bluuebunny/crossref_metadata_2025_split huggingface dataset:
Catalytic pyrolysis of biomass of solid compounds used for gasoline production
Authors: Igtisamova G R , Yangirova Z Z , Nosirov D Sh 
Published: July 2019

Abstract
The article examines the latest achievements of foreign researchers whose key focus is to obtain gasoline fractions from the biomass of solid compounds using catalytic pyrolysis for its further use in industrial sectors. The biomass of solid compounds is studied as a raw material for production of gasoline fractions due to its low cost and high availability. In addition, several ways for obtaining and converting biomass are studied. At high temperatures (up to 800° C) solid is used to produce synthesis gas by partial oxidation in an autothermal packed bed reactor over catalysts. Biomass is an acidic flammable liquid containing more than 300 compounds. Industrial biomass is not compatible with existing liquid transportation fuels, including gasoline and diesel. In order to use biomass as a conventional liquid transport fuel, it must be catalytically modernized.
Economic assessment of the need for processing of raw materials of animal origin
Authors: Popov V P , Dudorov V E , Sidorenko G A , Akhmadiyeva Z R , Tsyrkaeva E A , Sagitov R F 
Published: July 2019

Abstract
The search for new effective methods of processing of secondary raw materials in the food industry is a very urgent problem. The biological waste of the food and processing industry is considered to include veterinary confiscates, nonfood waste and little value food products, waste products of food, technical and special products, the corpses of livestock and poultry. This waste has been and remains a valuable secondary raw material. The reasons are our Russian mentality, which allows us to neglect the environment, certain economic reasons and the inefficiency of the supervisory bodies. In Soviet times, large processing plants had workshops for production of feed, fish, feather, horn and hoof and other flour. Waste of smaller enterprises was brought to special plants, where they were either burned or used for production of the same flour. Most of these plants had not been working for a long time, and the rest ones did not cope with the supplied volume of waste. The other side of the problem is that both these plants and the vast majority of enterprises that have their own production of feed and other animal flour use obsolete old technologies and old equipment. The result is a product with low consumer qualities. The variety of nonfood waste of the food industry and the diversity of their application imply the use of different technologies of utilization. And the more advanced these technologies, the higher the profitability of processing and the quality of the products.
Congruence Between 1994 WHO Classification of Endometrial Hyperplasia and Endometrial Intraepithelial Neoplasia System
Authors: Travaglino Antonio , Raffone Antonio , Saccone Gabriele , Mascolo Massimo , Guida Maurizio , Mollo Antonio , Insabato Luigi , Zullo Fulvio 
Published: July 2019

AbstractObjectivesTo assess congruence between World Health Organization (WHO) 1994 and endometrial intraepithelial neoplasia (EIN) classification systems of endometrial hyperplasia.MethodsSystematic review and meta-analysis were performed by searching electronic databases for studies that classified endometrial hyperplasia according to both WHO 1994 and EIN systems. Congruence was based on the rate of specimens classified as EIN in WHO categories, which should be virtually 0.000 in nonatypical hyperplasia (NAH) and 1.000 in atypical hyperplasia (AH). Subgroup analyses were performed based on architecture complexity.ResultsEight studies with 1,352 hyperplasias were included. Congruence with EIN criteria was fair in NAH (0.241) and moderate in AH (0.815). Subgroup analyses of NAH showed high congruence in simple NAH (0.065), null in complex NAH (0.517), null in simple AH (0.148), and high in complex AH (0.901).ConclusionsWHO 1994 system is not congruent with the EIN system and cannot be directly translated into a dual classification.
Quantile regression for challenging cases of eQTL mapping
Authors: Sun Bo , Chen Liang 
Published: July 2019

AbstractMapping of expression quantitative trait loci (eQTLs) facilitates interpretation of the regulatory path from genetic variants to their associated disease or traits. High-throughput sequencing of RNA (RNA-seq) has expedited the exploration of these regulatory variants. However, eQTL mapping is usually confronted with the analysis challenges caused by overdispersion and excessive dropouts in RNA-seq. The heavy-tailed distribution of gene expression violates the assumption of Gaussian distributed errors in linear regression for eQTL detection, which results in increased Type I or Type II errors. Applying rank-based inverse normal transformation (INT) can make the expression values more normally distributed. However, INT causes information loss and leads to uninterpretable effect size estimation. After comprehensive examination of the impact from overdispersion and excessive dropouts, we propose to apply a robust model, quantile regression, to map eQTLs for genes with high degree of overdispersion or large number of dropouts. Simulation studies show that quantile regression has the desired robustness to outliers and dropouts, and it significantly improves eQTL mapping. From a real data analysis, the most significant eQTL discoveries differ between quantile regression and the conventional linear model. Such discrepancy becomes more prominent when the dropout effect or the overdispersion effect is large. All the results suggest that quantile regression provides more reliable and accurate eQTL mapping than conventional linear models. It deserves more attention for the large-scale eQTL mapping.
Cooler: scalable storage for Hi-C data and other genomically labeled arrays
Authors: Abdennur Nezar , Mirny Leonid A 
Published: July 2019

Abstract

Motivation
Most existing coverage-based (epi)genomic datasets are one-dimensional, but newer technologies probing interactions (physical, genetic, etc.) produce quantitative maps with two-dimensional genomic coordinate systems. Storage and computational costs mount sharply with data resolution when such maps are stored in dense form. Hence, there is a pressing need to develop data storage strategies that handle the full range of useful resolutions in multidimensional genomic datasets by taking advantage of their sparse nature, while supporting efficient compression and providing fast random access to facilitate development of scalable algorithms for data analysis.

Results
We developed a file format called cooler, based on a sparse data model, that can support genomically labeled matrices at any resolution. It has the flexibility to accommodate various descriptions of the data axes (genomic coordinates, tracks and bin annotations), resolutions, data density patterns and metadata. Cooler is based on HDF5 and is supported by a Python library and command line suite to create, read, inspect and manipulate cooler data collections. The format has been adopted as a standard by the NIH 4D Nucleome Consortium.

Availability and implementation
Cooler is cross-platform, BSD-licensed and can be installed from the Python package index or the bioconda repository. The source code is maintained on Github at https://github.com/mirnylab/cooler.

Supplementary information
Supplementary data are available at Bioinformatics online.
MEpurity: estimating tumor purity using DNA methylation data
Authors: Liu Bowen , Yang Xiaofei , Wang Tingjie , Lin Jiadong , Kang Yongyong , Jia Peng , Ye Kai 
Published: July 2019

Abstract

Motivation
Tumor purity is a fundamental property of each cancer sample and affects downstream investigations. Current tumor purity estimation methods either require matched normal sample or report moderately high tumor purity even on normal samples. It is critical to develop a novel computational approach to estimate tumor purity with sufficient precision based on tumor-only sample.

Results
In this study, we developed MEpurity, a beta mixture model-based algorithm, to estimate the tumor purity based on tumor-only Illumina Infinium 450k methylation microarray data. We applied MEpurity to both The Cancer Genome Atlas (TCGA) cancer data and cancer cell line data, demonstrating that MEpurity reports low tumor purity on normal samples and comparable results on tumor samples with other state-of-art methods.

Availability and implementation
MEpurity is a C++ program which is available at https://github.com/xjtu-omics/MEpurity.

Supplementary information
Supplementary data are available at Bioinformatics online.
A 50-bp enhancer of the mouse acrosomal vesicle protein 1 gene activates round spermatid-specific transcription in vivo†
Authors: Urekar Craig , Acharya Kshitish K , Chhabra Preeti , Reddi Prabhakara P 
Published: July 2019

AbstractEnhancers are cis-elements that activate transcription and play critical roles in tissue- and cell type-specific gene expression. During spermatogenesis, genes coding for specialized sperm structures are expressed in a developmental stage- and cell type-specific manner, but the enhancers responsible for their expression have not been identified. Using the mouse acrosomal vesicle protein (Acrv1) gene that codes for the acrosomal protein SP-10 as a model, our previous studies have shown that Acrv1 proximal promoter activates transcription in spermatids; and the goal of the present study was to separate the enhancer responsible. Transgenic mice showed that three copies of the −186/−135 fragment (50 bp enhancer) placed upstream of the Acrv1 core promoter (−91/+28) activated reporter expression in testis but not somatic tissues (n = 4). Immunohistochemistry showed that enhancer activity was restricted to the round spermatids. The Acrv1 enhancer failed to activate transcription in the context of a heterologous core promoter (n = 4), indicating a likely requirement for enhancer-core promoter compatibility. Chromatin accessibility assays showed that the Acrv1 enhancer assumes a nucleosome-free state in male germ cells (but not liver), indicating occupancy by transcription factors. Southwestern assays (SWA) identified specific binding of the enhancer to a testis nuclear protein of 47 kDa (TNP47). TNP47 was predominantly nuclear and becomes abundant during the haploid phase of spermatogenesis. Two-dimensional SWA revealed the isoelectric point of TNP47 to be 5.2. Taken together, this study delineated a 50-bp enhancer of the Acrv1 gene for round spermatid-specific transcription and identified a putative cognate factor. The 50-bp enhancer could become useful for delivery of proteins into spermatids.
Follicle-stimulating hormone administration affects amino acid metabolism in mammalian oocytes†
Authors: Tetkova Anna , Susor Andrej , Kubelka Michal , Nemcova Lucie , Jansova Denisa , Dvoran Michal , Del Llano Edgar , Holubcova Zuzana , Kalous Jaroslav 
Published: July 2019

AbstractCulture media used in assisted reproduction are commonly supplemented with gonadotropin hormones to support the nuclear and cytoplasmic maturation of in vitro matured oocytes. However, the effect of gonadotropins on protein synthesis in oocytes is yet to be fully understood. As published data have previously documented a positive in vitro effect of follicle-stimulating hormone (FSH) on cytoplasmic maturation, we exposed mouse denuded oocytes to FSH in order to evaluate the changes in global protein synthesis. We found that dose-dependent administration of FSH resulted in a decrease of methionine incorporation into de novo synthesized proteins in denuded mouse oocytes and oocytes cultured in cumulus-oocyte complexes. Similarly, FSH influenced methionine incorporation in additional mammalian species including human. Furthermore, we showed the expression of FSH-receptor protein in oocytes. We found that major translational regulators were not affected by FSH treatment; however, the amino acid uptake became impaired. We propose that the effect of FSH treatment on amino acid uptake is influenced by FSH receptor with the effect on oocyte metabolism and physiology.
Shift in flowering time allows diploid and autotetraploid Anacamptis pyramidalis (Orchidaceae) to coexist by reducing competition for pollinators
Authors: Pegoraro Luca , De Vos Jurriaan M , Cozzolino Salvatore , Scopece Giovanni 
Published: July 2019

AbstractHow autopolyploids establish when competing with diploid progenitors is still poorly understood. Here, we investigate the effects of morphological and phenological divergence on the reproductive success of co-occurring diploid and autotetraploid individuals of Anacamptis pyramidalis to disentangle the mechanisms allowing their c-oexistence. We estimated reproductive success in terms of absolute and relative fruit production and recorded morphological and phenological traits of the two cytotypes. We also estimated correlations between traits within cytotypes and the related phenotypic selection patterns. The two cytotypes experience similar levels of reproductive success, but they differ significantly in their morphological and phenological traits. Correlations among floral traits were weaker in autotetraploids than in diploids, but among-individuals variation was higher in diploids. For most flower traits, the strength of phenotypic selection was different in the two cytotypes. We found selection on flower number in both cytotypes, whereas selection for earlier flowering time was only found in late-flowering diploids. Our results suggest that a shift in flowering time may have allowed diploid and autotetraploid A. pyramidalis individuals to reduce competition for naïve pollinators. Consequently, the two cytotypes can coexist by attaining similar levels of reproductive success and, at same time, reducing the likelihood of inter-cytotype mating.
Home run—results of a chronic kidney disease Telemedicine Patient Education Study
Authors: Easom Andrea M , Shukla Ashutosh M , Rotaru Dumitru , Ounpraseuth Songthip , Shah Sudhir V , Arthur John M , Singh Manisha 
Published: July 2019

Abstract

Background
Chronic kidney disease (CKD) incidence is increasing and associated mortality and morbidity are high. Educating patients is effective in delaying progression and establishing optimal renal replacement therapy (RRT). Tele-education/telemedicine (TM) can be an effective tool to provide such education, but there are no available data quantifying its effectiveness. We attempted to establish such evidence correlating the effect of education in patient choices and with the start of actual RRT. We present results from a 3-year pilot study evaluating the effectiveness of comprehensive predialysis education (CPE) through TM for CKD patients compared with a standard care group [face to face (FTF)]. The patient’s ability to choose RRT was the primary endpoint.

Methods
This was a randomized controlled study providing CPE over three classes at nine sites (one FTF and eight TM). Three assessment tools were utilized to compare groups: CKD knowledge, literacy and quality of life.

Results
A total of 47.1% of FTF and 52.2% of TM patients reported not having enough information to choose a modality. This decreased by the third visit (FTF 7.4%, TM 13.2%). Home modality choices more than doubled in both groups (FTF 25.8–67.7%, TM 22.2–50.1%). In patients that completed one visit and needed to start RRT, 47% started on a home modality or received a pre-emptive transplant (home hemodialysis 6%, peritoneal dialysis 38%, transplant 3%).

Conclusions
Results show almost 90% (TM 87%, FTF 95%) of the attendees could choose a modality after education. Home modality choices doubled. Patients were able to make an informed choice regardless of the modality of education.
Indian Interpreters in the Making of Colonial Historiography: New Light on Mark Wilks’s Historical Sketches of the South of India (1810–1817)
Authors: Ng Su Fang 
Published: July 2019

Abstract
A forgotten archive at Oxford, the working library of Mark Wilks (1759–1831), sometime Resident of Madras who wrote the influential Historical Sketches of the South of India (1810), offers evidence of Anglo-Indian collaboration in the early colonial period following the 1799 defeat of Tipu Sultan. Examining new manuscript evidence, this article shows how Wilks, a friend of Colin Mackenzie, the surveyor of Mysore, used texts from the vast Mackenzie Collection to compose his history, abstracting selected translations for his own library. Wilks had the help of Mackenzie’s assistants, in particular Kavali Venkata Lakshmayya. Lakshmayya (and others) provided Wilks with translations of land grants and genealogical narratives, both of which were used to establish historical chronology. Because the British saw themselves as restorers of ancient Indian practices, chronology was as important for public policy as for historiography. Working with Wilks, Lakshmayya compiled a large manuscript folio that was at once a table to convert dates among western, Islamic, and Indian calendars, and a historical abstract giving a timeline of key events. This and other manuscripts show Wilks’s use of the Mackenzie Collection beyond only inscriptions. Historical chronology was established through a mix of sources: inscriptions, narrative accounts, and published works. Moreover, Wilks incorporated narratives written by native interpreters into Historical Sketches. Indian history was the result of Anglo-Indian collaboration. Native interpreters contributed significant intellectual labour, and their historiographical work laid the foundation for the writing of the early history of South India.
Impact of pulmonary function on pulmonary complications after robotic-assisted thoracoscopic lobectomy
Authors: Cao Christopher , Louie Brian E , Melfi Franca , Veronesi Giulia , Razzak Rene , Romano Gaetano , Novellis Pierluigi , Ranganath Neel K , Park Bernard J 
Published: July 2019

Abstract

OBJECTIVES
Percentage-predicted forced expiratory volume in 1 s (FEV1) and diffusing capacity for carbon monoxide (DLCO), and their predicted postoperative (ppo) values are established prognostic factors for postoperative pulmonary complications after thoracotomy. However, their predictive value for minimally invasive pulmonary resections remains controversial. This study assessed the incidence of pulmonary complications after robotic lobectomy for primary lung cancer and analysed the predictive significance of FEV1 and DLCO.

METHODS
This was a retrospective analysis of patients who underwent robotic lobectomy from 4 institutions. Descriptive and comparative analyses were performed for patients who experienced pulmonary complications versus patients who did not, in relation to FEV1 and DLCO values. To identify thresholds for increased complications, patients were categorized into groups of 10% incremental increases in FEV1 and DLCO, and their ppo values.

RESULTS
From November 2002 to April 2018, 1088 patients underwent robotic lobectomy. Overall, 169 postoperative pulmonary complications occurred in 141 patients. Male gender and Eastern Cooperative Oncology Group grade ≥1 were associated with increased pulmonary complications on univariable analysis. Patients who experienced pulmonary complications had increased mortality (2.1% vs 0.2%, P = 0.017) and longer hospitalizations (9 vs 4 days, P &lt; 0.001). Pulmonary complications were associated when FEV1 ≤60% and DLCO ≤50%, and when ppo FEV1 or DLCO was ≤50%; ppo FEV1 ≤50% (P &lt; 0.001) and ppo DLCO ≤50% (P = 0.031) remained statistically significant on multivariable analysis.

CONCLUSIONS
Both FEV1 and DLCO were shown to be significant predictors of pulmonary complications. Furthermore, thresholds of percentage-predicted and ppo FEV1 and DLCO values were identified, below which pulmonary complications occurred significantly more frequently, suggesting their predictive values are particularly useful in patients with poorer pulmonary function.
Annuloplasty ring dehiscence after mitral valve repair: incidence, localization and reoperation
Authors: Noack Thilo , Kiefer Philipp , Vivell Nina , Sieg Franz , Marin-Cuartas Mateo , Leontyev Sergey , Holzhey David Michael , Garbade Jens , Pfannmueller Bettina , Davierwala Piroze , Misfeld Martin , Seeburger Joerg , Borger Michael Andrew 
Published: July 2019

Abstract

OBJECTIVES
Mitral valve (MV) annuloplasty ring dehiscence with subsequent recurrent mitral regurgitation represents an unusual but challenging clinical problem. Incidence, localization and outcomes for this complication have not been well defined.

METHODS
From 1996 to 2016, a total of 3478 patients underwent isolated MV repair with ring annuloplasty at the Leipzig Heart Centre. Of these patients, 57 (1.6%) underwent reoperation due to annuloplasty ring dehiscence. Echocardiographic data, operative and early postoperative characteristics as well as short- and long-term survival rates after MV reoperation were analysed.

RESULTS
Occurrences of ring dehiscence were acute (<30 days), early (≤1 year) and late (>1 year) in 44%, 33% and 23% of patients, respectively. Localization of annuloplasty ring dehiscence was found most frequently in the P3 segment (68%), followed by the P2 (51%) and the P1 segments (47%). The 30-day mortality rate and 1- and 5-year survival rates after MV reoperation were 2%, 89% and 74%, respectively. During reoperation, MV replacement was performed in 38 (67%) and MV re-repair in 19 (33%) patients.

CONCLUSIONS
Annuloplasty ring dehiscence is clinically less common, localized more frequently on the posterior annulus and occurs mostly acutely or early after MV repair. MV reoperation can be performed safely in such patients.
Periodontal effects and survival rates of different mandibular retainers: comparison of bonding technique and wire thickness
Authors: Gökçe Begüm , Kaya Burçak 
Published: July 2019

SummaryObjectivesThis non-randomized prospective cohort study aimed to compare the periodontal effects and success rates of mandibular canine-to-canine fixed retainers having different bonding techniques and wire thicknesses.Materials and methodsHundred patients requiring retention after orthodontic treatment were assigned to five study groups (n = 20 in each group, 61 females/39 males, median age range 16.5–18.0 years). Retention was provided by 0.0215”/direct, 0.0215”/indirect, 0.0175”/direct, 0.0175”/indirect bonded multistranded wires and removable Essix appliances. The primary and secondary outcomes were periodontal effects and success rates. The patients were examined in 1 week, 1 month, 3 months and 6 months follow-up appointments. Plaque index, gingival index, probing depth, marginal recession, bleeding on probing, failure rate per retainer wire and survival of retainer wires were analysed by Kruskal–Wallis H, Mann–Whitney U and chi-square tests.ResultsSignificant differences were observed between the fixed retainer (FR) and Essix (E) groups in gingival index scores at 1 month [mean FR: 1.13 (95% confidence interval (CI): 0.81–1.44), mean E: 0.40 (95% CI: 0.14–0.69), mean difference: 0.73, P < 0.01], 3 months [mean FR: 0.97/1.01 (95% CI: 0.65–1.30/0.72–1.30), mean E: 0.52 (95% CI: 0.25–0.82), mean differences: 0.45/0.49, P < 0.05], 6 months [mean FR: 0.94 (95% CI: 0.62–1.27), mean E: 0.35 (95% CI: 0.15–0.58), mean difference: 0.59, P < 0.05] and in bleeding on probing scores at 1 month [mean FR: 3.05 (95% CI: 2.12–3.98), mean E: 1.15 (95% CI: 0.42–1.88), mean difference: 1.90, P < 0.01]. The survival rates of retainer wires were 85 per cent for the 0.0215” direct/indirect and 90 per cent for the 0.0175” direct/indirect groups for the 6 months follow-up.LimitationsSix months follow-up period, which demonstrates only short-term outcomes.ConclusionsThe periodontal outcomes or survival rates of mandibular fixed retainers were not affected by bonding technique or wire thickness, whereas gingival health improved with Essix retainers but not with fixed retainers.