bluuebunny/crossref_metadata_2025_split huggingface dataset:
AMC: accurate mutation clustering from single-cell DNA sequencing data
Authors: Yu Zhenhua , Du Fang 
Published: December 2021

Abstract

Summary
Single-cell DNA sequencing (scDNA-seq) now enables high-resolution profiles of intra-tumor heterogeneity. Existing methods for phylogenetic inference from scDNA-seq data perform acceptably well on small datasets but suffer from low computational efficiency and/or degraded accuracy on large datasets. Motivated by the fact that mutations sharing common states over single cells can be grouped together, we introduce a new software called AMC (accurate mutation clustering) to accurately cluster mutations, thus improve the efficiency of phylogenetic inference. AMC first employs principal component analysis followed by K-means clustering to find mutation clusters, then infers the maximum likelihood estimates of the genotypes of each cluster. The inferred genotypes can subsequently be used to reconstruct the phylogenetic tree with high efficiency. Comprehensive evaluations on various simulated datasets demonstrate AMC is particularly useful to efficiently reason the mutation clusters on large scDNA-seq datasets.

Availability and implementation
AMC is freely available at https://github.com/qasimyu/amc.

Supplementary information
Supplementary data are available at Bioinformatics online.
Risk-dependent centrality in the Brazilian stock market
Authors: Alexandre Michel , De Moraes Kauê L , Rodrigues Francisco A 
Published: December 2021

Abstract
The purpose of this article is to calculate the risk-dependent centrality (RDC) assessing the Brazilian stock market. We computed the RDC for assets traded on the Brazilian stock market between January 2008 and June 2020 at different levels of external risk. We observed that the ranking of assets based on the RDC depends on the external risk. Rankings’ volatility is related to crisis events, capturing the recent Brazilian economic-political crisis. Moreover, we computed the RDC employing an empirically computed external risk level, relying on the Emerging Markets Bond Index index. We show that some economic sectors (oil, gas and biofuels and financial) become more central during crisis periods. Moreover, the volatility of the RDC is positively correlated with the external risk level.
When Should International Courts Intervene? How Populism, Democratic Decay and Crisis of Liberal Internationalism Complicate Things
Authors: Petrov Jan 
Published: December 2021

Abstract
Shai Dothan’s book International Judicial Review aims to refute criticism which stresses international courts’ (ICs) lack of legitimacy, epistemic inferiority, suffocation of public deliberation, susceptibility to capture and production of bad outcomes. This essay argues, however, that there is an important line of criticism of ICs stemming from a profounder disagreement with the post-Cold War international legal system – the critique related to ethno-national and/or authoritarian populism – which poses novel challenges to justifying ICs. Engaging with Dothan’s arguments through the prism of the populist backlash, this essay contributes to recent scholarship on populism and international law by explaining how populism challenges the justification of IC interventions. Populists treat majority will and national/regional identity as the exclusive sources of the common good, and this casts doubts on arguments favouring multilateralism, such as the Condorcet Jury Theorem used by Dothan. It also allows populists to re-frame IC interventions as threats to people’s well-being and disseminate ‘counter-myths’ delegitimizing ICs, which may impair ICs’ ability to produce good outcomes. Altogether, populism has the capacity to increase the costs of international judicial intervention for ICs and reduce the costs of non-compliance and exit for the populists, which confronts IC scholars and judges with new challenges.
A high-quality genome and comparison of short- versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck)
Authors: Mueller Ralf C , Ellström Patrik , Howe Kerstin , Uliano-Silva Marcela , Kuo Richard I , Miedzinska Katarzyna , Warr Amanda , Fedrigo Olivier , Haase Bettina , Mountcastle Jacquelyn , Chow William , Torrance James , Wood Jonathan M D , Järhult Josef D , Naguib Mahmoud M , Olsen Björn , Jarvis Erich D , Smith Jacqueline , Eöry Lél , Kraus Robert H S 
Published: December 2021

Abstract

Background
The tufted duck is a non-model organism that experiences high mortality in highly pathogenic avian influenza outbreaks. It belongs to the same bird family (Anatidae) as the mallard, one of the best-studied natural hosts of low-pathogenic avian influenza viruses. Studies in non-model bird species are crucial to disentangle the role of the host response in avian influenza virus infection in the natural reservoir. Such endeavour requires a high-quality genome assembly and transcriptome.

Findings
This study presents the first high-quality, chromosome-level reference genome assembly of the tufted duck using the Vertebrate Genomes Project pipeline. We sequenced RNA (complementary DNA) from brain, ileum, lung, ovary, spleen, and testis using Illumina short-read and Pacific Biosciences long-read sequencing platforms, which were used for annotation. We found 34 autosomes plus Z and W sex chromosomes in the curated genome assembly, with 99.6% of the sequence assigned to chromosomes. Functional annotation revealed 14,099 protein-coding genes that generate 111,934 transcripts, which implies a mean of 7.9 isoforms per gene. We also identified 246 small RNA families.

Conclusions
This annotated genome contributes to continuing research into the host response in avian influenza virus infections in a natural reservoir. Our findings from a comparison between short-read and long-read reference transcriptomics contribute to a deeper understanding of these competing options. In this study, both technologies complemented each other. We expect this annotation to be a foundation for further comparative and evolutionary genomic studies, including many waterfowl relatives with differing susceptibilities to avian influenza viruses.
Validation of existing risk scores for mortality prediction after a heart transplant in a Chinese population
Authors: Zheng Shanshan , Tang Hanwei , Zheng Zhe , Song Yunhu , Huang Jie , Liao Zhongkai , Liu Sheng 
Published: December 2021

Abstract

OBJECTIVES
The objectives of this study were to validate 3 existing heart transplant risk scores with a single-centre cohort in China and evaluate the efficacy of the 3 systems in predicting mortality.

METHODS
We retrospectively studied 428 patients from a single centre who underwent heart transplants from January 2015 to December 2019. All patients were scored using the Index for Mortality Prediction After Cardiac Transplantation (IMPACT) and the United Network for Organ Sharing (UNOS) and risk stratification scores (RSSs). We assessed the efficacy of the risk scores by comparing the observed and the predicted 1-year mortality. Binary logistic regression was used to evaluate the predictive accuracy of the 3 risk scores. Model discrimination was assessed by measuring the area under the receiver operating curves. Kaplan–Meier survival analyses were performed after the patients were divided into different risk groups.

RESULTS
Based on our cohort, the observed mortality was 6.54%, whereas the predicted mortality of the IMPACT and UNOS scores and the RSSs was 10.59%, 10.74% and 12.89%, respectively. Logistic regression analysis showed that the IMPACT [odds ratio (OR), 1.25; 95% confidence interval (CI), 1.15–1.36; P &lt; 0.001], UNOS (OR, 1.68; 95% CI, 1.37–2.07; P &lt; 0.001) and risk stratification (OR, 1.61; 95% CI, 1.30–2.00; P &lt; 0.001) scores were predictive of 1-year mortality. The discriminative power was numerically higher for the IMPACT score [area under the curve (AUC) of 0.691)] than for the UNOS score (AUC 0.685) and the RSS (AUC 0.648).

CONCLUSIONS
We validated the IMPACT and UNOS scores and the RSSs as predictors of 1-year mortality after a heart transplant, but all 3 risk scores had unsatisfactory discriminative powers that overestimated the observed mortality for the Chinese cohort.
Seven mysteries of LAG-3: a multi-faceted immune receptor of increasing complexity
Authors: Burnell Stephanie E A , Capitani Lorenzo , MacLachlan Bruce J , Mason Georgina H , Gallimore Awen M , Godkin Andrew 
Published: December 2021

Abstract
Despite three decades of research to its name and increasing interest in immunotherapies that target it, LAG-3 remains an elusive co-inhibitory receptor in comparison to the well-established PD-1 and CTLA-4. As such, LAG-3 targeting therapies have yet to achieve the clinical success of therapies targeting other checkpoints. This could, in part, be attributed to the many unanswered questions that remain regarding LAG-3 biology. Of these, we address: (i) the function of the many LAG-3-ligand interactions, (ii) the hurdles that remain to acquire a high-resolution structure of LAG-3, (iii) the under-studied LAG-3 signal transduction mechanism, (iv) the elusive soluble form of LAG-3, (v) the implications of the lack of (significant) phenotype of LAG-3 knockout mice, (vi) the reports of LAG-3 expression on the epithelium, and (vii) the conflicting reports of LAG-3 expression (and potential contributions to pathology) in the brain. These mysteries which surround LAG-3 highlight how the ever-evolving study of its biology continues to reveal ever-increasing complexity in its role as an immune receptor. Importantly, answering the questions which shroud LAG-3 in mystery will allow the maximum therapeutic benefit of LAG-3 targeting immunotherapies in cancer, autoimmunity and beyond.
Foreign Aid, Development, and US Strategic Interests in the Cold War
Authors: Lee James 
Published: December 2021

AbstractScholars have argued that during the Cold War, the United States gave aid to its allies to reward them for maintaining an anti-Communist foreign policy rather than to promote their economic development. This finding is mostly based on data starting in the 1970s and does not accurately characterize US grand strategy before the 1970s, when the United States used aid to promote development among its allies in order to strengthen them against Communism. Using original data collected from historical editions of USAID's “Greenbook,” this article identifies the amount of unconditional aid in the United States’ foreign-aid programs in the period 1955–1970. This type of aid was designed to be politically attractive rather than to be developmentally effective. This article also develops an original measure of aid recipients’ geopolitical alignment that draws on hand coding of 466 diplomatic documents. Using these data, this article finds that there was more unconditional aid in the United States’ aid programs to neutral and nonaligned countries than in the United States’ aid programs to its allies and security partners—a counterintuitive finding that shows how different the first half of the Cold War was from the second.1
Toxicity and Repellency of Magnolia grandiflora Seed Essential Oil and Selected Pure Compounds Against the Workers of Hybrid Imported Fire Ants (Hymenoptera: Formicidae)
Authors: Ali Abbas , Chen Jian , Khan Ikhlas A 
Published: December 2021

Abstract
We tested Magnolia grandiflora L. (Magnoliales: Magnoliaceae) seed essential oil and its pure compounds for their repellency and toxicity against workers of hybrid imported fire ants. Series of dosages were tested starting from 156 µg/g to the dose where the treatment failed. Workers removed significantly less sand from the vials with M. grandiflora seed essential oil and 1-octanol treated sand at serial dosages of 156–4.9 µg/g than the solvent control whereas the amount removed at 2.4–0.6 µg/g was similar to the solvent control. In 1-decanol treatments, workers removed significantly less sand at serial dosages of 156–0.15 µg/g than the solvent control whereas the removal of sand at the dose of 0.08 µg/g was similar to the solvent control. In DEET (N, N-diethyl-meta-toluamide) treatments, workers removed significantly less sand at serial dosages of 156–78 µg/g than the solvent control whereas the quantity of removed sand at 39 µg/g was similar to the solvent control. Based on the mean amount of sand removed, M. grandiflora essential oil, 1-decanol, and 1-octanol showed significantly higher repellency than DEET. 1-Decanol and 1-octanol, present in seed essential oil showed toxicity against fire ant workers. 1-Decanol with LC50 of 140.6 µg/g was the most toxic natural compound followed by 1-octanol (LC50 = 486.8 µg/g). Bifenthrin with LC50 value of 0.018 µg/g showed much higher toxicity than these natural compounds. High repellency and toxicity of 1-decanol makes it a natural compound of interest for further studies under field conditions.
Spatiotemporal patterns of riparian bat assemblages in a novel riparian ecosystem
Authors: Lin Jessica , Harris Leila S , Truan Melanie L , Engilis Andrew , Kelt Douglas A 
Published: December 2021

AbstractDespite increasing awareness of the ecological roles and ecosystem services that bats provide, spatiotemporal patterns in bat abundance and community assembly remain poorly understood outside of select sites in the tropics. We conducted systematic full-spectrum acoustic surveys of bats over the course of a year at eight permanent sites spanning nearly 50 km along Putah Creek, a stream in California’s Central Valley that has been subject to restoration efforts and changes to its in-stream flow regime over the past two decades. We surveyed all sites for 1 week each month. In 158 sampling nights over 11 months, we recorded 157,762 identifiable calls, thereby documenting a rich bat assemblage comprising 15 species from eight genera and two families. Seven species appeared to occur here year-round, whereas six others evidently migrated seasonally, and two were incidental visitors. Species richness and activity diversity were effectively invariant across this 50-km gradient, but assemblage composition varied both spatially and temporally. Spatial patterns suggest species-specific distributions that presumably reflect individualistic habitat preferences and responses to extrinsic factors. Species also varied temporally, with bat activity generally declining in winter, with an unexpected dip in richness and activity in late spring. For the three most commonly detected species, generalized linear models further highlighted the species-specific and individualistic nature of spatiotemporal activity patterns. When integrated with available data from other temperate sites, our results suggest that local species richness is high in temperate riparian systems. Additionally, our observations suggest that species responses to environmental variation are individualistic (e.g., “Gleasonian”) in nature and that local composition varies greatly over spatiotemporal gradients, but that emergent assemblage characteristics do not. The generality of these observations, and the underlying mechanism(s) leading to invariance in emergent characters, warrant further investigation. Similarly, the extent to which greater bat species richness provides complementary ecosystem services (hence, ecological insurance) is of both ecological and economic interest.
Salutogenic and Pathogenic Factors Among Young Adult Refugees in Germany: An Exploratory Study
Authors: Laufer Avital , Böttche Maria , Walg Marco , Khatib Anwar , Maoz-Dotan Carmel , Hassan Hiam , Finkelstein Michal 
Published: December 2021

Abstract
In this cross-sectional study, we explored the association of salutogenic variables—resilience and quality of life (QOL)—with posttraumatic stress (PTS) and depressive symptoms of 55 refugees who came to Germany as minors from various disputed Middle East and Africa countries. Results revealed that 53 per cent of participants showed a clinically relevant level of PTS, and 32 per cent scored in the clinical range for depression. Levels of resilience and QOL were moderate. Regression models revealed that resilience was the only significant variable associated with PTS over and above traumatic events and demographic variables. Pre-migration traumatic events and QOL were found to be significant variables associated with depression. Quality of life was found to mediate the relation between resilience and depression. Pre- and peri-traumatic events were not associated with resilience or QOL. Post-migration stressors were negatively associated with resilience and QOL. These findings suggest that the impact of forced migration on the young adults’ adjustment should be investigated not only in terms of psychological symptoms, but also in terms of resilience and QOL. In addition, therapeutic interventions should focus not only on diminishing psychological difficulties, but also in helping these young refugees increase, build, and maintain resilience and QOL.
Diffuse proliferative cerebral angiopathy: a case report and literature review on a very rare and misdiagnosed entity
Authors: Panthi Sagar , Khanal Nimesh , Poudel Sajana , Bhandari Siddhartha , Khatiwada Pradeep , Acharya Rochana , Bhattarai Raksha , Bhattarai Bharosha , Khanal Sandeep 
Published: December 2021

AbstractDiffuse proliferative cerebral angiopathy (DPCA) is an uncommon type of cerebral vascular malformation, mostly diagnosed in young females. It is characteristically different from other cerebral arteriovenous malformations and can be differentiated by its peculiar imaging findings. A nidus of normal brain parenchyma is present between the abnormal vascular channels. Therefore, it is crucial to diagnose it as a separate entity because unnecessary treatment of DPCA increases the risk of damage to the normal parenchyma leading to neurological deficits. Here we describe a case of a 60-year-old male who presented with severe neurological deficits and was later diagnosed with DPCA. He was managed conservatively with antiepileptics and almost completely recovered to normal within 2 weeks. A rare case of DPCA confused with other hemorrhagic disorders is discussed here. Rare cases are often overlooked. Correct diagnosis helps to prevent tragic consequences.
Adapting Nearest Neighbor for Multiple Imputation: Advantages, Challenges, and Drawbacks
Authors: Andridge Rebecca Roberts , Thompson Katherine Jenny 
Published: December 2021

AbstractThe U.S. Census Bureau has historically used nearest neighbor (NN) or random hot deck (RHD) imputation to handle missing data for many types of survey data. Using these methods removes the need to parametrically model values in imputation models. With strong auxiliary information, NN imputation is preferred because it produces more precise estimates than RHD. In addition, NN imputation is robust against a misspecified response mechanism if missingness depends on the auxiliary variable, in contrast to RHD which ignores the auxiliary information. A compromise between these two methods is k-NN imputation, which identifies a set of the k closest neighbors (“donor pool”) and randomly selects a single donor from this set. Recently these methods have been used for multiple imputation (MI), enabling variance estimation via the so-called Rubin’s Combining Rules. The Approximate Bayesian Bootstrap (ABB) is a simple-to-implement algorithm that makes the RHD “proper” for MI. In concept, ABB should work to propagate uncertainty for NN MI; bootstrapping respondents mean each nonrespondent’s one “nearest” donor will not be available for every imputation. However, we demonstrate through simulation that NN MI using ABB leads to variance underestimation. This underestimation is somewhat but not entirely attenuated with k-NN imputation. An alternative approach to variance estimation after MI, bootstrapped MI, eliminates the underestimation with NN imputation, but we show that it suffers from overestimation of variance with nonnegligible sampling fractions under both equal and unequal probability sampling designs. We propose a modification to bootstrapped MI to account for nonnegligible sampling fractions. We compare the performance of RHD and the various NN MI methods under a variety of sampling designs, sampling fractions, distribution shapes, and missingness mechanisms.
The National Quality Framework: The Benchmark for the Alcohol and Other Drug Sector in Australia
Authors: Henriksen Simone M 
Published: December 2021

Abstract
A National Quality Framework, developed by the Australian Government Department of Health, currently in a transitional phase, has been introduced to improve the quality of alcohol and other drug treatment services and provide a nationally consistent approach to treatment quality in the sector in Australia. This article examines how the National Quality Framework aims to achieve these goals. The article draws on the theory of quality frameworks to demonstrate how quality of treatment services may be improved under the National Quality Framework. The most difficult challenge for the National Quality Framework will be to deliver a nationally consistent approach to improving quality under the current structural arrangements for monitoring and enforcement of the framework.
Transcription factor GTF2B regulates AIP protein expression in growth hormone-secreting pituitary adenomas and influences tumor phenotypes
Authors: Cai Feng , Chen Shasha , Yu Xuebin , Zhang Jing , Liang Weiwei , Zhang Yan , Chen Yike , Chen Sheng , Hong Yuan , Yan Wei , Wang Wei , Zhang Jianmin , Wu Qun 
Published: December 2021

Abstract

Background
Clinically, the low expression of wild-type aryl hydrocarbon receptor-interacting protein (AIP) in patients with sporadic growth hormone (GH)-secreting pituitary adenoma (GHPA) is associated with a more aggressive phenotype. However, the mechanism by which AIP expression is regulated in GHPA remains unclear. Herein, we investigated a transcription factor that regulates AIP expression and explored its role in tumor phenotypes.

Methods
General transcription factor IIB (GTF2B) was predicted by several bioinformatic tools to regulate AIP expression transcriptionally. Regulation by GTF2B was evaluated using chromatin immunoprecipitation (ChIP), reverse transcription PCR, luciferase reporter, and western blot experiments in SH-SY5Y cells. Furthermore, the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) assay, transwell invasive assay, ELISA, western blot, immunohistochemical staining, and terminal deoxynucleotidyl transferase dUTP nick end labeling were performed to investigate the effects of GTF2B and AIP on tumor cell proliferation, apoptosis, growth hormone secretion, and invasiveness in GH3 cells and mouse xenograft models. Moreover, correlations between GTF2B and AIP expression were explored in GHPA cases.

Results
ChIP and luciferase reporter studies demonstrated that the regulation of AIP expression by GTF2B was dependent on the intergenic-5′ untranslated region element of AIP and the initial residual S65 of GTF2B. In vitro and in vivo experiments indicated that GTF2B regulated AIP expression to impact the GHPA phenotype; this was confirmed by data from 33 GHPA cases.

Conclusions
We determined the regulation by GTF2B of AIP transcription in GHPA and its impact on tumor phenotype. Our findings suggest that GTF2B may be a potential therapeutic target for GHPA with low AIP expression.