bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bugs in our pockets: the risks of client-side scanning
Authors: Abelson Harold , Anderson Ross , Bellovin Steven M , Benaloh Josh , Blaze Matt , Callas Jon , Diffie Whitfield , Landau Susan , Neumann Peter G , Rivest Ronald L , Schiller Jeffrey I , Schneier Bruce , Teague Vanessa , Troncoso Carmela 
Published: January 2024

Abstract
Our increasing reliance on digital technology for personal, economic, and government affairs has made it essential to secure the communications and devices of private citizens, businesses, and governments. This has led to pervasive use of cryptography across society. Despite its evident advantages, law enforcement and national security agencies have argued that the spread of cryptography has hindered access to evidence and intelligence. Some in industry and government now advocate a new technology to access targeted data: client-side scanning (CSS). Instead of weakening encryption or providing law enforcement with backdoor keys to decrypt communications, CSS would enable on-device analysis of data in the clear. If targeted information were detected, its existence and, potentially, its source would be revealed to the agencies; otherwise, little or no information would leave the client device. Its proponents claim that CSS is a solution to the encryption versus public safety debate: it offers privacy—in the sense of unimpeded end-to-end encryption—and the ability to successfully investigate serious crime. In this paper, we argue that CSS neither guarantees efficacious crime prevention nor prevents surveillance. Indeed, the effect is the opposite. CSS by its nature creates serious security and privacy risks for all society, while the assistance it can provide for law enforcement is at best problematic. There are multiple ways in which CSS can fail, can be evaded, and can be abused.
The Select Council of Philip I: A Spanish Institution in Tudor England, 1555–1558
Authors: Velasco Berenguer Gonzalo 
Published: January 2024

Abstract
Traditional interpretations of the reign of Philip and Mary in England and Ireland (1554–58) have tended to investigate this short-lived episode from a strongly Anglocentric perspective. Such an approach has often hindered interpretations of crucial aspects of the reign that have wider implications for the study of Britain, Spain and Europe in an increasingly globalised world. Philip’s creation of a new consultative body in 1555, the select council (consejo escogido), is a case in point. Conventionally viewed as a superfluous body that only worsened the alleged ungovernability of Mary’s privy council—from which, it was claimed, it was never truly separate—it has been assumed that the select council was allowed to function nominally for a while to sustain Philip’s ego. In fact, the creation of the select council responded to the deeply rooted conciliar traditions of Spain and England (based on Aristotelian notions of ‘political friendship’) and its actual level of activity disproves previous assumptions about its role and viability. The diplomatic negotiations undertaken by the English select councillors and their Spanish and Flemish counterparts place England firmly within the conciliar framework of the Spanish Monarchy and provide an invaluable window from which to explore the role of England as a fully integrated member of a composite monarchy extending from Naples and Oran to Lima and Mexico City.
Facultative symbiont virulence determines horizontal transmission rate without host specificity in Dictyostelium discoideum social amoebas
Authors: Noh Suegene , Peck Ron F , Larson Emily R , Covitz Rachel M , Chen Anna , Roy Prachee , Hamilton Marisa C , Dettmann Robert A 
Published: January 2024

Abstract
In facultative symbioses, only a fraction of hosts are associated with symbionts. Specific host and symbiont pairings may be the result of host–symbiont coevolution driven by reciprocal selection or priority effects pertaining to which potential symbiont is associated with a host first. Distinguishing between these possibilities is important for understanding the evolutionary forces that affect facultative symbioses. We used the social amoeba, Dictyostelium discoideum, and its symbiont, Paraburkholderia bonniea, to determine whether ongoing coevolution affects which host–symbiont strain pairs naturally cooccur within a facultative symbiosis. Relative to other Paraburkholderia, including another symbiont of D. discoideum, P. bonniea features a reduced genome size that indicates a significant history of coevolution with its host. We hypothesized that ongoing host–symbiont coevolution would lead to higher fitness for naturally cooccurring (native) host and symbiont pairings compared to novel pairings. We show for the first time that P. bonniea symbionts can horizontally transmit to new amoeba hosts when hosts aggregate together during the social stage of their life cycle. Here we find evidence for a virulence–transmission trade-off without host specificity. Although symbiont strains were significantly variable in virulence and horizontal transmission rate, hosts and symbionts responded similarly to associations in native and novel pairings. We go on to identify candidate virulence factors in the genomes of P. bonniea strains that may contribute to variation in virulence. We conclude that ongoing coevolution is unlikely for D. discoideum and P. bonniea. The system instead appears to represent a stable facultative symbiosis in which naturally cooccurring P. bonniea host and symbiont pairings are the result of priority effects.
RADseq data reveal widespread historical introgression in four familiar North American songbirds
Authors: Lait Linda A , Enciso-Romero Juan , Lekamlage Thilini T M , Veale Aaron , Abeyrama Dilini K , Burg Theresa M 
Published: January 2024

Abstract
Population genetic structure is influenced by a combination of contemporary and historical events; however, this structure can be complicated by ongoing gene flow. While it is well known that contemporary hybridization occurs frequently among many closely related species, it often remains uncertain as to which populations are involved in introgression events, and this can be even more difficult to infer when introgression is historical. Here we use restriction-site associated DNA sequencing to look at the level of introgression among four species of songbirds in North America: the black-capped, mountain, boreal, and chestnut-backed chickadee. Samples from both sympatric and allopatric sites across the species’ ranges supported limited ongoing mixing among the four species with Bayesian clustering and principal component analyses. In contrast, f4-statistics and admixture graphs revealed extensive historical introgression among geographically structured populations. Almost all historical admixture events were among populations west of the Rocky Mountains, and almost all populations west of the Rocky Mountains, excluding island and coastal populations, showed evidence of historical admixture. The inclusion of all four chickadee species proved crucial in differentiating which species were involved in hybridization events to avoid erroneous conclusions. Taken together, the results suggest a complex pattern of divergence with gene flow.
Effects of selfing on the evolution of sexual reproduction
Authors: Xu Kuangyi 
Published: January 2024

Abstract
Plants exhibit diverse breeding systems, with populations capable of outcrossing, selfing, and/or asexual reproduction. However, interactions between the three reproductive pathways remain not fully clear. Sexual reproduction introduces segregation and recombination, but incurs several costs. Selfing can affect the relative costs and benefits of sexual vs. asexual reproduction. Building population genetic models, I explore how selfing affects the evolution of a sexual reproduction rate modifier via (a) indirect selection due to segregation, (b) indirect selection from changes in recombination rates, and (c) selection from the cost of meiosis and mate limitation. The dominant selective force mediating the evolution of sex is found to vary with the rate of sexual reproduction and selfing, but selective force (a) and (c) are generally stronger than selective force (b). A modifier enhancing sexual reproduction tends to be favored by indirect selection generated by partially recessive, small-effect deleterious mutations, while hindered by highly recessive lethal mutations. Overall, evolution toward higher sexual reproduction is hindered at low sexual reproduction rates and intermediate selfing rates, but favored under high selfing rates. The results suggest that asexual reproduction may precede the evolution of selfing and offer insights into the evolution of mechanisms reducing geitonogamy in partially clonal populations.
Primary care physicians’ perspectives on the identification and management of postnatal mental health problems
Authors: Liow Yiyang , Lazarus Monica , Loh Victor , Shorey Shefaly , Chee Cornelia , Young Doris , Valderas Jose M 
Published: January 2024

Abstract

Background
Postnatal mental health problems (PMHPs) are prevalent and negatively affect mothers, children, and society. International and local guidelines recommend that Singapore primary care physicians (PCP) screen, assess, and manage mothers with PMHPs. However, little is known about their experiences and views.

Methods
We conducted semi-structured interviews with 14 PCPs in Singapore. Interview questions elicited perspectives on the identification and management of mothers with PMHPs. The interview guide was developed from a conceptual framework incorporating the knowledge-attitudes-practices, self-efficacy, and socio-ecological models. Interviews were audio-recorded and transcribed. Thematic analysis was used to identify emergent themes.

Results
Singapore PCPs viewed themselves as key providers of first-contact care to mothers with PMHPs. They believed mothers preferred them to alternative providers because of greater accessibility and trust. In detection, they were vigilant in identifying at-risk mothers and favoured clinical intuition over screening tools. PCPs were confident in diagnosing common PMHPs and believed that mothers not meeting diagnostic criteria must be readily recognized and supported. In managing PMHPs, PCPs expressed varying confidence in prescribing antidepressants, which were viewed as second-line to supportive counselling and psychoeducation. Impeding physician factors, constraining practice characteristics and health system limitations were barriers. Looking forward, PCPs aspired to leverage technology and multidisciplinary teams to provide comprehensive, team-based care for the mother-child dyad.

Conclusion
Singapore PCPs are key in identifying and managing mothers with PMHPs. To fully harness their potential in providing comprehensive care, PCPs need greater multidisciplinary support and technological solutions that promote remote disclosure and enhanced preparation for their role.
Calcineurin contributes to RNAi-mediated transgene silencing and small interfering RNA production in the human fungal pathogen Cryptococcus neoformans
Authors: Yadav Vikas , Mohan Riya , Sun Sheng , Heitman Joseph 
Published: January 2024

Abstract
Adaptation to external environmental challenges at the cellular level requires rapid responses and involves relay of information to the nucleus to drive key gene expression changes through downstream transcription factors. Here, we describe an alternative route of adaptation through a direct role for cellular signaling components in governing gene expression via RNA interference-mediated small RNA production. Calcium–calcineurin signaling is a highly conserved signaling cascade that plays central roles in stress adaptation and virulence of eukaryotic pathogens, including the human fungal pathogen Cryptococcus neoformans. Upon activation in C. neoformans, calcineurin localizes to P-bodies, membraneless organelles that are also the site for RNA processing. Here, we studied the role of calcineurin and its substrates in RNAi-mediated transgene silencing. Our results reveal that calcineurin regulates both the onset and the reversion of transgene silencing. We found that some calcineurin substrates that localize to P-bodies also regulate transgene silencing but in opposing directions. Small RNA sequencing in mutants lacking calcineurin or its targets revealed a role for calcineurin in small RNA production. Interestingly, the impact of calcineurin and its substrates was found to be different in genome-wide analysis, suggesting that calcineurin may regulate small RNA production in C. neoformans through additional pathways. Overall, these findings define a mechanism by which signaling machinery induced by external stimuli can directly alter gene expression to accelerate adaptative responses and contribute to genome defense.
Examining the Role of Frailty on Treatment Patterns and Complications Among Older Women Undergoing Procedure-Based Treatment for Urinary Incontinence
Authors: Parker-Autry Candace Y , Bauer Scott , Ford Cassie , Gregory W Thomas , Badlani Gopal , Scales Charles D 
Published: January 2024

Abstract

Background
Aging beyond 65 years is associated with increased prevalence of urinary incontinence (UI), frailty, and increased complication rate with UI treatments. To investigate this relationship, we examined frailty as a predictor of procedure-based UI treatment patterns and urologic complications in Medicare-eligible women.

Methods
We identified women undergoing procedures for UI between 2011 and 2018 in the 5% limited Medicare data set. A claims-based frailty index (CFI) using data from the 12 months prior to the index procedure defined frailty (CFI ≥0.25). Urologic complications were assessed during the 12 months following the index procedure. We used unadjusted logistic regression models to calculate odds of having a specific type of UI procedure based on frailty status. Odds of postprocedure urologic complications were examined with logistic regression adjusted for age and race.

Results
We identified 21 783 women who underwent a procedure-based intervention for UI, of whom 3 826 (17.5%) were frail. Frail women with stress UI were 2.6 times more likely to receive periurethral bulking (95% confidence interval [CI] 2.26–2.95), compared to nonfrail. Conversely, frailty was associated with lower odds of receiving a Sling or Burch colposuspension. Among women with urgency UI or overactive bladder, compared to nonfrail, frailty was associated with higher odds of both sacral neuromodulation (odds ratio [OR] = 1.21, 95% CI: 1.11–1.33) and intravesical Botox (OR = 1.16, 95% CI: 1.06–1.28), but lower odds of receiving posterior tibial nerve stimulation. Frailty was associated with higher odds of postprocedure urologic complications (OR = 1.64, 95% CI: 1.47–1.81).

Conclusions
Frailty status may influence treatment choice for treatment of stress or urgency UI symptoms and increase the odds of postprocedural complications in older women.
Parent–Child Relationships Following Gray Divorce: Stronger Ties With Mothers, Weaker Ties With Fathers
Authors: Buyukkececi Zafer , Leopold Thomas 
Published: January 2024

Abstract

Objectives
With rising gray divorce rates, older individuals face heightened risk of social isolation, highlighting the significance of adult children as a vital source of solidarity in the absence of a spouse. Simultaneously, gray divorce may undermine parent–adult child relationships and weaken the core of the family safety net of older persons. This study examined the consequences of gray divorce for parent–child relationships.

Methods
We used longitudinal data from the German Family Panel (Pairfam), a large-scale panel study collecting detailed information about family relationships and family structure. We focused on adult children aged 18–49 (n = 9,092) whose parents were married at first observation. During an observation period spanning up to 13 years (2008–2020), 606 individuals experienced parental divorce. Using fixed-effects models, we estimated changes in contact frequency, emotional closeness, and instrumental and emotional support provided to parents.

Results
Consequences of gray divorce varied strongly between mothers and fathers. Adult–child solidarity intensified for mothers but eroded for fathers. This impact was strongest for changes in contact frequency, moderate for changes in emotional closeness, and smaller for changes in support. The persistence of gender role differentiation was evident, as daughters displayed closer ties and provided greater support to their mothers following a gray divorce.

Discussion
Divorce alters relationships with adult children. A gray divorce tilts adult–child solidarity toward mothers and puts fathers at a higher risk of social isolation. Moreover, the observed gender dynamics underscore the continued influence of gender roles on family dynamics in the aftermath of gray divorce.
FAIR data retrieval for sensitive clinical research data in Galaxy
Authors: Ouwerkerk Jasper , Rasche Helena , Spalding John D , Hiltemann Saskia , Stubbs Andrew P 
Published: January 2024

Abstract

Background
In clinical research, data have to be accessible and reproducible, but the generated data are becoming larger and analysis complex. Here we propose a platform for Findable, Accessible, Interoperable, and Reusable (FAIR) data access and creating reproducible findings. Standardized access to a major genomic repository, the European Genome-Phenome Archive (EGA), has been achieved with API services like PyEGA3. We aim to provide a FAIR data analysis service in Galaxy by retrieving genomic data from the EGA and provide a generalized “omics” platform for FAIR data analysis.

Results
To demonstrate this, we implemented an end-to-end Galaxy workflow to replicate the findings from an RD-Connect synthetic dataset Beyond the 1 Million Genomes (synB1MG) available from the EGA. We developed the PyEGA3 connector within Galaxy to easily download multiple datasets from the EGA. We added the gene.iobio tool, a diagnostic environment for precision genomics, to Galaxy and demonstrate that it provides a more dynamic and interpretable view for trio analysis results. We developed a Galaxy trio analysis workflow to determine the pathogenic variants from the synB1MG trios using the GEMINI and gene.iobio tool. The complete workflow is available at WorkflowHub, and an associated tutorial was created in the Galaxy Training Network, which helps researchers unfamiliar with Galaxy to run the workflow.

Conclusions
We showed the feasibility of reusing data from the EGA in Galaxy via PyEGA3 and validated the workflow by rediscovering spiked-in variants in synthetic data. Finally, we improved existing tools in Galaxy and created a workflow for trio analysis to demonstrate the value of FAIR genomics analysis in Galaxy.
Toward genome assemblies for all marine vertebrates: current landscape and challenges
Authors: de Jong Emma , Parata Lara , Bayer Philipp E , Corrigan Shannon , Edwards Richard J 
Published: January 2024

Abstract
Marine vertebrate biodiversity is fundamental to ocean ecosystem health but is threatened by climate change, overharvesting, and habitat degradation. High-quality reference genomes are valuable foundational scientific resources that can inform conservation efforts. Consequently, global consortia are striving to produce reference genomes for representatives of all life. Here, we summarize the current landscape of available marine vertebrate reference genomes, including their phylogenetic diversity and geographic hotspots of production. We discuss key logistical and technical challenges that remain to be overcome if we are to realize the vision of a comprehensive reference genome library of all marine vertebrates.
OPA1 mutation affects autophagy and triggers senescence in autosomal dominant optic atrophy plus fibroblasts
Authors: Zanfardino Paola , Amati Alessandro , Doccini Stefano , Cox Sharon N , Tullo Apollonia , Longo Giovanna , D’Erchia Annamaria , Picardi Ernesto , Nesti Claudia , Santorelli Filippo M , Petruzzella Vittoria 
Published: January 2024

Abstract
In several cases of mitochondrial diseases, the underlying genetic and bioenergetic causes of reduced oxidative phosphorylation (OxPhos) in mitochondrial dysfunction are well understood. However, there is still limited knowledge about the specific cellular outcomes and factors involved for each gene and mutation, which contributes to the lack of effective treatments for these disorders. This study focused on fibroblasts from a patient with Autosomal Dominant Optic Atrophy (ADOA) plus syndrome harboring a mutation in the Optic Atrophy 1 (OPA1) gene. By combining functional and transcriptomic approaches, we investigated the mitochondrial function and identified cellular phenotypes associated with the disease. Our findings revealed that fibroblasts with the OPA1 mutation exhibited a disrupted mitochondrial network and function, leading to altered mitochondrial dynamics and reduced autophagic response. Additionally, we observed a premature senescence phenotype in these cells, suggesting a previously unexplored role of the OPA1 gene in inducing senescence in ADOA plus patients. This study provides novel insights into the mechanisms underlying mitochondrial dysfunction in ADOA plus and highlights the potential importance of senescence in disease progression.
Deletion of a conserved genomic region associated with adolescent idiopathic scoliosis leads to vertebral rotation in mice
Authors: McCallum-Loudeac Jeremy , Moody Edward , Williams Jack , Johnstone Georgia , Sircombe Kathleen J , Clarkson Andrew N , Wilson Megan J 
Published: January 2024

Abstract
Adolescent idiopathic scoliosis (AIS) is the most common form of scoliosis, in which spinal curvature develops in adolescence, and 90% of patients are female. Scoliosis is a debilitating disease that often requires bracing or surgery in severe cases. AIS affects 2%–5.2% of the population; however, the biological origin of the disease remains poorly understood. In this study, we aimed to determine the function of a highly conserved genomic region previously linked to AIS using a mouse model generated by CRISPR-CAS9 gene editing to knockout this area of the genome to understand better its contribution to AIS, which we named AIS_CRMΔ. We also investigated the upstream factors that regulate the activity of this enhancer in vivo, whether the spatial expression of the LBX1 protein would change with the loss of AIS-CRM function, and whether any phenotype would arise after deletion of this region. We found a significant increase in mRNA expression in the developing neural tube at E10.5, and E12.5, for not only Lbx1 but also other neighboring genes. Adult knockout mice showed vertebral rotation and proprioceptive deficits, also observed in human AIS patients. In conclusion, our study sheds light on the elusive biological origins of AIS, by targeting and investigating a highly conserved genomic region linked to AIS in humans. These findings provide valuable insights into the function of the investigated region and contribute to our understanding of the underlying causes of this debilitating disease.