bluuebunny/crossref_metadata_2025_split huggingface dataset:
Designing efficient randstrobes for sequence similarity analyses
Authors: Karami Moein , Soltani Mohammadi Aryan , Martin Marcel , Ekim Barış , Shen Wei , Guo Lidong , Xu Mengyang , Pibiri Giulio Ermanno , Patro Rob , Sahlin Kristoffer 
Published: April 2024

AbstractMotivationSubstrings of length k, commonly referred to as k-mers, play a vital role in sequence analysis. However, k-mers are limited to exact matches between sequences leading to alternative constructs. We recently introduced a class of new constructs, strobemers, that can match across substitutions and smaller insertions and deletions. Randstrobes, the most sensitive strobemer proposed in Sahlin (Effective sequence similarity detection with strobemers. Genome Res 2021a;31:2080–94. https://doi.org/10.1101/gr.275648.121), has been used in several bioinformatics applications such as read classification, short-read mapping, and read overlap detection. Recently, we showed that the more pseudo-random the behavior of the construction (measured in entropy), the more efficient the seeds for sequence similarity analysis. The level of pseudo-randomness depends on the construction operators, but no study has investigated the efficacy.ResultsIn this study, we introduce novel construction methods, including a Binary Search Tree-based approach that improves time complexity over previous methods. To our knowledge, we are also the first to address biases in construction and design three metrics for measuring bias. Our evaluation shows that our methods have favorable speed and sampling uniformity compared to existing approaches. Lastly, guided by our results, we change the seed construction in strobealign, a short-read mapper, and find that the results change substantially. We suggest combining the two results to improve strobealign’s accuracy for the shortest reads in our evaluated datasets. Our evaluation highlights sampling biases that can occur and provides guidance on which operators to use when implementing randstrobes.Availability and implementationAll methods and evaluation benchmarks are available in a public Github repository at https://github.com/Moein-Karami/RandStrobes. The scripts for running the strobealign analysis are found at https://github.com/NBISweden/strobealign-evaluation.
Practical causal mediation analysis: extending nonparametric estimators to accommodate multiple mediators and multiple intermediate confounders
Authors: Rudolph Kara E , Williams Nicholas T , Diaz Ivan 
Published: April 2024

Abstract
Mediation analysis is appealing for its ability to improve understanding of the mechanistic drivers of causal effects, but real-world data complexities challenge its successful implementation, including (i) the existence of post-exposure variables that also affect mediators and outcomes (thus, confounding the mediator-outcome relationship), that may also be (ii) multivariate, and (iii) the existence of multivariate mediators. All three challenges are present in the mediation analysis we consider here, where our goal is to estimate the indirect effects of receiving a Section 8 housing voucher as a young child on the risk of developing a psychiatric mood disorder in adolescence that operate through mediators related to neighborhood poverty, the school environment, and instability of the neighborhood and school environments, considered together and separately. Interventional direct and indirect effects (IDE/IIE) accommodate post-exposure variables that confound the mediator–outcome relationship, but currently, no readily implementable nonparametric estimator for IDE/IIE exists that allows for both multivariate mediators and multivariate post-exposure intermediate confounders. The absence of such an IDE/IIE estimator that can easily accommodate both multivariate mediators and post-exposure confounders represents a significant limitation for real-world analyses, because when considering each mediator subgroup separately, the remaining mediator subgroups (or a subset of them) become post-exposure intermediate confounders. We address this gap by extending a recently developed nonparametric estimator for the IDE/IIE to allow for easy incorporation of multivariate mediators and multivariate post-exposure confounders simultaneously. We apply the proposed estimation approach to our analysis, including walking through a strategy to account for other, possibly co-occurring intermediate variables when considering each mediator subgroup separately.
When the homo deamon went digital: writing Africa’s transgender refugee diaspora
Authors: Camminga B 
Published: April 2024

Abstract
From an online African lesbian, gay, bisexual, transgender and intersex (LGBTI) news and information website, launched in 2000, called Behind the Mask (BtM) to Sokari Ekine’s foundational 2004 blog Blacklooks, the digital has been crucial to queer African studies and, indeed, queer Africa. In this brief exploration, I navigate through the realms of queer African studies, African digital humanities, and African literary studies, using them as my guiding framework to uncover the digital emergence of an African transgender refugee diaspora. I suggest that this diaspora is producing content explicitly aimed back at the African continent to shape and deploy the reality of what it means to be transgender and African. In so doing, they are actively authoring themselves into existence.
Liveness Attacks On HotStuff: The Vulnerability Of Timer Doubling Mechanism
Authors: Guo Kaiwen , Hu Kexin , Zhang Zhenfeng 
Published: April 2024

Abstract
Byzantine fault-tolerant (BFT) consensus protocols are essential in distributed computing. Most partially synchronous BFT protocols proceed in views and rely on a view synchronizer module to guarantee liveness by synchronizing honest replicas to the same view. HotStuff is a leading BFT consensus protocol known for achieving linear view change and optimistic responsiveness. To achieve these desirable properties, HotStuff relies on a candidate solution for the view synchronizer based on a recomposed timer doubling mechanism. However, a formal analysis of this mechanism is currently lacking. This paper delves into HotStuff with the recomposed timer doubling mechanism. To facilitate accurate analysis, we introduce a new specification for the view synchronizer, incorporating two paths for view switching as in HotStuff’s setting. Surprisingly, we observe that the adversary can disrupt the view synchronization and launch a liveness attack, stalling the confirmation process. Besides, the adversary can further recover or control the confirmation process at will. A repairment that retains the desirable feature of HotStuff is also presented. We simulate the liveness attack and the repairment, demonstrating their effectiveness. Specifically, the liveness attack can cause HotStuff’s throughput to drop and remain at 0. When equipped with our repairment, HotStuff can resist the attack and retain the throughput performance.
Heterozygous gain of function variant in GUCY1A2 may cause autonomous ovarian hyperfunction
Authors: Wittrien Theresa , Ziegler Alban , Rühle Anne , Stomberg Svenja , Meyer Ruben , Bonneau Dominique , Rodien Patrice , Prunier-Mirebeau Delphine , Coutant Régis , Behrends Sönke 
Published: April 2024

Abstract

Purpose
The purpose of this study was to characterize the phenotype associated with a de novo gain-of-function variant in the GUCY1A2 gene.

Methods
An individual carrying the de novo heterozygous variant c.1458G&gt;T p.(E486D) in GUCY1A2 was identified by exome sequencing. The effect of the corresponding enzyme variant α2E486D/β1 was evaluated using concentration-response measurements with wild-type enzyme and the variant in cytosolic fractions of HEK293 cells, UV-vis absorbance spectra of the corresponding purified enzymes, and examination of overexpressed fluorescent protein-tagged constructs by confocal laser scanning microscopy.

Results
The patient presented with precocious peripheral puberty resembling the autonomous ovarian puberty seen in McCune-Albright syndrome. Additionally, the patient displayed severe intellectual disability. In vitro activity assays revealed an increased nitric oxide affinity for the mutant enzyme. The response to carbon monoxide was unchanged, while thermostability was decreased compared to wild type. Heme content, susceptibility to oxidation, and subcellular localization upon overexpression were unchanged.

Conclusion
Our data define a syndromic autonomous ovarian puberty likely due to the activating allele p.(E486D) in GUCY1A2 leading to an increase in cGMP. The overlap with the ovarian symptoms of McCune-Albright syndrome suggests an impact of this cGMP increase on the cAMP pathway in the ovary. Additional cases will be needed to ensure a causal link.
Coming of age: governance challenges in updated AMR national action plans in the EU
Authors: Carelli Daniel E , Ogne Josefin B , Pierre Jon 
Published: April 2024

Abstract

Background
National action plans (NAPs) are key instruments for governing antimicrobial resistance (AMR). In Europe, we can now observe many countries updating their NAPs which raise two key research questions; what substantial modifications are states opting for, and how do they wish to address challenges related to AMR governance in a comparative perspective?

Methods
Building on a previous analytical classification, we address these two questions by examining data of updated versions of NAPs in 13 European Union member states covering seventeen elements related to AMR governance.

Results
Our results substantiate the large variation with regard to both substantive issues and governance-related matters. Most tellingly, they highlight the growing importance of the One Health approach in updated versions of NAPs. Our analysis also shows that while substantive issues remain important, One Health and the coordination and collaboration issues it entails are becoming more salient in the second or third generation of NAPs.

Conclusions
Updated NAPs suggest that EU member states are becoming increasingly knowledgeable on the causes and consequences of AMR and how it needs to be addressed. The enhanced level of knowledge also leads these countries to address the next set of issues and challenges; to improve domestic and international coordination and collaboration. Thus, the revised NAPs present a noticeable development from substantive issues towards governance issues.
Microbial community structures and bacteria-Cylindrospermopsis raciborskii interactions in Yilong Lake
Authors: Jin Yuanpei , Ren Sanguo , Wu Yichi , Zhang Xu , Chen Zhengjun , Xie Bo 
Published: April 2024

Abstract
Cylindrospermopsis raciborskii-dominated harmful algae blooms have been reported globally in recent years. However, our understanding of the ecology of C. raciborskii in natural conditions is still poor. In this study, we collected the water samples from a C. raciborskii-blooming lake, Yilong Lake, in Yunnan province, China, and used both culture-dependent and culture-independent approaches to investigate their microbial communities and the interactions between C. raciborskii and the other bacteria. The composition and diversity of microbial communities were revealed with 16S rRNA gene high-throughput sequencing data analysis. Microbial co-occurrences analysis suggests C. raciborskii may have complex associations with other bacteria. Based on co-inoculation tests, we obtained 14 strains of bacterial strains from the water samples that exhibited either algicidal or promoting effects on a strain of C. raciborskii. Two bacterial isolates exhibited a consistent performance between co-occurrence analysis and experimental results. Effects of these bacteria-algae interspecies interactions on the bloom event are discussed. All these results may provide new insights into the C. raciborskii-dominated blooms and how its interspecies relationships with other bacteria may influence the bloom events in eutrophic waters throughout the world.
Reconquest, Reconstruction, Resumption: Churching Poland after the Second World War
Authors: Bjork James 
Published: April 2024

Abstract
This article examines how the Roman Catholic Church in Poland navigated the enormous increase in church buildings at its disposal at the end of the Second World War. This expansion was largely due to the mass acquisition of post-German churches in lands transferred from Germany to Poland. But rapid reconstruction of most of the churches destroyed during the war as well as the resumption of new construction also played a role. Although access to increased worship space might seem to have been a boon for Poland’s postwar Catholic Church, the appropriation, reconstruction and completion of thousands of church buildings presented the church with an array of challenges. Refounding local Polish religious life in post-German, and often post-Protestant, houses of worship raised difficult questions about how various constituencies in newly formed communities could be made to feel at home in their new surroundings. Trade-offs between the expectations and customs of divergent groups were exacerbated by the prominence within the postwar church of Catholics who were themselves post-German, having spent the war categorized as German before being recategorized as Polish after 1945. Close attention to how Polish Catholics encountered new sacred spaces and one another reveals the complex negotiations and balancing acts required to form an ostensibly homogeneous religious-national community.
The effects of immortalization on the N-glycome and proteome of CDK4-transformed lung cancer cells
Authors: Alvarez Michael Russelle S , Moreno Patrick Gabriel , Grijaldo-Alvarez Sheryl Joyce B , Yadlapati Anirudh , Zhou Qingwen , Narciso Michelle P , Completo Gladys Cherisse , Nacario Ruel C , Rabajante Jomar F , Heralde Francisco M , Lebrilla Carlito B 
Published: April 2024

Abstract
Biological experiments are often conducted in vitro using immortalized cells due to their accessibility and ease of propagation compared to primary cells and live animals. However, immortalized cells may present different proteomic and glycoproteomic characteristics from the primary cell source due to the introduction of genes that enhance proliferation (e.g. CDK4) or enable telomere lengthening. To demonstrate the changes in phenotype upon CDK4-transformation, we performed LC-MS/MS glycomic and proteomic characterizations of a human lung cancer primary cell line (DTW75) and a CDK4-transformed cell line (GL01) derived from DTW75. We observed that the primary and CDK4-transformed cells expressed significantly different levels of sialylated, fucosylated, and sialofucosylated N-glycans. Specifically, the primary cells expressed higher levels of hybrid- and complex-type sialylated N-glycans, while CDK4-transformed cells expressed higher levels of complex-type fucosylated and sialofucosylated N-glycans. Further, we compared the proteomic differences between the cell lines and found that CDK4-transformed cells expressed higher levels of RNA-binding and adhesion proteins. Further, we observed that the CDK4-transformed cells changed N-glycosylation after 31 days in cell culture, with a decrease in high-mannose and increase in fucosylated, sialylated, and sialofucosylated N-glycans. Identifying these changes between primary and CDK4-transformed cells will provide useful insight when adapting cell lines that more closely resemble in vivo physiological conditions.
Durability of the First Biologic in Children and Adults With Ulcerative Colitis: A Nationwide Study from the epi-IIRN
Authors: Atia Ohad , Friss Chagit , Focht Gili , Magen Rimon Ramit , Ledderman Natan , Greenfeld Shira , Ben-Tov Amir , Loewenberg Weisband Yiska , Matz Eran , Gorelik Yuri , Chowers Yehuda , Dotan Iris , Turner Dan 
Published: April 2024

Abstract

Background
In this nationwide study, our objective was to compare the durability of first-line biologics in ulcerative colitis (UC), categorized into monotherapy and combotherapy with immunomodulators.

Methods
We utilized data from the nationwide epi-IIRN cohort from 2005 to 2020. Durability was defined as consistent treatment without surgery. Comparisons were based on stringent propensity score-matching.

Results
We included 15 111 patients with UC, of whom 2322 (15%) received biologics, with a median follow-up of 7.0 years (interquartile range, 3.8-11.0). The durability rate was similar between pediatric-onset and adults after 1 and 5 years from initiation of treatment (72% and 43% vs 71% and 43%, respectively; P = .8). Durability of adalimumab vs infliximab after 1 or 5 years was similar, whether prescribed as monotherapy (65%/46% vs 63%/33%, respectively; n = 182 matched pairs, P = .3) or combotherapy (78%/56% vs 91%/58%, respectively; n = 46 matched pairs, P = .4). Durability of infliximab was higher as combotherapy (85%/50%) vs monotherapy (69%/42%; n = 174 matched pairs, P = .007), while it was similar for adalimumab (80%/52% vs 74%/52%; n = 53 matched pairs, P = .4). The durability rate was similar for vedolizumab monotherapy (77%/56%) compared with adalimumab monotherapy (69%/52%; n = 125 matched patients, P = .1), and infliximab monotherapy (73%/55% vs 62%/44%; n = 78 matched patients, P = .1). However, combotherapy of antitumor necrosis factors (TNFs) had longer durability than vedolizumab (85%/50% vs 75%/43%, respectively; n = 131 matched pairs, P = .02).

Conclusion
After 5 years of treatment, 43% of the patients with UC sustained their first biologic, with similar durability in pediatric and adult-onset onset disease. Anti-TNFs had similar durability to vedolizumab and superior durability when prescribed as combotherapy.
Modeling bycatch abundance in tropical tuna purse seine fisheries on floating objects using the Δ method
Authors: Dumont Agathe , Duparc Antoine , Sabarros Philippe S , Kaplan David M 
Published: April 2024

Abstract
Bycatch rates are essential to estimating fishery impacts and making management decisions, but data on bycatch are often limited. Tropical tuna purse seine (PS) fisheries catch numerous bycatch species, including vulnerable silky sharks. Even if bycatch proportion is relatively low, impacts on pelagic ecosystems may be important due to the large size of these fisheries. Partial observer coverage of bycatch is a major impediment to assessing impacts. Here we develop a generic Δ modeling approach for predicting catch of four major bycatch species, including silky sharks, in floating object-associated fishing sets of the French Indian Ocean PS fleet from 2011 to 2018 based on logbook and observer data. Cross-validation and variable selection are used to identify optimal models consisting of a random forest model for presence–absence and a negative binomial general-additive model for abundance when present. Though models explain small to moderate amounts of variance (5–15%), they outperform a simpler approach commonly used for reporting, and they allow us to estimate total annual bycatch for the four species with robust estimates of uncertainty. Interestingly, uncertainty relative to mean catch is lower for top predators than forage species, consistent with these species having similar behavior and ecological niches to tunas.
Why should scientists lead? To underpin policy on marine and polar ecosystems
Authors: Misund Ole Arve 
Published: April 2024

Abstract
I recount my personal history, beginning as a young fisherman, becoming an academic fisheries biologist, and ultimately a leader of institutions dedicated to marine and polar research, higher education, and advising policymakers. After my dissertation in the early 1990s, I embarked on an active research career at the Institute of Marine Research (IMR) in Bergen, Norway, developing a sonar method to estimate the abundance of schooling, pelagic fish. My career then transitioned to middle leadership—15 years as Section Leader and Research Director at IMR—followed by &gt;10 years as a top leader for The University Centre in Svalbard, the National Institute of Nutrition and Seafood Research, and finally the Norwegian Polar Institute. I describe the major challenges, opportunities, and processes these leadership roles have entailed. I hope to send a positive message about the influential role of science, and the necessity of clear communication of results and advice at a time when there is a sense of urgency.
Public Opinion and Drone Exports: Evidence from a Conjoint Experiment in the United States
Authors: Lushenko Paul 
Published: April 2024

Abstract
Drones are now a mainstay in war. Yet not all countries can manufacture armed and networked drones, heightening global demand. While some drone-manufacturing countries have adopted permissive export policies, U.S. policymakers have been more restrictive, citing international legal commitments and domestic export controls. In this study, I consider drone exports as a question of both political economy and public opinion. I derive and test hypotheses about public support for drone exports through a conjoint survey experiment administered in the United States. I find that perceived alignment between the recipient country and United States, as well as the intended use of drones, are the most important factors shaping public support for drone exports. Export control measures are less relevant to public opinion. These findings offer the first experimental evidence about public opinion for drone exports, which have implications for the political economy of security and policies relating to the export of military technologies.
Breakdown of a concavity property of mutual information for non-Gaussian channels
Authors: Kireeva Anastasia , Mourrat Jean-Christophe 
Published: April 2024

Abstract
Let $S$ and $\tilde S$ be two independent and identically distributed random variables, which we interpret as the signal, and let $P_{1}$ and $P_{2}$ be two communication channels. We can choose between two measurement scenarios: either we observe $S$ through $P_{1}$ and $P_{2}$, and also $\tilde S$ through $P_{1}$ and $P_{2}$; or we observe $S$ twice through $P_{1}$, and $\tilde{S}$ twice through $P_{2}$. In which of these two scenarios do we obtain the most information on the signal $(S, \tilde S)$? While the first scenario always yields more information when $P_{1}$ and $P_{2}$ are additive Gaussian channels, we give examples showing that this property does not extend to arbitrary channels. As a consequence of this result, we show that the continuous-time mutual information arising in the setting of community detection on sparse stochastic block models is not concave, even in the limit of large system size. This stands in contrast to the case of models with diverging average degree, and brings additional challenges to the analysis of the asymptotic behavior of this quantity.
Absent Objects and the Study of Material Religion
Authors: Patterson Sara M , Newell Quincy D 
Published: April 2024

Abstract
This article explores how absent objects continue to work on religious communities using two case studies: the gold plates from which Joseph Smith said he translated the Book of Mormon, and the first 116 manuscript pages of that translation. Neither of these objects are available to believers now, but they played and continue to play an outsized role in the early history of the Mormon tradition, but in different ways. Based on these case studies, this article argues that scholars of material religion need to attend to the absence of objects in their explorations of how religious assemblages operate.