bluuebunny/crossref_metadata_2025_split huggingface dataset:
scPNMF: sparse gene encoding of single cells to facilitate gene selection for targeted gene profiling
Authors: Song Dongyuan , Li Kexin , Hemminger Zachary , Wollman Roy , Li Jingyi Jessica 
Published: April 2021

ABSTRACT:

Motivation
Single-cell RNA sequencing (scRNA-seq) captures whole transcriptome information of individual cells. While scRNA-seq measures thousands of genes, researchers are often interested in only dozens to hundreds of genes for a closer study. Then, a question is how to select those informative genes from scRNA-seq data. Moreover, single-cell targeted gene profiling technologies are gaining popularity for their low costs, high sensitivity and extra (e.g. spatial) information; however, they typically can only measure up to a few hundred genes. Then another challenging question is how to select genes for targeted gene profiling based on existing scRNA-seq data.

Results
Here, we develop the single-cell Projective Non-negative Matrix Factorization (scPNMF) method to select informative genes from scRNA-seq data in an unsupervised way. Compared with existing gene selection methods, scPNMF has two advantages. First, its selected informative genes can better distinguish cell types. Second, it enables the alignment of new targeted gene profiling data with reference data in a low-dimensional space to facilitate the prediction of cell types in the new data. Technically, scPNMF modifies the PNMF algorithm for gene selection by changing the initialization and adding a basis selection step, which selects informative bases to distinguish cell types. We demonstrate that scPNMF outperforms the state-of-the-art gene selection methods on diverse scRNA-seq datasets. Moreover, we show that scPNMF can guide the design of targeted gene profiling experiments and the cell-type annotation on targeted gene profiling data.

Availability and implementation
The R package is open-access and available at https://github.com/JSB-UCLA/scPNMF. The data used in this work are available at Zenodo: https://doi.org/10.5281/zenodo.4797997.

Supplementary information
Supplementary data are available at Bioinformatics online.
Mapping the Pains of Neo-Colonialism: A Critical Elaboration of Southern Criminology
Authors: Ciocchini Pablo , Greener Joe 
Published: April 2021

Abstract
Recent appeals to decolonize criminology argue for a radical reorientation of the subject towards Global South relevant research agendas, theories and scholars. This paper begins by problematizing the current theoretical tendencies in Southern criminology’s view of coloniality and the vision for decolonization. First, Southern criminology has not directly engaged in investigating ‘empire’ in its current form; second, decolonization is viewed as primarily epistemological (transforming systems of knowledge production is seen as the central mode for decolonization); and, third, there is a tendency to reify Southern institutional responses to crime as preferable to Northern crime control. Launching from this critique, we argue that a successful Southern criminology should take seriously the continuing importance of structures of neo-colonialization: the Global system of accumulation founded on various matrixes of inequality, facilitating dispossession, appropriation and exploitation. We develop three criminological analyses of contemporary neo-colonization in Global South contexts: state-corporate ‘regimes of permission’, political economies of gender violence and racialization through criminalization regimes.
Simulating the outcome of amyloid treatments in Alzheimer's disease from imaging and clinical data
Authors: Abi Nader Clément , Ayache Nicholas , Frisoni Giovanni B , Robert Philippe , Lorenzi Marco ,   for the Alzheimer’s Disease Neuroimaging Initiative
Published: April 2021

Abstract
In this study, we investigate SimulAD, a novel quantitative instrument for the development of intervention strategies for disease-modifying drugs in Alzheimer's disease. SimulAD is based on the modeling of the spatio-temporal dynamics governing the joint evolution of imaging and clinical biomarkers along the history of the disease, and allows the simulation of the effect of intervention time and drug dosage on the biomarkers' progression. When applied to multi-modal imaging and clinical data from the Alzheimer's Disease Neuroimaging Initiative the method enables to generate hypothetical scenarios of amyloid lowering interventions. The results quantify the crucial role of intervention time, and provide a theoretical justification for testing amyloid modifying drugs in the pre-clinical stage. Our experimental simulations are compatible with the outcomes observed in past clinical trials, and suggest that anti-amyloid treatments should be administered at least 7 years earlier than what is currently being done in order to obtain statistically powered improvement of clinical endpoints.
Circulating concentrations of thyroid hormones and cortisol in wild and semi-natural Yangtze finless porpoise (Neophocaena asiaeorientalis)
Authors: Nabi Ghulam , Robeck Todd R , Yujiang Hao , Tang Bin , Zheng Jinsong , Wang Kexiong , Wang Ding 
Published: April 2021

AbstractOur understanding about how environmental and biological variables may influence circulating thyroid and adrenal hormones in free-ranging cetaceans is limited. As such, we used liquid chromatography–mass spectrometry to determine concentrations of circulating cortisol and thyroid hormones (THs; tT3, tT4) in 132 Yangtze finless porpoises (YFPs) located in Poyang Lake, (PL, n = 92) and Tian-E-Zhou Oxbow reserve (TZO, n = 40). For overall hormone comparisons, animals were partitioned by age [juvenile and adult (male and non-pregnant, non-lactating female)], sex, season (winter or spring) and geographical location. Geographically, during winter, circulating THs were significantly higher in the PL versus TZO population. Seasonally, within PL, THs were significantly higher in the winter versus spring season. Animals were further binned into groups as follows: juvenile male (JM) and juvenile female (JF), adult male (AM), non-pregnant adult female, pregnant female and non-pregnant lactating female. Intra-group comparisons between locations showed a significant increase in JM THs at PL. Significant increases in THs during winter compared to spring were detected between JM and JF groups. Mean comparisons of cortisol within and between locations for each group identified a significant increase for TZO AM versus TZO pregnant female and JM and JF. Seasonally, in PL, only JF has significantly higher cortisol in winter versus spring. Finally, we established reference values of THs and cortisol for YFPs in different geographical locations. These references are important baselines from which the effects of environmental and biological variables on THs and cortisol may be evaluated.
Cardiovascular risk factors, cardiovascular disease, and COVID-19: an umbrella review of systematic reviews
Authors: Harrison Stephanie L , Buckley Benjamin J R , Rivera-Caravaca José Miguel , Zhang Juqian , Lip Gregory Y H 
Published: April 2021

Abstract

Aims
To consolidate evidence to determine (i) the association between cardiovascular risk factors and health outcomes with coronavirus 2019 (COVID-19); and (ii) the impact of COVID-19 on cardiovascular health.

Methods and results
An umbrella review of systematic reviews was conducted. Fourteen medical databases and pre-print servers were searched from 1 January 2020 to 5 November 2020. The review focused on reviews rated as moderate or high-quality using the AMSTAR 2 tool. Eighty-four reviews were identified; 31 reviews were assessed as moderate quality and one was high-quality. The following risk factors were associated with higher mortality and severe COVID-19: renal disease [odds ratio (OR) (95% confidence interval) for mortality 3.07 (2.43–3.88)], diabetes mellitus [OR 2.09 (1.80–2.42)], hypertension [OR 2.50 (2.02–3.11)], smoking history [risk ratio (RR) 1.26 (1.20–1.32)], cerebrovascular disease [RR 2.75 (1.54–4.89)], and cardiovascular disease [OR 2.65 (1.86–3.78)]. Liver disease was associated with higher odds of mortality [OR 2.81 (1.31–6.01)], but not severe COVID-19. Current smoking was associated with a higher risk of severe COVID-19 [RR 1.80 (1.14–2.85)], but not mortality. Obesity associated with higher odds of mortality [OR 2.18 (1.10–4.34)], but there was an absence of evidence for severe COVID-19. In patients hospitalized with COVID-19, the following incident cardiovascular complications were identified: acute heart failure (2%), myocardial infarction (4%), deep vein thrombosis (7%), myocardial injury (10%), angina (10%), arrhythmias (18%), pulmonary embolism (19%), and venous thromboembolism (25%).

Conclusion
Many of the risk factors identified as associated with adverse outcomes with COVID-19 are potentially modifiable. Primary and secondary prevention strategies that target cardiovascular risk factors may improve outcomes for people following COVID-19.
Primary cardiovascular risk prediction by LDL-cholesterol in Caucasian middle-aged and older adults: a joint analysis of three cohorts
Authors: Hilvo Mika , Dhar Indu , Lääperi Mitja , Lysne Vegard , Sulo Gehard , Tell Grethe S , Jousilahti Pekka , Nygård Ottar K , Brenner Hermann , Schöttker Ben , Laaksonen Reijo 
Published: April 2021

AbstractAimsLow-density lipoprotein cholesterol (LDL-C) is an established causal driver of atherosclerotic cardiovascular disease (ASCVD), but its performance and age-dependency as a biomarker for incident events and mortality arising from ASCVD is less clear. The aim was to determine the value of LDL-C as a susceptibility/risk biomarker for incident coronary heart disease (CHD), ASCVD, and stroke events and deaths, for the age groups &lt;50 and ≥50 years.Methods and resultsThe performance of LDL-C was evaluated in three cohorts, FINRISK 2002 (n = 7709), HUSK (n = 5431), and ESTHER (n = 4559), by Cox proportional hazards models, C-statistics, and net reclassification index calculations. Additionally, the hazard ratios (HRs) for the three cohorts were pooled by meta-analysis. The most consistent association was observed for CHD [95% confidence interval (CI) for HRs per standard deviation ranging from 0.99 to 1.37], whereas the results were more modest for ASCVD (0.96–1.18) due to lack of association with stroke (0.77–1.24). The association and discriminatory value of LDL-C with all endpoints in FINRISK 2002 and HUSK were attenuated in subjects 50 years and older [HRs (95% CI) obtained from meta-analysis 1.11 (1.04–1.18) for CHD, 1.15 (1.02–1.29) for CHD death, 1.02 (0.98–1.06) for ASCVD, 1.12 (1.02–1.23) for ASCVD death, and 0.97 (0.89–1.05) for stroke].ConclusionIn middle-aged and older adults, associations between LDL-C and all the studied cardiovascular endpoints were relatively weak, while LDL-C showed stronger association with rare events of pre-mature CHD or ASCVD death among middle-aged adults. The predictive performance of LDL-C also depends on the studied cardiovascular endpoint.
Household food spending, parental and childhood’s diet quality, in financial crisis: a cross-sectional study in Greece
Authors: Kosti Rena I , Kanellopoulou Aikaterini , Notara Venetia , Antonogeorgos George , Rojas-Gil Andrea Paola , Kornilaki Ekaterina N , Lagiou Areti , Panagiotakos Demosthenes B 
Published: April 2021

Abstract

Background
Over the past decade, the financial crisis has affected harshly the household income of Greek people. This study aimed to investigate whether the effect of the financial crisis on food spending has affected the dietary habits in the family environment.

Methods
Under a cross-sectional study conducted during 2014–2016, 1145 children and their parents completed questionnaires examining socio-economic and dietary characteristics. The MedDietScore and the KIDMED Score were used to assess parental and childhood adherence to the Mediterranean diet, respectively.

Results
The parents who reported that the financial crisis has affected food spending used to consume weekly fewer fruits (3.26 ± 0.94 vs. 3.41 ± 0.90, P = 0.016), carbohydrate foods (3.16 ± 0.57 vs. 2.99 ± 0.55, P &lt; 0.001) and legumes (3.28 ± 0.76 vs. 3.14 ± 0.67, P = 0.001) and more nutrient-poor/energy-dense foods (2.55 ± 0.98 vs. 2.20 ± 0.82, P &lt; 0.001) compared with non-affected parents. Their children showed a decreased weekly consumption of vegetables (2.82 ± 0.90 vs. 2.97 ± 0.98, P = 0.019) and increased weekly consumption of nutrient-poor/energy-dense foods (2.38 ± 0.97 vs. 2.19 ± 0.80, P &lt; 0.001). The affected parents had a lower MedDietScore than non-affected parents (25.76 ± 8.10 vs. 27.03 ± 8.11, P = 0.034). No difference was revealed on the KIDMED Score (P = 0.294).

Conclusions
The constrained food spending due to financial crisis has an independent and inverse impact on parent’s diet quality while keeping unaffected preadolescent’s diet quality. This finding highlights the role of parents as a protective ‘wall’ against the deterioration of their children’s diet quality. The modification on the prices of healthy food and the provision of food aid particularly in economically disadvantaged households is underlined.
The US Congress and Rogue States
Authors: Kotb Shereen , Jeong Gyung-Ho 
Published: April 2021

Abstract
Foreign policy has become one of the most polarizing issues in American politics. This paper investigates the extent to which this division extends to arguably one of the most bipartisan foreign policy issues: policies toward rogue states. Our examination of congressional voting and sponsorship data related to rogue states since 1991 finds that, while there is a high degree of bipartisanship on the issue, there are nuanced but significant partisan differences. First, we find that Democrats are significantly more likely to support a rogue state bill dealing with human rights concerns, whereas Republicans are significantly less likely to support a conciliatory bill. We also find that members of Congress are less likely to propose and support a rogue state bill in the presence of a co-partisan president. We thus conclude that, despite the overall high degree of bipartisanship on rogue state issues, partisanship plays an important role in influencing legislative behavior.
Efficient Recovery of Centric Heterochromatin P-Element Insertions in Drosophila melanogaster
Authors: Yan Christopher M , Dobie Kenneth W , Le Hiep D , Konev Alexander Y , Karpen Gary H 
Published: April 2021

Abstract
Approximately one-third of the human and Drosophila melanogaster genomes are heterochromatic, yet we know very little about the structure and function of this enigmatic component of eukaryotic genomes. To facilitate molecular and cytological analysis of heterochromatin we introduced a yellow+ (y+)-marked P element into centric heterochromatin by screening for variegated phenotypes, that is, mosaic gene inactivation. We recovered &gt;110 P insertions with variegated yellow expression from ∼3500 total mobilization events. FISH analysis of 71 of these insertions showed that 69 (97%) were in the centric heterochromatin, rather than telomeres or euchromatin. High-resolution banding analysis showed a wide but nonuniform distribution of insertions within centric heterochromatin; variegated insertions were predominantly recovered near regions of satellite DNA. We successfully used inverse PCR to clone and sequence the flanking DNA for ∼63% of the insertions. BLAST analysis of the flanks demonstrated that either most of the variegated insertions could not be placed on the genomic scaffold, and thus may be inserted within novel DNA sequence, or that the flanking DNA hit multiple sites on the scaffold, due to insertions within different transposons. Taken together these data suggest that screening for yellow variegation is a very efficient method for recovering centric insertions and that a large-scale screen for variegated yellow P insertions will provide important tools for detailed analysis of centric heterochromatin structure and function.
Subfunctionalization of DuplicatemitfGenes Associated With Differential Degeneration of Alternative Exons in Fish
Authors: Altschmied Joachim , Delfgaauw Jacqueline , Wilde Brigitta , Duschl Jutta , Bouneau Laurence , Volff Jean-Nicolas , Schartl Manfred 
Published: April 2021

AbstractThe microphthalmia-associated transcription factor (MITF) exists in at least four isoforms. These are generated in higher vertebrates using alternative 5′ exons and promoters from a single gene. Two separate genes (mitf-m and mitf-b), however, are present in different teleost fish species including the poeciliid Xiphophorus, the pufferfishes Fugu rubripes and Tetraodon nigroviridis, and the zebrafish Danio rerio. Fish proteins MITF-m and MITF-b correspond at both the structural and the expression levels to one particular bird/mammalian MITF isoform. In the teleost lineage subfunctionalization of mitf genes after duplication at least 100 million years ago is associated with the degeneration of alternative exons and, probably, regulatory elements and promoters. For example, a remnant of the first exon specific for MITF-m is detected within the pufferfish gene encoding MITF-b. Retracing the evolutionary history of mitf genes in vertebrates uncovered the differential recruitment of new introns specific for either the teleost or the bird/mammalian lineage.
Codon Bias Differentiates Between the Duplicated Amylase Loci Following Gene Duplication in Drosophila
Authors: Zhang Ze , Inomata Nobuyuki , Ohba Tomohiro , Cariou Marie-Louise , Yamazaki Tsuneyuki 
Published: April 2021

Abstract
We examined the pattern of synonymous substitutions in the duplicated Amylase (Amy) genes (called the Amy1- and Amy3-type genes, respectively) in the Drosophila montium species subgroup. The GC content at the third synonymous codon sites of the Amy1-type genes was higher than that of the Amy3-type genes, while the GC content in the 5′-flanking region was the same in both genes. This suggests that the difference in the GC content at third synonymous sites between the duplicated genes is not due to the temporal or regional changes in mutation bias. We inferred the direction of synonymous substitutions along branches of a phylogeny. In most lineages, there were more synonymous substitutions from G/C (G or C) to A/T (A or T) than from A/T to G/C. However, in one lineage leading to the Amy1-type genes, which is immediately after gene duplication but before speciation of the montium species, synonymous substitutions from A/T to G/C were predominant. According to a simple model of synonymous DNA evolution in which major codons are selectively advantageous within each codon family, we estimated the selection intensity for specific lineages in a phylogeny on the basis of inferred patterns of synonymous substitutions. Our result suggested that the difference in GC content at synonymous sites between the two Amy-type genes was due to the change of selection intensity immediately after gene duplication but before speciation of the montium species.
Genetic Analysis of Sunflower Domestication
Authors: Burke John M , Tang Shunxue , Knapp Steven J , Rieseberg Loren H 
Published: April 2021

AbstractQuantitative trait loci (QTL) controlling phenotypic differences between cultivated sunflower and its wild progenitor were investigated in an F3 mapping population. Composite interval mapping revealed the presence of 78 QTL affecting the 18 quantitative traits of interest, with 2–10 QTL per trait. Each QTL explained 3.0–68.0% of the phenotypic variance, although only 4 (corresponding to 3 of 18 traits) had effects &gt;25%. Overall, 51 of the 78 QTL produced phenotypic effects in the expected direction, and for 13 of 18 traits the majority of QTL had the expected effect. Despite being distributed across 15 of the 17 linkage groups, there was a substantial amount of clustering among QTL controlling different traits. In several cases, regions influencing multiple traits harbored QTL with antagonistic effects, producing a cultivar-like phenotype for some traits and a wild-like phenotype for others. On the basis of the directionality of QTL, strong directional selection for increased achene size appears to have played a central role in sunflower domestication. None of the other traits show similar evidence of selection. The occurrence of numerous wild alleles with cultivar-like effects, combined with the lack of major QTL, suggests that sunflower was readily domesticated.
Estimating Mutation Parameters, Population History and Genealogy Simultaneously From Temporally Spaced Sequence Data
Authors: Drummond Alexei J , Nicholls Geoff K , Rodrigo Allen G , Solomon Wiremu 
Published: April 2021

Abstract
Molecular sequences obtained at different sampling times from populations of rapidly evolving pathogens and from ancient subfossil and fossil sources are increasingly available with modern sequencing technology. Here, we present a Bayesian statistical inference approach to the joint estimation of mutation rate and population size that incorporates the uncertainty in the genealogy of such temporally spaced sequences by using Markov chain Monte Carlo (MCMC) integration. The Kingman coalescent model is used to describe the time structure of the ancestral tree. We recover information about the unknown true ancestral coalescent tree, population size, and the overall mutation rate from temporally spaced data, that is, from nucleotide sequences gathered at different times, from different individuals, in an evolving haploid population. We briefly discuss the methodological implications and show what can be inferred, in various practically relevant states of prior knowledge. We develop extensions for exponentially growing population size and joint estimation of substitution model parameters. We illustrate some of the important features of this approach on a genealogy of HIV-1 envelope (env) partial sequences.
Multileveled Selection on Plasmid Replication
Authors: Paulsson Johan 
Published: April 2021

Abstract
The replication control genes of bacterial plasmids face selection at two conflicting levels. Plasmid copies that systematically overreplicate relative to their cell mates have a higher chance of fixing in descendant cells, but these cells typically have a lower chance of fixing in the population. Apart from identifying the conflict, this mathematical discussion characterizes the efficiency of the selection levels and suggests how they drive the evolution of kinetic mechanisms. In particular it is hypothesized that: (1) tighter replication control is more vulnerable to selfishness; (2) cis-acting replication activators are relics of a conflict where a plasmid outreplicated its intracellular competitors by monopolizing activators; (3) high-copy plasmids with sloppy replication control arise because intracellular selection favors overreplication, thereby relieving intercellular selection for lower loss rates; (4) the excessive synthesis of cis-acting replication activators and trans-acting inhibitors is the result of an arms race between cis selfishness and trans retaliations; (5) site-specific recombination of plasmid dimers is equivalent to self-policing; and (6) plasmids modify their horizontal transfer to spread without promoting selfishness. It is also discussed how replication control may be subject to a third level of selection acting on the entire population of plasmid-containing cells.