bluuebunny/crossref_metadata_2025_split huggingface dataset:
BAMscale: quantification of next-generation sequencing peaks and generation of scaled coverage tracks
Authors: Pongor Lorinc , Gross Jacob M , Alvarez Roberto Vera , Murai Junko , Jang Sang-Min , Zhang Hongliang , Redon Christophe , Fu Haiqing , Huang Shar-Yin , Thakur Bhushan , Baris Adrian , Marino-Ramirez Leonardo , Landsman David , Aladjem Mirit I , Pommier Yves 
Published: January 2020

Abstract
Background: Next-generation sequencing allows genome-wide analysis of changes in chromatin states and gene expression. Data analysis of these increasingly used methods either requires multiple analysis steps, or extensive computational time. We sought to develop a tool for rapid quantification of sequencing peaks, and an efficient method to produce coverage tracks for accurate visualization that can be intuitively interpreted by experimentalists with minimal bioinformatics background. We demonstrate its strength by integrating data from several types of sequencing approaches. Results: We have developed BAMscale, a one-step tool that processes a wide set of sequencing datasets. To demonstrate the usefulness of BAMscale, we analyzed multiple sequencing datasets from chromatin immunoprecipitation sequencing (ChIP-seq) data, chromatin state change data (Assay for Transposase-Accessible Chromatin using sequencing: ATAC-seq, DNA double strand break mapping sequencing: END-seq), DNA replication data (Okazaki fragments sequencing: OK-seq, Nascent-strand sequencing: NS-seq, single-cell replication timing sequencing: scRepli-seq) and RNA-seq data. The outputs consist of raw and normalized peak scores (multiple normalizations) in text format and scaled bigWig coverage tracks that are directly accessible to data visualization programs. Our tool can effectively analyze large sequencing datasets (~100Gb size) in minutes, outperforming currently available tools.Conclusions: BAMscale is a tool that can be used to accurately quantify and normalize identified peaks directly from BAM files, as well as create coverage tracks for visualization in genome browsers. BAMScale can be implemented for a wide set of methods for calculating coverage tracks such as ChIP-seq / ATAC-seq, as well as splice aware RNA-seq, END-seq and OK-seq for which no dedicated software is available. BAMscale is freely available on github (https://github.com/ncbi/BAMscale).
Porous gold nanoparticles for attenuating infectivity of influenza A virus
Authors: Kim Jinyoung , Yeom Minjoo , Lee Taeksu , Kim Hyun-Ouk , Na Woonsung , Kang Aram , Lim Jong-Woo , Park Geunseon , Park Chaewon , Song Daesub , Haam Seungjoo 
Published: January 2020

Abstract
Background: Influenza viruses (IVs) have become increasingly resistant to antiviral drugs that target neuraminidase and matrix protein 2 due to gene mutations that alter their drug-binding target protein regions. Consequently, almost all recent IV pandemics have exhibited resistance to commercial antiviral vaccines. To overcome this challenge, an antiviral target is needed that is effective regardless of genetic mutations.Main body: In particular, hemagglutinin (HA), a highly conserved surface protein across many IV strains, could be an effective antiviral target as it mediates binding of IVs with host cell receptors, which is crucial for membrane fusion. HA has 6 disulfide bonds that can easily bind with the surfaces of gold nanoparticles. Herein, we fabricated porous gold nanoparticles (PoGNPs) via a surfactant-free emulsion method that exhibited strong affinity for disulfide bonds due to gold-thiol interactions, and provided extensive surface area for these interactions. A remarkable decrease in viral infectivity was demonstrated by increased cell viability results after exposing MDCK cells to various IV strains (H1N1, H3N2, and H9N2) treated with PoGNP. Most of all, the viability of MDCK cells infected with all IV strains increased to 96.8% after PoGNP treatment of the viruses compared to 33.9% cell viability with non-treated viruses. Intracellular viral RNA quantification by real-time RT-PCR also confirmed that PoGNP successfully inhibited viral membrane fusion by blocking the viral entry process through conformational deformation of HA. Conclusion: We believe that the technique described herein can be further developed for PoGNP-utilized antiviral protection as well as metal nanoparticle-based therapy to treat viral infection. Additionally, facile detection of IAV can be achieved by developing PoGNP as a multiplatform for detection of the virus.KEYWORDS: Virus inactivation, Influenza A virus, Porous gold nanoparticle, Membrane fusion, disulfide bond
WITHDRAWN: High Failure Rate after Beta-tricalcium Phosphate Grafting for the Treatment of Femoral Head Osteonecrosis: a Retrospective Analysis
Authors: Liu Pei , Mu Xiao-hong , Yu Hua-chen , Jian-lei Guan , Liu Zhao-hui , Wang Wei-guo , Zhang Qi-dong , Guo Wanshou 
Published: January 2020

Abstract

Background: Non-vascularized bone grafting is a promising head-preserving technique for younger patients diagnosed as non-traumatic osteonecrosis of the femoral head (NONFH). Among the various types of bone grafting techniques, “light-bulb” procedure grafting with synthetic bone substitute is an attractive option. We aimed to assess the effectiveness of using beta-tricalcium phosphate (β-TCP) for the treatment of pre-collapse and early post-collapse lesions NONFH. Methods: From April 2010 to June 2014, 33 patients (47 hips) with NONFH were treated using the afore-mentioned technique. The clinical and radiological outcomes were compared between pre- and post-operation. Harris hip score (HHS) was used to evaluate the clinical results, and Association Research Circulation Osseous (ARCO) stage was applied to assess the radiological outcomes. Results: After 5 years’ follow-up, the failure rate of using β-TCP grafting was accounting for 74.5%. 2 hips collapsed more than 2 mm were awaiting for THA, and 33 of the 47 hips had converted to THAs in an average time to failure of 24.1±14.6 months postoperatively. Meanwhile, only 4 hips survived without collapse, and 8 hips collapsed less than 2 mm. After surgery, the time onset of head collapse was 3.6±1.4 months on average, and the first conversion to THA was performed at 5 months postoperative. Conclusions: Our results suggest that “light-bulb” procedure grafting with β-TCP sticks presented with a high failure rate in the early postoperative period. It is not proposed for the treatment of pre-collapse and early post-collapse lesions NONFH.
Granular computing–neural network model for prediction of longitudinal dispersion coefficients in rivers
Authors: Ghiasi Behzad , Sheikhian Hossein , Zeynolabedin Amin , Niksokhan Mohammad Hossein 
Published: January 2020

Abstract
Successful application of one-dimensional advection–dispersion models in rivers depends on the accuracy of the longitudinal dispersion coefﬁcient (LDC). In this regards, this study aims to introduce an appropriate approach to estimate LDC in natural rivers that is based on a hybrid method of granular computing (GRC) and an artificial neural network (ANN) model (GRC-ANN). Also, adaptive neuro-fuzzy inference system (ANFIS) and ANN models were developed to investigate the accuracy of three credible artificial intelligence (AI) models and the performance of these models in different LDC values. By comparing with empirical models developed in other studies, the results revealed the superior performance of GRC-ANN for LDC estimation. The sensitivity analysis of the three intelligent models developed in this study was done to determine the sensitivity of each model to its input parameters, especially the most important ones. The sensitivity analysis results showed that the W/H parameter (W: channel width; H: flow depth) has the most significant impact on the output of all three models in this research.
Research on the coagulant aid effects of modified diatomite on coal microbial flocculation
Authors: Jingshen Dong , Quanjun Liu 
Published: January 2020

Abstract
Diatomite was modified by chitosan to prepare modified diatomite, and the modified diatomite in an optimized ratio was utilized in coal bio-flocculation. The interaction behavior and flocculation mechanism of modified diatomite on coal slurry water were investigated by single factor experiments, infrared spectroscopy, Brunauer-Emmett-Teller (BET) measurements, and zeta potential measurements. The single factor experiments showed that when the amount of microbial flocculant added was 1.5 ml, the temperature of coal slurry water was 39 °C, the pH was 5, and the amount of modified diatomite was 0.2 g, after 30 min of sedimentation, the flocculation transmittance of the coal slurry water reached 84.3%. The infrared spectra showed that the -NH2 and -OH of the chitosan molecule had a polar interaction with the Si-OH bond in diatomite. The BET measurements showed that the specific surface area of diatomite was not a decisive factor affecting the flocculation effect. Zeta potential measurements indicated that the amino protonation of chitosan increased the isoelectric point (IEP) of modified diatomite. These results showed that modified diatomite has a good effect on coal bio-flocculation.
Aptamers Which Target Proteins: What Proteotronics Suggests to Pharmaceutics
Authors: Cataldo Rosella , De Nunzio Giorgio , Millithaler Jean-Francois , Alfinito Eleonora 
Published: January 2020

Aptamers represent a challenging field of research, relevant for diagnosis in macular degeneration, cancer, thrombosis and many inflammatory diseases, and promising in drug discovery and development. Their selection is currently performed by a stable in vitro technology, namely, SELEX. Furthermore, computationalstatistical tools have been developed to complement the SELEX selection; they work both in the preliminary stage of selection, by designing high affinity aptamers for the assigned target, and also in the final stage, analyzing the features of the best performers to implement the selection technique further. A massive use of the in silico approach is, at present, only restricted by the limited knowledge of the specific aptamer-target topology. Actually, only about fifty X-ray structures of aptamer-protein complexes have been experimentally resolved, highlighting how this knowledge has to be improved. The structure of biomolecules like aptamer-protein complexes can be represented by networks, from which several parameters can be extracted. This work briefly reviews the literature, discussing if and how general network parameters in the framework of Proteotronics and graph theory (such as electrical features, link number, free energy change, and assortativity), are important in characterizing the complexes, anticipating some features of the biomolecules.To better explain this topic, a case-study is proposed, constituted by a set of anti-angiopoietin (Ang2) aptamers, whose performances are known from the experiments, and for which two different types of conformers were predicted. A topological indicator is proposed, named Möbius (M), which combines local and global information, and seems able to discriminate between the two possible types of conformers, so that it can be considered as a useful complement to the in vitro screening for pharmaceutical aims.
Pathophysiological Features of Obesity and its Impact on Cognition: Exercise Training as a Non-Pharmacological Approach
Authors: Inoue Daniela S. , Antunes Bárbara M. , Maideen Mohammad F.B. , Lira Fábio S. 
Published: January 2020

Background:
The number of individuals with obesity is growing worldwide and this is a worrying
trend, as obesity has shown to cause pathophysiological changes, which result in the emergence of comorbidities
such as cardiovascular disease, diabetes mellitus type 2 and cancer. In addition, cognitive performance may be
compromised by immunometabolic deregulation of obesity. Although in more critical cases, the use of medications
is recommended, a physically active lifestyle is one of the main foundations for health maintenance, making
physical training an important tool to reduce the harmful effects of excessive fat accumulation.

Aim:
The purpose of this review of the literature is to present the impact of immunometabolic alterations on cognitive
function in individuals with obesity, and the role of exercise training as a non-pharmacological approach to
improve the inflammatory profile, energy metabolism and neuroplasticity in obesity.

Method:
An overview of the etiology and pathophysiology of obesity to establish a possible link with cognitive
performance in obese individuals, with the executive function being one of the most affected cognitive components.
In addition, the brain-derived neurotrophic factor (BDNF) profile and its impact on cognition in obese
individuals are discussed. Lastly, studies showing regular resistance and/or aerobic training, which may be able to
improve the pathophysiological condition and cognitive performance through the improvement of the inflammatory
profile, decreased insulin resistance and higher BDNF production are discussed.

Conclusion:
Exercise training is essential for reestablishment and maintenance of health by increasing energy
expenditure, insulin resistance reduction, anti-inflammatory proteins and neurotrophin production corroborating
to upregulation of body function.
Effect of Environmental Exposure and Pharmacogenomics on Drug Metabolism
Authors: Banerjee Basu Dev , Kumar Ranjeet , Thamineni Krishna Latha , Shah Harendra , Thakur Gaurav Kumar , Sharma Tusha 
Published: January 2020

Background:Pesticides are major xenobiotic compounds and environmental pollutants, which are able to alter drug-metabolizing enzyme as well as pharmacokinetics of drugs. Subsequent to the release of the human genome project, genetic variations (polymorphism) become an integral part of drug development due to their influence on disease susceptibility/ progression of the disease and their impact on drug absorption, distribution, metabolism of active metabolites and finally excretion of the drug. Genetic polymorphisms crucially regulate pharmacokinetics and pharmacodynamics of drugs under the influence of physiological condition, lifestyle, as well as pathological conditions collectively.Objective:To review all the evidence concerning the effect of environmental exposure on drug metabolism with reference to pharmacogenomics.Method:Scientific data search and review of basic, epidemiological, pharmacogenomics and pharmacokinetics studies were undertaken to evaluate the influence of environmental contaminants on drug metabolism.Result:Various environmental contaminants like pesticides effectively alter drug metabolism at various levels under the influence of pharmacogenomics, which interferes with pharmacokinetics of drug metabolism. Genetic polymorphism of phase I and phase II xenobiotic-metabolizing enzymes remarkably alters disease susceptibility as well as the progression of disease under the influence of various environmental contaminants at various levels.Conclusion:Individual specific drug response may be attributed to a large variety of factors alone or in combination ranging from genetic variations (SNP, insertion, deletion, duplication etc.) to physiological setting (gender, age, body size, and ethnicity), environmental or lifestyle factors (radiation exposure, smoking, alcohol, nutrition, exposure to toxins, etc.); and pathological conditions (obesity, diabetes, liver and renal function).
‘New/Designer Benzodiazepines’: An Analysis of the Literature and Psychonauts’ Trip Reports
Authors: Orsolini Laura , Corkery John M. , Chiappini Stefania , Guirguis Amira , Vento Alessandro , De Berardis Domenico , Papanti Duccio , Schifano Fabrizio 
Published: January 2020

Background:
NPS belonging to the benzodiazepine (BZD) class, e.g., ‘legal/designer
BZDs’/‘research chemicals’, have recently emerged in the drug (mainly online/virtual) market.

Objective:
While certain NPS belonging to the BZD class possess pharmacological profiles similar
to controlled pharmaceutical BZDs, clinical and pharmacological profiles of current emerging
BZDs are still not well-described. Therefore, there is a need to increase clinicians’/public health
knowledge/awareness, to incentive harm reduction strategies.

Methods:
A comprehensive overview was carried out by using the EMCDDA/EDND database regularly
monitored by our research team, by specifically looking at the ‘new BZDs’ so far notified.
Furthermore, given the limitation of peer-reviewed data published so far, a nonparticipant multilingual
qualitative netnographic study was conducted to obtain further clinical/pharmacological/
toxicological data, including psychonauts’ online trip reports.

Results:
First designer BZDs appeared as NPS around 2007. So far, 29 designer BZDs have been
notified to the EMCDDA, being some of them extremely powerful, also at lower dosages. They are
sold as tablets/powder/pellets/capsules/blotters/liquids, at very affordable prices, and variably administered.
Some are also sold on the illicit drugmarket as counterfeit forms of traditional BZDs or
as either adulterants or diluents in heroin or other synthetic opioids/cannabinoids. Nowadays, there
is no guarantee of the quality of designer BZDs composition/purification and, hence, most NPS
consumers may be inadvertently exposed to unsafe and harmful compounds.

Conclusions:
Given the limited information on their pharmacology/toxicity, variations in dosage,
onset of effects, combination of substances, potency, and general patient or individual variability,
the concomitant use of these substances with other drugs entails several and unpredictable risks.
Molecular Mechanism of Autophagy: Its Role in the Therapy of Alzheimer’s Disease
Authors: Zhao Yuan , Zhang Yidan , Zhang Jian , Zhang Xiangjian , Yang Guofeng 
Published: January 2020

:
Alzheimer’s disease (AD) is a neurodegenerative disorder of progressive dementia that is
characterized by the accumulation of beta-amyloid (Aβ)-containing neuritic plaques and intracellular
Tau protein tangles. This distinctive pathology indicates that the protein quality control is compromised
in AD. Autophagy functions as a “neuronal housekeeper” that eliminates aberrant protein
aggregates by wrapping then into autophagosomes and delivering them to lysosomes for degradation.
Several studies have suggested that autophagy deficits in autophagy participate in the accumulation
and propagation of misfolded proteins (including Aβ and Tau). In this review, we summarize
current knowledge of autophagy in the pathogenesis of AD, as well as some pathways targeting the
restoration of autophagy. Moreover, we discuss how these aspects can contribute to the development
of disease-modifying therapies in AD.
A Numerical Study: Transitional Hydrodynamic Behaviour of a Moored Barge in Different Ultra-shallow Water Depths of Malaysia
Authors: Patel M.S. , Azizan Nurliyana , Liew M.S. , Mustaffa Zahiraniza , Ali Montasir Osman , Whyte Andrew 
Published: January 2020

Background:
Malaysia has most of its oil reservoirs in the South China sea. The water depth ranges from 50 m to 200 m. The effects of ultra-shallow water are of prime importance in the exploration of marginal oil fields. Hence, there is an increasing demand for understanding the hydrodynamic behavior of FPSO in ultra-shallow water depths.

Objective:
A simulation study in both frequency-domain and time-domain analyses has been performed to understand the dynamic responses of a moored barge in varying shallow water depths. The objective of this study was to observe the transitional hydrodynamic behavior of the moored barge under varying shallow water depths.

Methods:
The moored barge was administered under regular and irregular waves. Operating conditions for irregular waves in terms of significant wave height and peak time period were incorporated from PETRONAS Technical Standards (PTS). The wave-body interactions and mooring effects have been numerically modelled using a commercial Computational Fluid Dynamics (CFD) and simulation software (ANSYS AQWA) successfully. In order to gain confidence in the simulation software, additional experimental validation was performed for a FPSO model.

Results:
Though the barge was primarily free to rotate in all Degrees Of Freedom (DOF), however, only three DOFs were considered for our study; viz, heave, roll and yaw respectively. The force spectral density, cable RAO’s in addition to the time series of cable forces, along with the effect of significant motions on the mooring cables behavior have been discussed.

Conclusion:
In irregular beam sea state, the significant motions in ultra-shallow water were greater than that for deep waters, this was primarily the main reason for higher cable responses in ultra-shallow water.
Effect of Feeding Different Mixtures of Short Milled Wheat and Sesame Seed Cake on Intake, Digestibility, and Live Bodyweight Changes for Abergelle Sheep in Tigray
Authors: Gebremariam Berihu 
Published: January 2020

Background:
The use of agro-industrial by-products is an alternative to enhance the performance of animals.

Objective:
To improve feed intake, digestibility, and live bodyweight changes for Abergelle sheep fed different mixtures prepared using short milled wheat and sesame seed cake mixtures.

Methods:
The experiment was designed using yearling male rams and was divided into four blocks based on initial live weight and assigned to each dietary feed randomly. The diets were prepared at a level of 0, 120, 240, and 360 gram dry matter base/day for diet1, diet2, diet3, and diet4, respectively, with a proportion of 65:35 (short milled wheat: sesame seed cake) combinations. Digestibility trial was conducted for 7 consecutive days following the 90 days feeding stage.

Results:
Total dry matter and nutrient intake were significant (P<0.001) in the order of diet4> diet3> diet2 level of supplementation than the control group (diet1). Feed conversion efficiency and final bodyweight gain were significant (P<0.01) for the supplemented groups. Apparent digestibility of crude protein was observed highest in diet4 (81.32) and lowest in diet1 (61.55). Similarly, dry matter and organic matter digestibility were significantly higher in diet4 (74.47, 76.38) and lowest in diet1 (58.71, 60.42), respectively. In general, supplementation with different levels of sesame seed cake and short milled wheat improves the biological performance of Abergelle sheep.

Conclusion:
The growth performance of rams can be realized supplementing with diets prepared using short milled wheat and sesame seed cake mixtures.
A Variable Temperature Study of the π–π Stacking Interaction in the Co-Crystal Naphthalene-Octafluoronaphthalene
Authors: Burrows Judith , Sain Prithwish , Saunders Graham C. 
Published: January 2020

Introduction:
The structure of the 1:1 co-crystal of naphthalene and octafluoronaphthalene, which has been previously determined at room temperature, was determined at 100, 150, 200 and 250 K.

Results:
Reductions in intermolecular distances and unit cell dimensions are observed on cooling. DFT calculations reveal that the energies of interaction between pairs of molecules vary little with temperature.

Conclusion:
The strongest interaction is the π–π stacking between virtually parallel naphthalene and octafluoronaphthalene molecules and this displays less change with temperature than the other, weaker, interactions, which have much shallower energy minima.