bluuebunny/crossref_metadata_2025_split huggingface dataset:
NeuroCirc: an integrative resource of circular RNA expression in the human brain
Authors: Walsh Kieran , Gokool Akira , Alinejad-Rokny Hamid , Voineagu Irina 
Published: May 2021

Abstract

Motivation
CircRNAs are covalently closed RNA molecules that are particularly abundant in the brain. While circRNA expression data from the human brain is rapidly accumulating, integration of large-scale datasets remains challenging and time-consuming, and consequently an integrative view of circRNA expression in the human brain is currently lacking.

Results
NeuroCirc is a web-based resource that allows interactive exploration of multiple types of circRNA data from the human brain, including large-scale expression datasets, circQTL data and circRNA expression across neuronal differentiation and cellular maturation time-courses. NeuroCirc also allows users to upload their own circRNA expression data and explore it in the integrative platform, thereby supporting circRNA prioritization for experimental validation and functional studies.

Availability and implementation
NeuroCirc is freely available at: https://voineagulab.github.io/NeuroCirc/. The source code and user documentation are available at: https://github.com/Voineagulab/NeuroCirc.

Supplementary information
Supplementary data are available at Bioinformatics online.
Interfacing Seurat with the R tidy universe
Authors: Mangiola Stefano , Doyle Maria A , Papenfuss Anthony T 
Published: May 2021

Abstract

Motivation
Seurat is one of the most popular software suites for the analysis of single-cell RNA sequencing data. Considering the popularity of the tidyverse ecosystem, which offers a large set of data display, query, manipulation, integration and visualization utilities, a great opportunity exists to interface the Seurat object with the tidyverse. This interface gives the large data science community of tidyverse users the possibility to operate with familiar grammar.

Results
To provide Seurat with a tidyverse-oriented interface without compromising efficiency, we developed tidyseurat, a lightweight adapter to the tidyverse. Tidyseurat displays cell information as a tibble abstraction, allowing intuitively interfacing Seurat with dplyr, tidyr, ggplot2 and plotly packages powering efficient data manipulation, integration and visualization. Iterative analyses on data subsets are enabled by interfacing with the popular nest-map framework.

Availability and implementation
The software is freely available at cran.r-project.org/web/packages/tidyseurat and github.com/stemangiola/tidyseurat.

Supplementary information
Supplementary data are available at Bioinformatics online.
Still New Chronic Q Fever Cases Diagnosed 8 Years After a Large Q Fever Outbreak
Authors: Buijs Sheila B , Bleeker-Rovers Chantal P , van Roeden Sonja E , Kampschreur Linda M , Hoepelman Andy I M , Wever Peter C , Oosterheert Jan Jelrik 
Published: May 2021

Abstract

Background
Chronic Q fever usually develops within 2 years after primary infection with Coxiella burnetii. We determined the interval between acute Q fever and diagnosis of chronic infection, assessed what factors contribute to a longer interval, and evaluated the long-term follow-up.

Methods
From 2007 to 2018, patients with chronic Q fever were included from 45 participating hospitals. The interval between acute and chronic infection was calculated in patients with a known day of first symptoms and/or serological confirmation of acute Q fever. Chronic Q fever-related complications and mortality were assessed by 2 investigators based on predefined criteria.

Results
In total, 313 (60.3%) proven, 81 (15.6%) probable, and 125 (24.1%) possible chronic Q fever patients were identified. The date of acute Q fever was known in 200 patients: in 45 (22.5%), the interval was longer than 2 years, with the longest observed interval being 9.2 years. Patients in whom serological follow-up was performed after acute Q fever were diagnosed less often after this 2-year interval (odds ratio, 0.26; 95% confidence interval, 0.12–0.54). Chronic Q fever-related complications occurred in 216 patients (41.6%). Chronic Q fever-related mortality occurred in 83 (26.5%) of proven and 3 (3.7%) of probable chronic Q fever patients.

Conclusions
Chronic Q fever is still being diagnosed and mortality keeps occurring 8 years after a large outbreak. Intervals between acute Q fever and diagnosis of chronic infection can reach more than 9 years. We urge physicians to perform microbiological testing for chronic Q fever even many years after an outbreak or acute Q fever disease.
The Humanization of Jus ad Bellum: Prospects and Perils
Authors: Lieblich Eliav 
Published: May 2021

Abstract
In its recent General Comment no. 36 (GC 36), the Human Rights Committee (HRC) engaged for the first time, in a substantial manner, with the relations between the law on the use of force (jus ad bellum) and the right to life. This article uses the HRC’s position on these relations as a platform for a long-needed discussion on the theoretical underpinnings, and implications, of a possible human rights law on the resort to force between states. This article identifies and conceptualizes three pillars in GC 36’s position, which subject traditional questions of jus ad bellum to international human rights law considerations: first, the view that aggression is not only a violation of jus ad bellum but also that the killings it entails are ipso facto violations of the right to life, even in cases where these killings would be lawful under the laws of armed conflict (jus in bello); second, that states bear the ‘responsibility’ to oppose aggression as a matter of human rights; and, third, that a state’s failure to reasonably attempt to resolve disputes peacefully could amount to a violation of the duty to ensure the right to life of its people. The article analyses these pillars doctrinally and then moves to discuss the theoretical commitments required to accept each of them as well as their costs. Namely, they all require breaking with the traditional view that jus ad bellum is strictly an interstate issue. Although, as the article argues, this development is based on sound ethical premises, the humanization of jus ad bellum through human rights law carries risks that should not be overlooked: chiefly, the securitization of human rights and the depoliticization of war. The prospects and perils of the humanization of jus ad bellum, as this article demonstrates, open a new area of theoretical inquiry and legal possibilities.
The impact of orthognathic surgery on quality of life in individuals with oral clefts
Authors: Feitosa Mariana Chaves Petri , Garib Daniela , de Cássia Moura Carvalho Lauris Rita , Herkrath Ana Paula Queiroz , Vettore Mario Vianna 
Published: May 2021

Summary

Background/objectives
To evaluate the relationships between individual, environmental, clinical factors and oral health-related quality of life (OHRQoL) in patients with cleft lip and palate (CLP) following orthognathic surgery.

Materials and methods
A follow-up study was conducted involving 69 adults with unilateral and bilateral CLP under orthodontic treatment. Interviews and oral examinations were conducted prior to orthognathic surgery (T0) to evaluate age, gender, psychological well-being, dental caries, malocclusion, social support, social networks, family income and education and OHRQoL. All participants were reviewed after 6 months (T1) to re-assess psychological well-being, malocclusion and OHRQoL. Structural equation modeling estimated the associations between the variables.

Results
OHRQoL total scores reduced following orthognathic surgery, from 11.7 to 6.9 (P &lt; 0.01). Occlusal characteristics and psychological well-being improved between T0 and T1. In the structural equation modeling, reduction of malocclusion (β = 0.02) between T0 and T1 directly predicted poor OHRQoL at T1. Improvement of psychological well-being between T0 and T1 was associated with better OHRQoL at T1 (β = −0.07). Dental caries and malocclusion at T0 were indirectly linked to poor OHRQoL at T1 (β = 0.02).

Limitations
The short follow-up period of 6 months after orthognathic surgery.

Conclusions/implications
This represents the first prospective study examining the interrelationships of predictors of OHRQoL in patients with CLP after orthognathic surgery. OHRQoL and psychological well-being improved after orthognathic surgery. Clinical and psychological characteristics were important determinants of OHRQoL. These findings suggest the importance of the biopsychosocial model of health and the patient-centered approach in oral health care in individuals with CLP.
Birds of a Feather, Do Sanctioned States Flock Together?
Authors: Early Bryan R 
Published: May 2021

Abstract
Despite several high-profile cases of cooperation between sanctioned states, little is understood about how being sanctioned affects target states’ incentives to cooperate with one another and what forms that cooperation might take. I theorize that sanctioned states will tend to seek out sanctions-surviving assistance from nonsanctioned states in most cases. Being sanctioned constrains how much useful assistance that sanctioned states can provide to one another, as they suffer from similar trade constraints, levels of economic turmoil, and governmental resource limitations. I test my theory's predictions that sanctioned states are less likely to cooperate with one another via two different large-n tests involving cooperation via engaging in trade-based sanctions-busting and civil nuclear cooperation. Both of these distinct tests provide strong support for my theory. The final portion of the study conducts an exploratory analysis of why sanctioned states still sometimes cooperate with one another, finding that such cooperation may involve risky or taboo transactions, like arms sales, and that sanctioned parties have incentives to keep their cooperation a secret in such cases. These findings improve our understanding of the various cooperative strategies that states employ to survive sanctions.
Going Nativist: How Nativism and Economic Ideology Interact to Shape Beliefs about Global Trade
Authors: Powers Kathleen E , Reifler Jason , Scotto Thomas J 
Published: May 2021

AbstractExisting research explains variation in trade attitudes by pitting explanations rooted in the foreign part of foreign economic policy, like nativism, against economic beliefs like a commitment to free market principles. But what happens when these factors create significant cross-pressures—how do free market-oriented nativists think about trade? We argue that nativism is a higher-order belief that constrains the relationship between lower-order economic attitudes and beliefs about international trade. We test our argument using representative samples from the United States and United Kingdom. First, we analyze observational data and find a significant interaction whereby nativism moderates the relationship between free market attitudes and beliefs that trade provides national and global benefits. Second, we report results from a survey experiment to show that a message about the long-term benefits from free trade increases support for free trade in both samples. Importantly, we also find that nativist values weaken the treatment effect in the US sample. As long as international relations scholars focus on cultural or economic antecedents on their own, we miss much about how elements in belief systems interact.
Committed Moderates and Uncommitted Extremists: Ideological Leaning and Parties’ Narratives on Military Interventions in Italy
Authors: Curini Luigi , Vignoli Valerio 
Published: May 2021

AbstractCurrent research highlights that ideology decisively affects political contestation concerning peace and security operations in European countries. In particular, recent studies suggest that party preferences on this issue follow a curvilinear distribution along the left-right axis, delineating a conflict between moderate and extreme parties. However, the impact of this cleavage on the use of strategic narratives to either support or criticize these missions requires more attention. This article aims to fill this gap by employing seeded latent Dirichlet allocation, a semi-supervised automated text analysis method, to analyze parliamentary debates on Italy's most significant troop deployments between 1994 and 2013. We expect to find that while moderates express a supportive narrative aimed at justifying the use of force, extremists attempt to delegitimize military interventions. Accordingly, we hypothesize that moderate parties emphasize more on the multilateral and humanitarian framework of a mission, while extremist parties focus more on its military means. The empirical findings largely confirm our hypotheses. By means of its method and results, the article contributes both empirically and methodologically to the debate on the party politics of military interventions in Europe.
Our Tangled Family Tree: New Genomic Methods Offer Insight into the Legacy of Archaic Admixture
Authors: Ahlquist K D , Bañuelos Mayra M , Funk Alyssa , Lai Jiaying , Rong Stephen , Villanea Fernando A , Witt Kelsey E 
Published: May 2021

AbstractThe archaic ancestry present in the human genome has captured the imagination of both scientists and the wider public in recent years. This excitement is the result of new studies pushing the envelope of what we can learn from the archaic genetic information that has survived for over 50,000 years in the human genome. Here, we review the most recent ten years of literature on the topic of archaic introgression, including the current state of knowledge on Neanderthal and Denisovan introgression, as well as introgression from other as-yet unidentified archaic populations. We focus this review on four topics: 1) a reimagining of human demographic history, including evidence for multiple admixture events between modern humans, Neanderthals, Denisovans, and other archaic populations; 2) state-of-the-art methods for detecting archaic ancestry in population-level genomic data; 3) how these novel methods can detect archaic introgression in modern African populations; and 4) the functional consequences of archaic gene variants, including how those variants were co-opted into novel function in modern human populations. The goal of this review is to provide a simple-to-access reference for the relevant methods and novel data, which has changed our understanding of the relationship between our species and its siblings. This body of literature reveals the large degree to which the genetic legacy of these extinct hominins has been integrated into the human populations of today.
Sperm donation: an alternative to improve post-ICSI live birth rates in advanced maternal age patients
Authors: Mignini Renzini M , Dal Canto M , Guglielmo M C , Garcia D , De Ponti E , La Marca A , Vassena R , Buratini J 
Published: May 2021

Abstract

STUDY QUESTION
Can sperm donation increase live birth rates following ICSI in advanced maternal age (AMA) patients?

SUMMARY ANSWER
Sperm donation increases the live birth rate in AMA ICSI cycles.

WHAT IS KNOWN ALREADY
In ICSI practice, sperm donation has been predominantly applied to overcome male infertility. The involvement of paternal age and lower sperm quality in the severe reduction in fertility observed in AMA patients remains to be clarified.

STUDY DESIGN, SIZE, DURATION
Retrospective multicenter cohort study including data generated between 2015 and 2019 from 755 ICSI cycles achieving a fresh embryo transfer, of which 337 were first homologous cycles (normozoospermic partner sperm and homologous oocytes) and 418 were first sperm donation cycles (donor sperm and homologous oocytes). The association of sperm origin (partner vs donor) with live birth was assessed by multivariate analysis in non-AMA (&lt;37 years, n = 278) and AMA (≥37 years, n = 477) patients, separately, including in the model all variables previously found to be associated with live birth in a univariate analysis (number of MII oocytes recovered, number of embryos transferred, and maternal age). ICSI outcomes were compared between sperm donation and homologous cycles in overall, non-AMA and AMA patients.

PARTICIPANTS/MATERIALS, SETTING, METHODS
The study was conducted in three fertility clinics and included 755 Caucasian patients aged 24–42 years undergoing their first homologous or sperm donation ICSI cycle achieving a fresh embryo transfer.

MAIN RESULTS AND THE ROLE OF CHANCE
The multivariate analysis revealed that sperm donation was positively associated with the likelihood of a live birth independently of all other variables tested in AMA (P = 0.02), but not in non-AMA patients. Live birth, delivery, and miscarriage rates differed substantially between sperm donation and homologous AMA cycles; live birth and delivery rates were 70–75% higher (25.4% vs 14.5% and 22.5% vs 13.5%, respectively; P &lt; 0.01), while miscarriage occurrence was less than half (18.0% vs 39.5%; P &lt; 0.01) in sperm donation compared to homologous AMA cycles.

LIMITATIONS, REASONS FOR CAUTION
This study is limited by its retrospective nature, differences in patients profiles between sperm donation and homologous-control groups and varying proportion of donor cycles between fertility centers, although these variations have been controlled for in the statistical analysis.

WIDER IMPLICATIONS OF THE FINDINGS
The findings suggest that sperm donation increases live birth rates while reducing miscarriage occurrence in AMA patients, and thus may be a valid strategy to improve ICSI outcomes in this growing and challenging patient group.

STUDY FUNDING/COMPETING INTEREST(S)
N/A.

TRIAL REGISTRATION NUMBER
N/A.
Analysing different exposures identifies that wearing masks and establishing COVID-19 areas reduce secondary-attack risk in aged-care facilities
Authors: Reyné Bastien , Selinger Christian , Sofonea Mircea T , Miot Stéphanie , Pisoni Amandine , Tuaillon Edouard , Bousquet Jean , Blain Hubert , Alizon Samuel 
Published: May 2021

Abstract

Background
The COVID-19 epidemic has spread rapidly within aged-care facilities (ACFs), where the infection-fatality ratio is high. It is therefore urgent to evaluate the efficiency of infection prevention and control (IPC) measures in reducing SARS-CoV-2 transmission.

Methods
We analysed the COVID-19 outbreaks that took place between March and May 2020 in 12 ACFs using reverse transcription–polymerase chain reaction (RT–PCR) and serological tests for SARS-CoV-2 infection. Using maximum-likelihood approaches and generalized linear mixed models, we analysed the proportion of infected residents in ACFs and identified covariates associated with the proportion of infected residents.

Results
The secondary-attack risk was estimated at 4.1%, suggesting a high efficiency of the IPC measures implemented in the region. Mask wearing and the establishment of COVID-19 zones for infected residents were the two main covariates associated with lower secondary-attack risks.

Conclusions
Wearing masks and isolating potentially infected residents appear to be associated with a more limited spread of SARS-CoV-2 in ACFs.
The Presence or Absence of Symptoms Among Cases of Urethral Gonorrhoea Occurring in a Cohort of Men Taking Human Immunodeficiency Virus Pre-exposure Prophylaxis in the PrEPX Study
Authors: Donovan Lucy C , Fairley Christopher K , Aung Ei T , Traeger Michael W , Wright Edwina J , Stoové Mark A , Chow Eric P F 
Published: May 2021

Abstract
We aimed to estimate how often urethral gonorrhoea is symptomatic among men in the Pre-Exposure Prophylaxis Expanded Victoria study. Eighty-seven percent of 213 cases of urethral gonorrhoea were symptomatic. Ensuring men with urethral gonorrhoea both recognize and present early for treatment is critical to reduce transmission.
First Reported Case of Invasive Cutaneous Penicillium cluniae Infection in a Patient With Acute Myelogenous Leukemia: A Case Report and Literature Review
Authors: Mehta Devanshi , Hofacker Samuel A , Villalba Julian A , Duncan Lyn M , Branda John A , Cañete-Gibas Connie , Wiederhold Nathan , Moran Jenna , Fathi Amir T , Chen Steven T , Cervantes Jessica , Hammond Sarah P 
Published: May 2021

Abstract
Certain Penicillium species are emerging opportunistic pathogens. While these can be common causes of airborne contamination of clinical cultures, an increasing number of reports describe clinically significant disease in the immunocompromised population, particularly in patients with hematologic malignancy. The typical site of infection is respiratory, but disseminated infection is also reported with some frequency. Therefore, culture growth of Penicillium in respiratory and other clinical samples from immunocompromised patients requires thorough investigation with clinical correlation. Here we report a case of angioinvasive Penicillium cluniae infection of the right shin in a patient with acute myeloid leukemia and review reported cases of invasive Penicillium infection (excluding Talaromyces marneffei) in hematologic malignancy patients to characterize the emerging pathogen in this vulnerable population.
Infected Aneurysm of the Native Aorta due to Coccidioides posadasii
Authors: Huang Jeffrey , Cano Edison J , Shweta Fnu , Shah Aditya S , Schuetz Audrey N , Bois Melanie , Gurram Pooja R 
Published: May 2021

Abstract
Coccidioidomycosis is an endemic fungal infection that is typically asymptomatic or associated with pulmonary disease. Extrapulmonary disease may involve the skin, bones, or central nervous system, yet endovascular infections are exceedingly rare. We report the first case, to our knowledge, of coccidioidomycosis of the native aorta in an immunocompromised host.
Heterologous vaccination strategy for containing COVID-19 pandemic
Authors: Lin Ang , Liu JingJing , Ma Xiaopin , Zhao Fanfan , Yu Bo , He Jiaxin , Shen Mingyun , Huang Lei , Tang Hongming , Jiang Erpeng , Wang Yue , Cui Pingfang , Zhang Yujian , Yao Weiguo , Zhang Aihua , Wang Youchun , Li Yuhua , Huang Weijin , Li Qihan , Liu Zhongmin , Li Hangwen 
Published: May 2021

SummaryAn unequitable vaccine allocation and continuously emerging SARS-CoV-2 variants pose challenges to contain the pandemic, which underscores the need for licensing more vaccine candidates, increasing manufacturing capacity and implementing better immunization strategy. Here, we report data from a proof-of-concept investigation in two healthy individuals who received two doses of inactivated whole-virus COVID-19 vaccines, followed by a single heterologous boost vaccination after 7 months with an mRNA vaccine candidate (LPP-Spike-mRNA) developed by Stemirna Therapeutics. Following the boost, Spike-specific antibody (Ab), memory B cell and T cell responses were significantly increased. These findings indicate that a heterologous immunization strategy combining inactivated and mRNA vaccines can generate robust vaccine responses and therefore provide a rational and effective vaccination regimen.