly C. , Palmer William E. 
Published: June 2016

Background: Limited research is available regarding return-to-running (RTR) time after femoral neck stress fractures. While studies have shown the prognostic value of image-based grading scales for stress fractures at other sites, few have included femoral neck stress fractures. Purpose: To determine if the grade of femoral neck stress fractures based on magnetic resonance imaging (MRI) characteristics correlates with RTR time. Study Design: Cohort study; Level of evidence, 3. Methods: This study included 24 patients (mean age, 32.9 years; range, 18-51 years) who were diagnosed with 27 femoral neck stress fractures by MRI from 2009 to 2015 at a single sports medicine clinic. All fractures were compression sided and were treated nonoperatively. Charts were reviewed for patient demographics and RTR time. Images were graded from 1 to 4 using the Arendt stress fracture severity scale. Statistical analysis was performed using survival analysis and Cox proportional hazard model to compare the RTR time between grades. Cox regression was repeated, adjusted for age, bone mineral density (BMD), and body mass index (BMI). Results: The mean (±standard error of the mean) RTR time in weeks for patients with fractures graded 1 to 4 was 7.4 ± 2.7 (range, 4-11), 13.8 ± 3.8 (range, 6-21), 14.7 ± 3.5 (range, 8.5-24), and 17.5 ± 3.4 (range, 10-32), respectively. Survival analysis indicated that there was a statistically significant effect of fracture grade on RTR time ( P = .0065). The Cox model indicated a statistically significant difference in RTR time between grades 1 and 2 ( P = .036), 1 and 3 ( P = .014), and 1 and 4 ( P = .002). The unadjusted hazard ratio was significant ( P = .037). There were no statistically significant differences between the remaining grades ( P = .82 for grades 2 and 3, P = .37 for grades 2 and 4, and P = .31 for grades 3 and 4). Age ( P = .71) and BMD ( P = .81) did not have an effect on RTR time. The hazard ratio remained significant ( P = .05) after adjusting for age and BMD. BMI tended to have an effect on RTR time ( P = .09). After adding BMI to the adjustment, the hazard ratio decreased in significance ( P = .13), although sample size also decreased. Conclusion: Grade 2 to 4 femoral neck stress fractures require longer RTR time than do grade 1 injuries. Patients with lower BMI tend to require a longer RTR time.
Are Female Soccer Players at an Increased Risk of Second Anterior Cruciate Ligament Injury Compared With Their Athletic Peers?
Authors: Allen Melissa M. , Pareek Ayoosh , Krych Aaron J. , Hewett Timothy E. , Levy Bruce A. , Stuart Michael J. , Dahm Diane L. 
Published: June 2016

Background: Female soccer players have a well-known risk for anterior cruciate ligament (ACL) injury, but few studies have reported on second ACL injuries in this population. Purpose: To (1) report the rates of subsequent ACL injury (ipsilateral graft rupture or contralateral tear) in competitive female soccer players, (2) compare these rates with those of other female athletes of similar competitive level, (3) determine risk factors for second ACL injury, and (4) report clinical outcome scores in this population. Study Design: Cohort study; Level of evidence, 3. Methods: The medical records at a single institution were reviewed for female patients who were injured during a competitive athletic event and treated with primary ACL reconstruction (ACLR) between 1998 and 2013. Patients were followed for a mean of 68.8 months postoperatively (range, 24-115.2 months). Clinical outcome was obtained via Lysholm and International Knee Documentation Committee (IKDC) scores. Soccer players were matched 1:1 to non-soccer athletes for age, activity level, and graft type. Results: A total of 180 female ACLR patients with a mean ± SD age of 19.6 ± 6.9 years met the study inclusion and exclusion criteria (90 soccer players and 90 non-soccer players). Soccer players sustained more second ACL injuries, including both graft failures (11% vs 1%; P < .01) and contralateral ACL tears (17% vs 4%; P < .01), compared with non-soccer players. Of the 67 patients who returned to soccer after ACLR (mean age, 17.5 years; range, 13-27 years), significantly more had graft tears compared with those who did not return to soccer (15% vs 0%, respectively; P = .04); however, the difference in contralateral ACL tears (19% for returning players vs 9% for those who did not return; P = .34) was not significant. Relatively older age (odds ratio, 1.5 per year; P = .03) was a significant risk factor for ACL graft tear but not for contralateral ACL injury. Both groups had similar mean Lysholm (96 vs 95) and IKDC scores (95 vs 96) at final follow-up. Conclusion: Twenty-eight percent of all female soccer players and 34% of those players who returned to soccer had a second ACL tear. Soccer players had an increased rate of both graft tear and contralateral ACL injury compared with similar non-soccer athletes. Older age and return to soccer were significant risk factors for graft rupture.