bluuebunny/crossref_metadata_2025_split huggingface dataset:
Justification of the Need and Feasibility of Switching to Renewable Energy Sources for the Implementation of Sustainable Development Principles
Authors: Tyaglov S , Sheveleva A , Guseva T 
Published: August 2019

Abstract
Reduction of the negative impact on the environment, improvement of the energy efficiency, optimization in the structure of the global energy balance and ensuring innovative energy development are important tasks in achieving sustainable development. The aim of this article is to justify the need for the development and feasibility of switching to renewable energy sources (RES) in order to solve the abovementioned issues. In this regard, it is necessary to study the prerequisites for intensifying the process of transition from traditional energy sources made up of renewable ones, analyze their current state and prospects for further development. In addition, it is necessary to identify the necessary measures to stimulate the transition from traditional energy sources to RES. Eventually, the expected results of transition to RES are identified and allow proving the economic, social and environmental efficiency of their use.
PTRF/CAVIN1, regulated by SHC1 through the EGFR pathway, is found in urine exosomes as a potential biomarker of ccRCC
Authors: Zhao Yubo , Wang Yunfei , Zhao Enyang , Tan Yanli , Geng Bo , Kang Chunsheng , Li Xuedong 
Published: August 2019

Abstract
Polymerase I and transcript release factor (PTRF)/Cavin1 regulates RNA polymerase I during transcription and plays a critical role in endocytosis. Abnormal expressions of PTRF were detected in multiple cancers according to increasing research. PTRF has been showed to involve in the formation and secretion of exosomes and can be detected in the exosomes, which suggests that PTRF would be a potential biomarker for diagnosis of clear cell renal cell carcinoma (ccRCC) using urine samples. Approximately 50–90% of ccRCC cases suffered abnormal epidermal growth factor receptor (EGFR), which activates a variety of signaling pathways, including the mitogen-activated protein kinase/extracellular signal-regulated kinase and Phosphoinositide 3-Kinase/Akt pathway. According to bioinformatic analysis of gene expression arrays of kidney clear cell carcinoma from The Cancer Genome Atlas, we found SHC1 was significantly overexpressed in high-grade ccRCC and correlated to poor prognosis, and also SHC1 was annotated in extracellular matrix process, which was regulated by EGFR. Further studies showed that the expression of PTRF was regulated by SHC1 through EGFR-Phosphoinositide 3-Kinase/Akt pathway. PTRF was detected in the exosomes isolated from ccRCC patients' urine and ccRCC cancer cells culture medium. It suggested that the abnormal SHC1-increased PTRF, which is detected in exosomes from urine, would be a potential marker for ccRCC diagnose and treatment.
The Flexible Loop is a New Sweetness Determinant Site of the Sweet-Tasting Protein: Characterization of Novel Sweeter Mutants of the Single-Chain Monellin (MNEI)
Authors: Yang Liu , Zhu Kongkai , Yu Haifeng , Zhang Xinlei , Liu Bo 
Published: August 2019

AbstractThe single-chain monellin (MNEI) displays same sweet potency as the natural monellin protein. To identify critical residues determining its sweetness, residues located at the loops region were selected for mutagenesis analysis. Mutations of positive-charge residues R31, R53, and R82 consistently led to obvious decrease of sweetness, whereas mutations of negative-charge residues resulted in variable sweet potency. Of note, the E50N mutant in the loop region linking the 2 natural chains showed significantly increased sweetness. Mutations of this residue to M or K led to similar effects, in accordance with the so-called wedge model for explanation of the sweet protein–receptor interaction. Homology modeling was carried out with the firstly reported crystal structure of sweet taste receptor (from medaka fish) as the template, and molecular docking and dynamics simulations suggested that flexible conformations of specific residues located in the loops region play essential roles for the interaction with the receptor and the sweetness of the protein. Moreover, obvious additive effects were found for the sweetness as 2 double-site mutants (E50N/Y65R and E2N/E50N) displayed increased sweetness than their single-site mutants. Our results revealed the flexible loop L23 linking the 2 natural chains as a novel sweetness determinant site of the sweet protein monellin and raised a series of new sweeter mutants, which could provide helpful guidance for molecular designing the sweet-tasting proteins.
Neurosyphilis Treatment Outcomes After Intravenous Penicillin G Versus Intramuscular Procaine Penicillin Plus Oral Probenecid
Authors: Dunaway Shelia B , Maxwell Clare L , Tantalo Lauren C , Sahi Sharon K , Marra Christina M 
Published: August 2019

AbstractBackgroundData comparing neurosyphilis treatment regimens are limited.MethodsParticipants were enrolled in a study of cerebrospinal fluid (CSF) abnormalities in syphilis that was conducted at the University of Washington between April 2003 to May 2014. They were diagnosed with syphilis and referred by their providers due to concerns for neurosyphilis. We evaluated 150 people with CSF abnormalities who were treated with either intravenous aqueous penicillin G (PenG) or intramuscular aqueous procaine penicillin G plus oral probenecid (APPG-P). An abnormal CSF diagnosis was defined as a white blood cell (WBC) count &gt;20/µL, a CSF protein reading &gt;50 mg/dL, or a reactive CSF–Venereal Disease Research Laboratory test (VDRL). Hazard ratios for normalization of CSF or serum measures were determined using Cox regression.ResultsIn individuals treated with either PenG or APPG-P, CSF WBCs and CSF-VDRL reactivity normalized within 12 months after treatment, while protein normalized more slowly and less completely. There was no relationship between treatment regimen or human immunodeficiency virus (HIV) status and likelihood of normalization of any measure. Among those living with HIV, CSF WBC counts and CSF-VDRL reactivity were more likely to normalize in those treated with antiretrovirals. Unexpectedly, CSF WBCs were more likely to normalize in those with low CD4+ T cell counts. When neurosyphilis was more stringently defined as a reactive CSF-VDRL, the relationship with the CD4+ T cell count remained unchanged.ConclusionsIn the current antiretroviral treatment era, neurosyphilis treatment outcomes are not different for PenG and APPG-P, regardless of HIV status. The relationship between the normalization of CSF WBC counts and CD4+ T cell counts may indicate continued imprecision in neurosyphilis diagnostic criteria, due to HIV-related CSF pleocytosis.
An Informational Theory of Privacy
Authors: Jann Ole , Schottmüller Christoph 
Published: August 2019

Abstract
Privacy of consumers or citizens is often seen as an inefficient information asymmetry. We challenge this view by showing that privacy can increase welfare in an informational sense. It can also improve information aggregation and prevent inefficient statistical discrimination. We show how and when the different informational effects of privacy line up to make privacy efficient or even Pareto-optimal. Our theory can be applied to decide who should have which information and how privacy and information disclosure should be regulated. We discuss applications to online privacy, credit decisions and transparency in government.
Machine learning of clinical variables and coronary artery calcium scoring for the prediction of obstructive coronary artery disease on coronary computed tomography angiography: analysis from the CONFIRM registry
Authors: Al’Aref Subhi J , Maliakal Gabriel , Singh Gurpreet , van Rosendael Alexander R , Ma Xiaoyue , Xu Zhuoran , Alawamlh Omar Al Hussein , Lee Benjamin , Pandey Mohit , Achenbach Stephan , Al-Mallah Mouaz H , Andreini Daniele , Bax Jeroen J , Berman Daniel S , Budoff Matthew J , Cademartiri Filippo , Callister Tracy Q , Chang Hyuk-Jae , Chinnaiyan Kavitha , Chow Benjamin J W , Cury Ricardo C , DeLago Augustin , Feuchtner Gudrun , Hadamitzky Martin , Hausleiter Joerg , Kaufmann Philipp A , Kim Yong-Jin , Leipsic Jonathon A , Maffei Erica , Marques Hugo , Gonçalves Pedro de Araújo , Pontone Gianluca , Raff Gilbert L , Rubinshtein Ronen , Villines Todd C , Gransar Heidi , Lu Yao , Jones Erica C , Peña Jessica M , Lin Fay Y , Min James K , Shaw Leslee J 
Published: August 2019

Abstract

Aims
Symptom-based pretest probability scores that estimate the likelihood of obstructive coronary artery disease (CAD) in stable chest pain have moderate accuracy. We sought to develop a machine learning (ML) model, utilizing clinical factors and the coronary artery calcium score (CACS), to predict the presence of obstructive CAD on coronary computed tomography angiography (CCTA).

Methods and results
The study screened 35 281 participants enrolled in the CONFIRM registry, who underwent ≥64 detector row CCTA evaluation because of either suspected or previously established CAD. A boosted ensemble algorithm (XGBoost) was used, with data split into a training set (80%) on which 10-fold cross-validation was done and a test set (20%). Performance was assessed of the (1) ML model (using 25 clinical and demographic features), (2) ML + CACS, (3) CAD consortium clinical score, (4) CAD consortium clinical score + CACS, and (5) updated Diamond-Forrester (UDF) score. The study population comprised of 13 054 patients, of whom 2380 (18.2%) had obstructive CAD (≥50% stenosis). Machine learning with CACS produced the best performance [area under the curve (AUC) of 0.881] compared with ML alone (AUC of 0.773), CAD consortium clinical score (AUC of 0.734), and with CACS (AUC of 0.866) and UDF (AUC of 0.682), P &lt; 0.05 for all comparisons. CACS, age, and gender were the highest ranking features.

Conclusion
A ML model incorporating clinical features in addition to CACS can accurately estimate the pretest likelihood of obstructive CAD on CCTA. In clinical practice, the utilization of such an approach could improve risk stratification and help guide downstream management.
Comparison of single-nucleotide variants identified by Illumina and Oxford Nanopore technologies in the context of a potential outbreak of Shiga toxin–producing Escherichia coli
Authors: Greig David R , Jenkins Claire , Gharbia Saheer , Dallman Timothy J 
Published: August 2019

Abstract

Background
We aimed to compare Illumina and Oxford Nanopore Technology sequencing data from the 2 isolates of Shiga toxin–producing Escherichia coli (STEC) O157:H7 to determine whether concordant single-nucleotide variants were identified and whether inference of relatedness was consistent with the 2 technologies.

Results
For the Illumina workflow, the time from DNA extraction to availability of results was ~40 hours, whereas with the ONT workflow serotyping and Shiga toxin subtyping variant identification were available within 7 hours. After optimization of the ONT variant filtering, on average 95% of the discrepant positions between the technologies were accounted for by methylated positions found in the described 5-methylcytosine motif sequences, CC(A/T)GG. Of the few discrepant variants (6 and 7 difference for the 2 isolates) identified by the 2 technologies, it is likely that both methodologies contain false calls.

Conclusions
Despite these discrepancies, Illumina and Oxford Nanopore Technology sequences from the same case were placed on the same phylogenetic location against a dense reference database of STEC O157:H7 genomes sequenced using the Illumina workflow. Robust single-nucleotide polymorphism typing using MinION-based variant calling is possible, and we provide evidence that the 2 technologies can be used interchangeably to type STEC O157:H7 in a public health setting.
SNV identification from single-cell RNA sequencing data
Authors: Schnepp Patricia M , Chen Mengjie , Keller Evan T , Zhou Xiang 
Published: August 2019

Abstract
Integrating single-cell RNA sequencing (scRNA-seq) data with genotypes obtained from DNA sequencing studies facilitates the detection of functional genetic variants underlying cell type-specific gene expression variation. Unfortunately, most existing scRNA-seq studies do not come with DNA sequencing data; thus, being able to call single nucleotide variants (SNVs) from scRNA-seq data alone can provide crucial and complementary information, detection of functional SNVs, maximizing the potential of existing scRNA-seq studies. Here, we perform extensive analyses to evaluate the utility of two SNV calling pipelines (GATK and Monovar), originally designed for SNV calling in either bulk or single-cell DNA sequencing data. In both pipelines, we examined various parameter settings to determine the accuracy of the final SNV call set and provide practical recommendations for applied analysts. We found that combining all reads from the single cells and following GATK Best Practices resulted in the highest number of SNVs identified with a high concordance. In individual single cells, Monovar resulted in better quality SNVs even though none of the pipelines analyzed is capable of calling a reasonable number of SNVs with high accuracy. In addition, we found that SNV calling quality varies across different functional genomic regions. Our results open doors for novel ways to leverage the use of scRNA-seq for the future investigation of SNV function.
Surgical treatment of pulmonary oligorecurrence after curative resection for non-small-cell lung cancer
Authors: Han Sung Joon , Cho Sukki , Yum Sungwon , Kim Kwhanmien , Jheon Sanghoon 
Published: August 2019

Abstract

OBJECTIVES
The most appropriate therapeutic strategy for patients with pulmonary oligorecurrence after curative resection of non-small-cell lung cancer (NSCLC) is unclear; therefore, characterizing the results of various treatments for pulmonary oligorecurrence would be valuable. This study compared the prognosis of operative and non-operative treatment for pulmonary oligorecurrence after complete resection of NSCLC.

METHODS
Among 2230 patients from a prospective lung cancer database who underwent surgical resection between 2004 and 2014, 486 patients (22%) experienced recurrence, including 254 with pulmonary recurrence and 102 with pulmonary oligorecurrence (5 or fewer metastatic lesions). Post-recurrence survival (PRS) rates were compared between those who received operative or non-operative treatment, including chemotherapy, radiotherapy, chemoradiotherapy and best supportive care.

RESULTS
Among 102 patients with pulmonary oligorecurrence, 41 patients received operative treatment and 61 received non-operative treatment (34 chemotherapy, 15 radiotherapy, 9 chemoradiotherapy and 3 best supportive care). The patients who received operative treatment were significantly younger at the first operation than those in the non-operative group and had better performance status, lower pathological T stage at the first operation, younger age at recurrence and fewer metastatic lesions. The median PRS was 46.4 months, and the 5-year PRS rates were 67% and 26% in the operative and non-operative groups, respectively. The multivariable analysis revealed that undergoing video-assisted thoracoscopic surgery at the first operation and receiving operative treatment for recurrence were independent prognostic factors for more favourable PRS.

CONCLUSIONS
Operative treatment of pulmonary oligorecurrence after curative resection significantly prolonged the PRS in patients who underwent curative resection for NSCLC.
Precision Medicine and Precision Public Health in the Era of Pathogen Next-Generation Sequencing
Authors: Leguia Mariana , Vila-Sanjurjo Anton , Chain Patrick S G , Berry Irina Maljkovic , Jarman Richard G , Pollett Simon 
Published: August 2019

Abstract
This brief report serves as an introduction to a supplement of the Journal of Infectious Diseases entitled “Next-Generation Sequencing (NGS) Technologies to Advance Global Infectious Disease Research.” We briefly discuss the history of NGS technologies and describe how the techniques developed during the past 40 years have impacted our understanding of infectious diseases. Our focus is on the application of NGS in the context of pathogen genomics. Beyond obvious clinical and public health applications, we also discuss the challenges that still remain within this rapidly evolving field.
Functional Human CD141+ Dendritic Cells in Human Immune System Mice
Authors: Coelho-Dos-Reis Jordana G A , Funakoshi Ryota , Huang Jing , Pereira Felipe Valença , Iketani Sho , Tsuji Moriya 
Published: August 2019

AbstractBackgroundFor the purpose of studying functional human dendritic cells (DCs) in a humanized mouse model that mimics the human immune system (HIS), a model referred to as HIS mice was established.MethodsHuman immune system mice were made by engrafting NOD/SCID/IL2Rgammanull (NSG) mice with human hematopoietic stem cells (HSCs) following the transduction of genes encoding human cytokines and human leukocyte antigen (HLA)-A2.1 by adeno-associated virus serotype 9 (AAV9) vectors.ResultsOur results indicate that human DC subsets, such as CD141+CD11c+ and CD1c+CD11c+ myeloid DCs, distribute throughout several organs in HIS mice including blood, bone marrow, spleen, and draining lymph nodes. The CD141+CD11c+ and CD1c+CD11c+ human DCs isolated from HIS mice immunized with adenoviruses expressing malaria/human immunodeficiency virus (HIV) epitopes were able to induce the proliferation of malaria/HIV epitopes-specific human CD8+ T cells in vitro. Upregulation of CD1c was also observed in human CD141+ DCs 1 day after immunization with the adenovirus-based vaccines.ConclusionsEstablishment of such a humanized mouse model that mounts functional human DCs enables preclinical assessment of the immunogenicity of human vaccines in vivo.
The IARC Monographs: Updated Procedures for Modern and Transparent Evidence Synthesis in Cancer Hazard Identification
Authors: Samet Jonathan M , Chiu Weihsueh A , Cogliano Vincent , Jinot Jennifer , Kriebel David , Lunn Ruth M , Beland Frederick A , Bero Lisa , Browne Patience , Fritschi Lin , Kanno Jun , Lachenmeier Dirk W , Lan Qing , Lasfargues Gérard , Le Curieux Frank , Peters Susan , Shubat Pamela , Sone Hideko , White Mary C , Williamson Jon , Yakubovskaya Marianna , Siemiatycki Jack , White Paul A , Guyton Kathryn Z , Schubauer-Berigan Mary K , Hall Amy L , Grosse Yann , Bouvard Véronique , Benbrahim-Tallaa Lamia , El Ghissassi Fatiha , Lauby-Secretan Béatrice , Armstrong Bruce , Saracci Rodolfo , Zavadil Jiri , Straif Kurt , Wild Christopher P 
Published: August 2019

Abstract
The Monographs produced by the International Agency for Research on Cancer (IARC) apply rigorous procedures for the scientific review and evaluation of carcinogenic hazards by independent experts. The Preamble to the IARC Monographs, which outlines these procedures, was updated in 2019, following recommendations of a 2018 expert advisory group. This article presents the key features of the updated Preamble, a major milestone that will enable IARC to take advantage of recent scientific and procedural advances made during the 12 years since the last Preamble amendments. The updated Preamble formalizes important developments already being pioneered in the Monographs program. These developments were taken forward in a clarified and strengthened process for identifying, reviewing, evaluating, and integrating evidence to identify causes of human cancer. The advancements adopted include the strengthening of systematic review methodologies; greater emphasis on mechanistic evidence, based on key characteristics of carcinogens; greater consideration of quality and informativeness in the critical evaluation of epidemiological studies, including their exposure assessment methods; improved harmonization of evaluation criteria for the different evidence streams; and a single-step process of integrating evidence on cancer in humans, cancer in experimental animals, and mechanisms for reaching overall evaluations. In all, the updated Preamble underpins a stronger and more transparent method for the identification of carcinogenic hazards, the essential first step in cancer prevention.
ERECTA receptor-kinases play a key role in the appropriate timing of seed germination under changing salinity
Authors: Nanda Amrit K , El Habti Abdeljalil , Hocart Charles H , Masle Josette 
Published: August 2019

AbstractAppropriate timing of seed germination is crucial for the survival and propagation of plants, and for crop yield, especially in environments prone to salinity or drought. However, the exact mechanisms by which seeds perceive changes in soil conditions and integrate them to trigger germination remain elusive, especially once the seeds are non-dormant. In this study, we determined that the Arabidopsis ERECTA (ER), ERECTA-LIKE1 (ERL1), and ERECTA-LIKE2 (ERL2) leucine-rich-repeat receptor-like kinases regulate seed germination and its sensitivity to changes in salt and osmotic stress levels. Loss of ER alone, or in combination with ERL1 and/or ERL2, slows down the initiation of germination and its progression to completion, or arrests it altogether under saline conditions, until better conditions return. This function is maternally controlled via the tissues surrounding the embryo, with a primary role being played by the properties of the seed coat and its mucilage. These relate to both seed-coat expansion and subsequent differentiation and to salinity-dependent interactions between the mucilage, subtending seed coat layers and seed interior in the germinating seed. Salt-hypersensitive er105, er105 erl1.2, er105 erl2.1 and triple-mutant seeds also exhibit increased sensitivity to exogenous ABA during germination, and under salinity show an enhanced up-regulation of the germination repressors and inducers of dormancy ABA-insensitive-3, ABA-insensitive-5, DELLA-encoding RGL2, and Delay-Of-Germination-1. These findings reveal a novel role of the ERECTA receptor-kinases in the sensing of conditions at the seed surface and the integration of developmental, dormancy and stress signalling pathways in seeds. They also open novel avenues for the genetic improvement of plant adaptation to changing drought and salinity patterns.
The density distribution of accreting cosmic filaments as shaped by Kelvin–Helmholtz instability
Authors: Vossberg Ann-Christine E , Cantalupo Sebastiano , Pezzulli Gabriele 
Published: August 2019

ABSTRACT
Cosmic filaments play a crucial role in galaxy evolution, transporting gas from the intergalactic medium into galaxies. However, little is known about the efficiency of this process and whether the gas is accreted in a homogenous or clumpy way. Recent observations suggest the presence of broad gas density distributions in the circumgalactic medium, which could be related to the accretion of filaments. By means of two-dimensional high-resolution hydrodynamical simulations, we explore here the evolution of cold accreting filaments flowing through the hot circumgalactic medium (CGM) of high-z galaxies. We focus on the purely adiabatic case, not including cooling, gravity, or magnetic fields. In particular, we examine the non-linear effects of Kelvin–Helmholtz instability on the development of broad gas density distributions and on the formation of cold, dense clumps. We explore a large parameter space in the filament and perturbation properties, such as filament Mach number, initial perturbation wavelength, and thickness of the interface between the filament and the halo. We find that the time-averaged density distribution of the cold gas is qualitatively consistent with a skewed lognormal probability distribution function plus an additional component in the form of a high-density tail for high Mach numbers. Our results suggest a tight correlation between the accreting velocity and the maximum densities developing in the filament, which is consistent with the variance–Mach number relation for turbulence. Therefore, cosmological accretion could be a viable mechanism to produce turbulence and broad gas density distributions within the CGM.