bluuebunny/crossref_metadata_2025_split huggingface dataset:
Empirical comparison of analytical approaches for identifying molecular HIV-1 clusters
Authors: Novitsky Vlad , Steingrimsson Jon A. , Howison Mark , Gillani Fizza S. , Li Yuanning , Manne Akarsh , Fulton John , Spence Matthew , Parillo Zoanne , Marak Theodore , Chan Philip A. , Bertrand Thomas , Bandy Utpala , Alexander-Scott Nicole , Dunn Casey W. , Hogan Joseph , Kantor Rami 
Published: October 2020

AbstractPublic health interventions guided by clustering of HIV-1 molecular sequences may be impacted by choices of analytical approaches. We identified commonly-used clustering analytical approaches, applied them to 1886 HIV-1 Rhode Island sequences from 2004–2018, and compared concordance in identifying molecular HIV-1 clusters within and between approaches. We used strict (topological support ≥ 0.95; distance 0.015 substitutions/site) and relaxed (topological support 0.80–0.95; distance 0.030–0.045 substitutions/site) thresholds to reflect different epidemiological scenarios. We found that clustering differed by method and threshold and depended more on distance than topological support thresholds. Clustering concordance analyses demonstrated some differences across analytical approaches, with RAxML having the highest (91%) mean summary percent concordance when strict thresholds were applied, and three (RAxML-, FastTree regular bootstrap- and IQ-Tree regular bootstrap-based) analytical approaches having the highest (86%) mean summary percent concordance when relaxed thresholds were applied. We conclude that different analytical approaches can yield diverse HIV-1 clustering outcomes and may need to be differentially used in diverse public health scenarios. Recognizing the variability and limitations of commonly-used methods in cluster identification is important for guiding clustering-triggered interventions to disrupt new transmissions and end the HIV epidemic.
Color image encryption based on chaotic compressed sensing and two-dimensional fractional Fourier transform
Authors: Wang Xingyuan , Su Yining 
Published: October 2020

AbstractCombining the advantages of structured random measurement matrix and chaotic structure, this paper introduces a color image encryption algorithm based on a structural chaotic measurement matrix and random phase mask. The Chebyshev chaotic sequence is used in the algorithm to generate the flip permutation matrix, the sampling subset and the chaotic cyclic matrix for constructing the structure perceptual matrix and the random phase mask. The original image is compressed and encrypted simultaneously by compressed sensing, and re-encrypted by two-dimensional fractional Fourier transform. Simulation experiments show the effectiveness and reliability of the algorithm.
Successful post-glacial colonization of Europe by single lineage of freshwater amphipod from its Pannonian Plio-Pleistocene diversification hotspot
Authors: Csapó Hedvig , Krzywoźniak Paula , Grabowski Michał , Wattier Remi , Bącela-Spychalska Karolina , Mamos Tomasz , Jelić Mišel , Rewicz Tomasz 
Published: October 2020

AbstractGammarus roeseliiGervais, 1835 is a morphospecies with a wide distribution range in Europe. The Balkan Peninsula is known as an area of pre-Pleistocene cryptic diversification within this taxon, resulting in at least 13 Molecular Operational Taxonomic Units (MOTUs). The morphospecies diversified there during Neogene and has probably invaded other parts of the continent very recently, in postglacial or even historical times. Thus, the detailed goals of our study were to (1) identify which lineage(s) colonized Central-Western Europe (CWE), (2) determine their possible geographical origin, (3) verify, whether the colonisation was associated with demographic changes. In total, 663 individuals were sequenced for the cytochrome oxidase I (COI) barcoding fragment and 137 individuals for the internal transcribed spacer II (ITS2). We identified two MOTUs in the study area with contrasting Barcode Index Number and haplotype diversities. The Pannonian Basin (PB) appeared to be a potential ice age refugium for the species, while CWE was colonised by a single lineage (also present in PB), displaying low genetic diversity. Our results suggest thatG. roeseliiis a relatively recent coloniser in CWE, starting demographic expansion around 10 kya.
Molecular imaging analysis of microvesicular and macrovesicular lipid droplets in non-alcoholic fatty liver disease by Raman microscopy
Authors: Minamikawa Takeo , Ichimura-Shimizu Mayuko , Takanari Hiroki , Morimoto Yuki , Shiomi Ryosuke , Tanioka Hiroki , Hase Eiji , Yasui Takeshi , Tsuneyama Koichi 
Published: October 2020

AbstractPredominant evidence of non-alcoholic fatty liver disease (NAFLD) is the accumulation of excess lipids in the liver. A small group with NAFLD may have a more serious condition named non-alcoholic steatohepatitis (NASH). However, there is a lack of investigation of the accumulated lipids with spatial and molecular information. Raman microscopy has the potential to characterise molecular species and structures of lipids based on molecular vibration and can achieve high spatial resolution at the organelle level. In this study, we aim to demonstrate the feasibility of Raman microscopy for the investigation of NAFLD based on the molecular features of accumulated lipids. By applying the Raman microscopy to the liver of the NASH model mice, we succeeded in visualising the distribution of lipid droplets (LDs) in hepatocytes. The detailed analysis of Raman spectra revealed the difference of molecular structural features of the LDs, such as the degree of saturation of lipids in the LDs. We also found that the inhomogeneous distribution of cholesterol in the LDs depending on the histology of lipid accumulation. We visualised and characterised the lipids of NASH model mice by Raman microscopy at organelle level. Our findings demonstrated that the Raman imaging analysis was feasible to characterise the NAFLD in terms of the molecular species and structures of lipids.
Metabolomic profiles associated with a mouse model of antipsychotic-induced food intake and weight gain
Authors: Zapata Rizaldy C. , Rosenthal Sara Brin , Fisch Kathleen , Dao Khoi , Jain Mohit , Osborn Olivia 
Published: October 2020

AbstractAntipsychotic drugs (AP) are used to treat a multitude of psychiatric conditions including schizophrenia and bipolar disorder. However, APs also have metabolic side effects including increased food intake and body weight, but the underlying mechanisms remain unknown. We previously reported that minocycline (MINO) co-treatment abrogates olanzapine (OLZ)-induced hyperphagia and weight gain in mice. Using this model, we investigated the changes in the pharmacometabolome in the plasma and hypothalamus associated with OLZ-induced hyperphagia and weight gain. Female C57BL/6 mice were divided into groups and fed either i) control, CON (45% fat diet) ii) CON + MINO, iii) OLZ (45% fat diet with OLZ), iv) OLZ + MINO. We identified one hypothalamic metabolite indoxylsulfuric acid and 389 plasma metabolites (including 19 known metabolites) that were specifically associated with AP-induced hyperphagia and weight gain in mice. We found that plasma citrulline, tricosenoic acid, docosadienoic acid and palmitoleic acid were increased while serine, asparagine and arachidonic acid and its derivatives were decreased in response to OLZ. These changes were specifically blocked by co-treatment with MINO. These pharmacometabolomic profiles associated with AP-induced hyperphagia and weight gain provide candidate biomarkers and mechanistic insights related to the metabolic side effects of these widely used drugs.
Tailored flavoproteins acting as light-driven spin machines pump nuclear hyperpolarization
Authors: Ding Yonghong , Kiryutin Alexey S. , Zhao Ziyue , Xu Qian-Zhao , Zhao Kai-Hong , Kurle Patrick , Bannister Saskia , Kottke Tilman , Sagdeev Renad Z. , Ivanov Konstantin L. , Yurkovskaya Alexandra V. , Matysik Jörg 
Published: October 2020

AbstractThe solid-state photo-chemically induced dynamic nuclear polarization (photo-CIDNP) effect generates non-Boltzmann nuclear spin magnetization, referred to as hyperpolarization, allowing for high gain of sensitivity in nuclear magnetic resonance (NMR). Well known to occur in photosynthetic reaction centers, the effect was also observed in a light-oxygen-voltage (LOV) domain of the blue-light receptor phototropin, in which the functional cysteine was removed to prevent photo-chemical reactions with the cofactor, a flavin mononucleotide (FMN). Upon illumination, the FMN abstracts an electron from a tryptophan to form a transient spin-correlated radical pair (SCRP) generating the photo-CIDNP effect. Here, we report on designed molecular spin-machines producing nuclear hyperpolarization upon illumination: a LOV domain of aureochrome1a from Phaeodactylum tricornutum, and a LOV domain named 4511 from Methylobacterium radiotolerans (Mr4511) which lacks an otherwise conserved tryptophan in its wild-type form. Insertion of the tryptophan at canonical and novel positions in Mr4511 yields photo-CIDNP effects observed by 15N and 1H liquid-state high-resolution NMR with a characteristic magnetic-field dependence indicating an involvement of anisotropic magnetic interactions and a slow-motion regime in the transient paramagnetic state. The heuristic biomimetic design opens new categories of experiments to analyze and apply the photo-CIDNP effect.
Kinetics of SARS-CoV-2 positivity of infected and recovered patients from a single center
Authors: Huang Jia , Zheng Le , Li Zhen , Hao Shiying , Ye Fangfan , Chen Jun , Gans Hayley A. , Yao Xiaoming , Liao Jiayu , Wang Song , Zeng Manfei , Qiu Liping , Li Chunyang , Whitin John C. , Tian Lu , Chubb Henry , Hwa Kuo-Yuan , Ceresnak Scott R. , Zhang Wei , Lu Ying , Maldonado Yvonne A. , McElhinney Doff B. , Sylvester Karl G. , Cohen Harvey J. , Liu Lei , Ling Xuefeng B. 
Published: October 2020

AbstractRecurrence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) positive detection in infected but recovered individuals has been reported. Patients who have recovered from coronavirus disease 2019 (COVID-19) could profoundly impact the health care system. We sought to define the kinetics and relevance of PCR-positive recurrence during recovery from acute COVID-19 to better understand risks for prolonged infectivity and reinfection. A series of 414 patients with confirmed SARS-Cov-2 infection, at The Second Affiliated Hospital of Southern University of Science and Technology in Shenzhen, China from January 11 to April 23, 2020. Statistical analyses were performed of the clinical, laboratory, radiologic image, medical treatment, and clinical course of admission/quarantine/readmission data, and a recurrence predictive algorithm was developed. 16.7% recovered patients with PCR positive recurring one to three times, despite being in strict quarantine. Younger patients with mild pulmonary respiratory syndrome had higher risk of PCR positivity recurrence. The recurrence prediction model had an area under the ROC curve of 0.786. This case series provides characteristics of patients with recurrent SARS-CoV-2 positivity. Use of a prediction algorithm may identify patients at high risk of recurrent SARS-CoV-2 positivity and help to establish protocols for health policy.
Trimethylamine N-oxide and the reverse cholesterol transport in cardiovascular disease: a cross-sectional study
Authors: Bordoni Laura , Samulak Joanna J. , Sawicka Angelika K. , Pelikant-Malecka Iwona , Radulska Adrianna , Lewicki Lukasz , Kalinowski Leszek , Gabbianelli Rosita , Olek Robert A. 
Published: October 2020

AbstractThe early atherosclerotic lesions develop by the accumulation of arterial foam cells derived mainly from cholesterol-loaded macrophages. Therefore, cholesterol and cholesteryl ester transfer protein (CETP) have been considered as causative in atherosclerosis. Moreover, recent studies indicate the role of trimethylamine N-oxide (TMAO) in development of cardiovascular disease (CVD). The current study aimed to investigate the association between TMAO and CETP polymorphisms (rs12720922 and rs247616), previously identified as a genetic determinant of circulating CETP, in a population of coronary artery disease (CAD) patients (n = 394) and control subjects (n = 153). We also considered age, sex, trimethylamine (TMA) levels and glomerular filtration rate (GFR) as other factors that can potentially play a role in this complex picture. We found no association of TMAO with genetically determined CETP in a population of CAD patients and control subjects. Moreover, we noticed no differences between CAD patients and control subjects in plasma TMAO levels. On the contrary, lower levels of TMA in CAD patients respect to controls were observed. Our results indicated a significant correlation between GFR and TMAO, but not TMA. The debate whether TMAO can be a harmful, diagnostic or protective marker in CVD needs to be continued.
Cost–benefit of limited isolation and testing in COVID-19 mitigation
Authors: Eilersen Andreas , Sneppen Kim 
Published: October 2020

AbstractThe international community has been put in an unprecedented situation by the COVID-19 pandemic. Creating models to describe and quantify alternative mitigation strategies becomes increasingly urgent. In this study, we propose an agent-based model of disease transmission in a society divided into closely connected families, workplaces, and social groups. This allows us to discuss mitigation strategies, including targeted quarantine measures. We find that workplace and more diffuse social contacts are roughly equally important to disease spread, and that an effective lockdown must target both. We examine the cost–benefit of replacing a lockdown with tracing and quarantining contacts of the infected. Quarantine can contribute substantially to mitigation, even if it has short duration and is done within households. When reopening society, testing and quarantining is a strategy that is much cheaper in terms of lost workdays than a long lockdown. A targeted quarantine strategy is quite efficient with only 5 days of quarantine, and its effect increases when testing is more widespread.
Accurate detection of cerebellar smooth pursuit eye movement abnormalities via mobile phone video and machine learning
Authors: Chang Zhuoqing , Chen Ziyu , Stephen Christopher D. , Schmahmann Jeremy D. , Wu Hau-Tieng , Sapiro Guillermo , Gupta Anoopum S. 
Published: October 2020

AbstractEye movements are disrupted in many neurodegenerative diseases and are frequent and early features in conditions affecting the cerebellum. Characterizing eye movements is important for diagnosis and may be useful for tracking disease progression and response to therapies. Assessments are limited as they require an in-person evaluation by a neurology subspecialist or specialized and expensive equipment. We tested the hypothesis that important eye movement abnormalities in cerebellar disorders (i.e., ataxias) could be captured from iPhone video. Videos of the face were collected from individuals with ataxia (n = 102) and from a comparative population (Parkinson’s disease or healthy participants, n = 61). Computer vision algorithms were used to track the position of the eye which was transformed into high temporal resolution spectral features. Machine learning models trained on eye movement features were able to identify abnormalities in smooth pursuit (a key eye behavior) and accurately distinguish individuals with abnormal pursuit from controls (sensitivity = 0.84, specificity = 0.77). A novel machine learning approach generated severity estimates that correlated well with the clinician scores. We demonstrate the feasibility of capturing eye movement information using an inexpensive and widely accessible technology. This may be a useful approach for disease screening and for measuring severity in clinical trials.
Waist-height ratio and waist are the best estimators of visceral fat in type 1 diabetes
Authors: Parente Erika B. , Mutter Stefan , Harjutsalo Valma , Ahola Aila J. , Forsblom Carol , Groop Per-Henrik 
Published: October 2020

AbstractVisceral fat is associated with cardiovascular and kidney disease. However, the relationship between body composition and anthropometric measures in type 1 diabetes is unknown. Using z-statistics, we ranked the ability of body mass index (BMI), waist circumference (WC), waist-hip ratio (WHR), waist-height ratio (WHtR) and a body shape index (ABSI) to capture measures of body composition from 603 Dual-energy-X-Ray-Absorptiometry scans of adults with type 1 diabetes. Albuminuria was defined as urinary albumin excretion rate of at least 30 mg/24 h. Women with albuminuria had higher visceral fat mass % (VFM%) (0.9 vs. 0.5%, p = 0.0017) and lower appendicular lean mass % (AppLM%) (25.4 vs 26.4%, p = 0.03) than those without. Men with albuminuria had higher VFM% (1.5 vs. 1.0%, p = 0.0013) and lower AppLM% (30.0 vs 32.3, p < 0.0001) than those without. In men, WHtR estimated VFM% best (z-statistics = 21.1), followed by WC (z = 19.6), BMI (z = 15.1), WHR (z = 14.6) and ABSI (z = 10.1). In women, the ranking was WC (z = 28.9), WHtR (z = 27.3), BMI (z = 20.5), WHR (z = 12.7) and ABSI (z = 10.5). Overall, the ranking was independent of albuminuria. Adults with type 1 diabetes and albuminuria have greater VFM% and lower AppLM% than those without. WHtR and WC best estimate the VFM% in this population, independently of albuminuria and sex.
Transformation of non-water sorbing fly ash to a water sorbing material for drought management
Authors: Saha Abhisekh , Sekharan Sreedeep , Manna Uttam , Sahoo Lingaraj 
Published: October 2020

AbstractSecuring water in the soil through suitable amendments is one of the methods for drought management in arid regions. In this study, a poor water sorbing fly ash was transformed into a high water-absorbing material for improving soil water retention during the drought period. The fly ash water absorbent (FAWA) exhibited high water-absorbing capacity (WAC) of 310 g/g at par with commercially available superabsorbent hydrogel (SAH). The FAWA showed excellent re-swelling behavior for more than eight alternate wetting–drying cycles. The WAC of FAWA was sensitive to salt type, pH, and ionic strength of the solution. At maximum salinity level permitted for plant growth, the WAC of FAWA was 80 g/g indicating its suitability for drought management. There was only a marginal WAC variation in the range of pH (5.5–7.5) considered most suitable for plant growth. The drying characteristics of FAWA amended soil exhibited an increase in desaturation time by 3.3, 2.2, and 1.5 times for fine sand, silt loam, and clay loam, respectively. The study demonstrates the success of using a low rate of FAWA for drought management with the advantage of offering a non-toxic and eco-friendly solution to mass utilization of industrial solid waste for agricultural applications.
Interspecific grafting between Gossypium hirsutum, G. barbadense and G. herbaceum lines
Authors: Karaca Mehmet , Ince Ayse Gul , Reddy Umesh K. 
Published: October 2020

AbstractSeedling grafting could provide additional crop improvement strategies for cotton. However, there existed limited studies on interspecific grafting and approaches. Four different grafting approaches were developed and compared between lines representing three of the four cultivated cotton species G. hirsutum, G. barbadense and G. herbaceum. Grafting approaches of this study focused on the cotyledon node and cotyledon leaves retained on scions, rootstocks, without cotyledon node and cotyledon leaves on scions and rootstocks or halved cotyledon node and single cotyledon leaf on scions and rootstocks. Evaluations of the grafting approaches were made by comparing survival and growth rate during the second and fifth weeks after transplantation, respectively. The formation of any lateral shoots at the grafted sites were studied in two of four grafting approaches in the first and the second year during flowering stage. DNA alterations due to grafting were investigated using microsatellite markers. There were no statistically significant differences between grafts and their control in survival rate and locus specific DNA alteration. Growth rate and lateral shoot formation, on the other hand, were different among grafting types and grafts. We concluded that grafting without cotyledon node and cotyledon leaves on rootstocks, and with cotyledon node but without cotyledon leaves on scions were easy to perform and suitable for interspecific cotton grafting. Results suggested that grafting seedlings and allowing time to heal graft wounds prior to spring transplanting or double cropping is suitable for wheat–cotton intercropping to prevent late or early chilling damage associated with seed sowing or conventional transplanting of susceptible seedlings. Furthermore, the rapid and consistent wound healing in seedling grafts along with lateral shoot formation occurring in two of four grafting approaches make them a suitable approach to investigate possible genetic and epigenetic movement between scions and rootstocks, especially across species.
Analysis of open chromatin regions in bladder cancer links β-catenin mutations and Wnt signaling with neuronal subtype of bladder cancer
Authors: Eray Aleyna , Güneri Perihan Yağmur , Yılmaz Gülden Özden , Karakülah Gökhan , Erkek-Ozhan Serap 
Published: October 2020

AbstractUrothelial carcinoma of the bladder is the most frequent bladder cancer affecting more than 400,000 people each year. Histopathologically, it is mainly characterized as muscle invasive bladder cancer (MIBC) and non-muscle invasive bladder cancer (NMIBC). Recently, the studies largely driven by consortiums such as TCGA identified the mutational landscape of both MIBC and NMIBC and determined the molecular subtypes of bladder cancer. Because of the exceptionally high rate of mutations in chromatin proteins, bladder cancer is thought to be a disease of chromatin, pointing out to the importance of studying epigenetic deregulation and the regulatory landscape of this cancer. In this study, we have analyzed ATAC-seq data generated for MIBC and integrated our findings with gene expression and DNA methylation data to identify subgroup specific regulatory patterns for MIBC. Our computational analysis revealed three MIBC regulatory clusters, which we named as neuronal, non-neuronal and luminal outlier. We have identified target genes of neuronal regulatory elements to be involved in WNT signaling, while target genes of non-neuronal and luminal outlier regulatory regions were enriched in epithelial differentiation and drug metabolism, respectively. Neuronal regulatory elements were determined to be ß-catenin targets (p value = 3.59e−08) consisting of genes involved in neurogenesis such as FGF9, and PROX1, and significantly enriched for TCF/LEF binding sites (p value = 1e−584). Our results showed upregulation of ß-catenin targets regulated by neuronal regulatory elements in three different cohorts, implicating ß-catenin signature in neuronal bladder cancer. Further, integration with mutation data revealed significantly higher oncogenic exon 3 ß-catenin mutations in neuronal bladder cancer compared to non-neuronal (odds ratio = 31.33, p value = 1.786e−05). Our results for the first time identify regulatory elements characterizing neuronal bladder cancer and links these neuronal regulatory elements with WNT signaling via mutations in β-catenin and its destruction complex components.