bluuebunny/crossref_metadata_2025_split huggingface dataset:
Local coherence by thermalized intra-system coupling
Authors: Kolář Michal , Filip Radim 
Published: June 2024

Abstract
Quantum superposition of energy eigenstates can appear autonomously in a single quantum two-level system coupled to a low-temperature thermal bath, if such coupling has a proper composite nature. We propose here a principally different and more feasible approach employing engineered interactions between two-level systems being thermalized into a global Gibbs state by weakly coupled thermal bath at temperature T. Therefore, in such case quantum coherence appears by a different mechanism, whereas the system-bath coupling does not have to be engineered. We demonstrate such autonomous coherence generation reaching maximum values of coherence. Moreover, it can be alternatively built up by using weaker but collective interaction with several two-level systems. This approach surpasses the coherence generated by the engineered system-bath coupling for comparable interaction strengths and directly reduces phase estimation error in quantum sensing. This represents a necessary step towards the autonomous quantum sensing.
Unavoidable structures in infinite tournaments
Authors: Benford Alistair , DeBiasio Louis , Larson Paul 
Published: June 2024

We prove a strong dichotomy result for countably-infinite oriented graphs; that is, we prove that for all countably-infinite oriented graphs

G
G

, either (i) there is a countably-infinite tournament

K
K

such that

G
⊈
K

G\not \subseteq K

, or (ii) every countably-infinite tournament contains a spanning copy of

G
G

. Furthermore, we are able to give a concise characterization of such oriented graphs. Our characterization becomes even simpler in the case of transitive acyclic oriented graphs (i.e. strict partial orders).

For uncountable oriented graphs, we are able to extend the dichotomy result mentioned above to all regular cardinals

κ
\kappa

; however, we are only able to provide a concise characterization in the case when

κ
=

ℵ
1

\kappa =\aleph _1

.
Grassroots Archives
Authors: McDonald Daniel 
Published: June 2024

Abstract
In recent years, coalitions of activists, artists, scholars, and community members have created archives composed of material related to social movements past and present with increasing frequency. These grassroots archives raise questions about the potential role of archives as generative spaces for democratizing history. This article explores this potential and the attendant challenges through a case study on an effort to preserve the memory of activism in São Paulo’s urban peripheries during Brazil’s civil-military dictatorship (1964–85)—an effort in which the author took part amid the rise of the far-right president and former dictatorship supporter Jair Bolsonaro. The postdictatorship culture of censorship and an ever-changing city relentlessly militated against the permanence of memory, not least through the destruction of physical archives and reference points in the urban landscape. The effort to organize and digitize precarious materials unfolded amid a larger campaign by activists to create an archive as part of a new university in the periphery. In this article, the author reflects on his experience working with communities through grassroots archiving to preserve at-risk historical sources, enhance local capacity, and broaden the practice of history beyond the academy.
Ploidy as a leaky reproductive barrier: mechanisms, rates and evolutionary significance of interploidy gene flow
Authors: Bartolić Paolo , Morgan Emma J , Padilla-García Nélida , Kolář Filip 
Published: June 2024

Abstract

Background
Whole-genome duplication (polyploidization) is a dominant force in sympatric speciation, particularly in plants. Genome doubling instantly poses a barrier to gene flow owing to the strong crossing incompatibilities between individuals differing in ploidy. The strength of the barrier, however, varies from species to species and recent genetic investigations revealed cases of rampant interploidy introgression in multiple ploidy-variable species.

Scope
Here, we review novel insights into the frequency of interploidy gene flow in natural systems and summarize the underlying mechanisms promoting interploidy gene flow. Field surveys, occasionally complemented by crossing experiments, suggest frequent opportunities for interploidy gene flow, particularly in the direction from diploid to tetraploid, and between (higher) polyploids. However, a scarcity of accompanying population genetic evidence and a virtual lack of integration of these approaches leave the underlying mechanisms and levels of realized interploidy gene flow in nature largely unknown. Finally, we discuss potential consequences of interploidy genome permeability on polyploid speciation and adaptation and highlight novel avenues that have just recently been opened by the very first genomic studies of ploidy-variable species. Standing in stark contrast with rapidly accumulating evidence for evolutionary importance of homoploid introgression, similar cases in ploidy-variable systems are yet to be documented.

Conclusions
The genomics era provides novel opportunity to re-evaluate the role of interploidy introgression in speciation and adaptation. To achieve this goal, interdisciplinary studies bordering ecology and population genetics and genomics are needed.
Did She or Didn't She? Perceptions of Operative Status of Female Genitalia
Authors: Sasson Daniel C , Sharp Gemma , Placik Otto J 
Published: June 2024

Abstract

Background
Although extensive research has explored why women undergo labiaplasty, little attention has been paid to societal and professional abilities to distinguish between altered and unaltered labia, impacting both patient concerns and broader societal perceptions.

Objectives
This study aimed to evaluate the accuracy of the general public and healthcare professionals in identifying labiaplasty and to pinpoint the misconceptions driving their perceptions. The goal was to inform more effective patient counseling strategies and challenge existing stigmas around cosmetic genital surgery.

Methods
The authors conducted an online survey of 511 lay adults and a group of 21 gynecologists and aesthetic vulvar surgeons. The survey assessed the participants’ ability to detect labiaplasty from images, focusing on aesthetic appearance, hair patterns, and size. The analysis involved Pearson correlation and Z-tests to compare perceptions against actual operative status.

Results
Analysis of the survey findings revealed a pronounced difficulty among participants in accurately discerning labiaplasty, with neither group showing a significant ability to identify surgical alterations. Misinterpretations were notably influenced by expectations of aesthetic appearance, with 49% associating an “odd” or “fake” look with surgery, and hair and size misconceptions also misleading respondents. Additionally, 20% of participants mistakenly related surgical changes to gender-affirming surgery or female genital mutilation.

Conclusions
The study highlights a gap in the ability of both the general public and medical professionals to accurately identify labiaplasty, pointing to a broad misunderstanding of cosmetic genital surgery's visual outcomes. Addressing these misconceptions through targeted education could substantially improve patient counseling and help dismantle the stigmas associated with labiaplasty.

Level of Evidence: 3
An amplicon panel for high-throughput and low-cost genotyping of Pacific oyster
Authors: Sutherland Ben J G , Thompson Neil F , Surry Liam B , Gujjula Krishna Reddy , Carrasco Claudio D , Chadaram Srinivas , Lunda Spencer L , Langdon Christopher J , Chan Amy M , Suttle Curtis A , Green Timothy J 
Published: June 2024

Abstract
Maintaining genetic diversity in cultured shellfish can be challenging due to high variance in individual reproductive success, founder effects, and rapid genetic drift, but is important to retain adaptive potential and avoid inbreeding depression. To support broodstock management and selective breeding in cultured Pacific oysters (Crassostrea (Magallana) gigas), we developed an amplicon panel targeting 592 genomic regions and SNP variants with an average of 50 amplicons per chromosome. Target SNPs were selected based on elevated observed heterozygosity or differentiation in Pacific oyster populations in British Columbia, Canada. The use of the panel for parentage applications was evaluated using multiple generations of oysters from a breeding program on Vancouver Island, Canada (n = 181) and families selected for Ostreid herpesvirus-1 resistance from the Molluscan Broodstock Program in Oregon, USA (n = 136). Population characterization was evaluated using wild, naturalized, farmed, or hatchery oysters sampled throughout the Northern Hemisphere (n = 189). Technical replicates showed high genotype concordance (97.5%; n = 68 replicates). Parentage analysis found suspected pedigree and sample handling errors, demonstrating the panel's value for quality control in breeding programs. Suspected null alleles were identified and found to be largely population dependent, suggesting population-specific variation impacting target amplification. Null alleles were identified using existing data without the need for pedigree information, and once they were removed, assignment rates increased to 93.0 and 86.0% of possible assignments in the two breeding program datasets. A pipeline for analyzing the amplicon sequence data from sequencer output, amplitools, is also provided.
Dogs and their genes: what ever will they think of next?
Authors: Ostrander Elaine A 
Published: June 2024

Abstract
The Edward Novitski Prize recognizes creativity and intellectual ingenuity in the solution of problems in genetics research. The prize honors scientific experimental work—either a single experimental accomplishment or a body of work.
Ostrander is recognized for work developing the domestic dog as an experimental system for solving fundamental biological problems and identifying genetic sequences of relevance to human health and disease. Including work on disease and behavioral health, Ostrander has shown a dedication to creative methods for understanding canine genetics and the value of translating research organisms to human genetics.
Genome size and chromosome number are critical metrics for accurate genome assembly assessment in Eukaryota
Authors: Hjelmen Carl E 
Published: June 2024

Abstract
The number of genome assemblies has rapidly increased in recent history, with NCBI databases reaching over 41,000 eukaryotic genome assemblies across about 2,300 species. Increases in read length and improvements in assembly algorithms have led to increased contiguity and larger genome assemblies. While this number of assemblies is impressive, only about a third of these assemblies have corresponding genome size estimations for their respective species on publicly available databases. In this paper, genome assemblies are assessed regarding their total size compared to their respective publicly available genome size estimations. These deviations in size are assessed related to genome size, kingdom, sequencing platform, and standard assembly metrics, such as N50 and BUSCO values. A large proportion of assemblies deviate from their estimated genome size by more than 10%, with increasing deviations in size with increased genome size, suggesting nonprotein coding and structural DNA may be to blame. Modest differences in performance of sequencing platforms are noted as well. While standard metrics of genome assessment are more likely to indicate an assembly approaching the estimated genome size, much of the variation in this deviation in size is not explained with these raw metrics. A new, proportional N50 metric is proposed, in which N50 values are made relative to the average chromosome size of each species. This new metric has a stronger relationship with complete genome assemblies and, due to its proportional nature, allows for a more direct comparison across assemblies for genomes with variation in sizes and architectures.
The maternal protein NLRP5 stabilizes UHRF1 in the cytoplasm: implication for the pathogenesis of multilocus imprinting disturbance
Authors: Unoki Motoko , Uemura Shuhei , Fujimoto Akihiro , Sasaki Hiroyuki 
Published: June 2024

Abstract
We have recently discovered that the so-called subcortical maternal complex (SCMC) proteins composing of cytoplasmic lattices are destabilized in Uhrf1 knockout murine fully grown oocytes (FGOs). Here we report that human UHRF1 interacts with human NLRP5 and OOEP, which are core components of the SCMC. Moreover, NLRP5 and OOEP interact with DPPA3, which is an essential factor for exporting UHRF1 from the nucleus to the cytoplasm in oocytes. We identify that NLRP5, not OOEP, stabilizes UHRF1 protein in the cytoplasm utilizing specifically engineered cell lines mimicking UHRF1 status in oocytes and preimplantation embryos. Further, UHRF1 is destabilized both in the cytoplasm and nucleus of Nlrp5 knockout murine FGOs. Since pathogenic variants of the SCMC components frequently cause multilocus imprinting disturbance and UHRF1 is essential for maintaining CpG methylation of imprinting control regions during preimplantation development, our results suggest possible pathogenesis behind the disease, which has been a long-standing mystery.
Modeling Fertilization Outcome in a Changing World
Authors: Chan Kit Yu Karen , KO Wing Ho 
Published: June 2024

Synopsis
Marine organisms have complex life histories. For broadcast spawners, successful continuation of the population requires their small gametes to make contact in the water column for sufficiently long periods for fertilization to occur. Anthropogenic climate change has been shown to impact fertilization success in various marine invertebrates, including sea urchins, which are key grazers in their habitats. Gamete performance of both sexes declined when exposed to elevated temperatures and/or pCO2 levels. Examples of reduced performance included slower sperm swimming speed and thinning egg jelly coat. However, such responses to climate change stress were not uniform between individuals. Such variations could serve as the basis for selection. Fertilization kinetics have long been modeled as a particle collision process. Here, we present a modified fertilization kinetics model that incorporates individual variations in performance in a more environmentally relevant regime, and which the performance of groups with different traits can be separately tracked in a mixture. Numerical simulations highlight that fertilization outcomes are influenced by changes in gamete traits as they age in sea water and the presence of competition groups (multiple dams or sires). These results highlight the importance of considering multiple individuals and at multiple time points during in vivo assays. We also applied our model to show that interspecific variation in climate stress vulnerabilities elevates the risk of hybridization. By making a numerical model open-source, we aim to help us better understand the fate of organisms in the face of climate change by enabling the community to consider the mean and variance of the response to capture adaptive potential.
Resistance towards and biotransformation of a Pseudomonas-produced secondary metabolite during community invasion
Authors: Hansen Morten L , Dénes Zsófia , Jarmusch Scott A , Wibowo Mario , Lozano-Andrade Carlos N , Kovács Ákos T , Strube Mikael L , Andersen Aaron J C , Jelsbak Lars 
Published: June 2024

Abstract
The role of antagonistic secondary metabolites produced by Pseudomonas protegens in suppression of soil-borne phytopathogens has been clearly documented. However, their contribution to the ability of P. protegens to establish in soil and rhizosphere microbiomes remains less clear. Here, we use a four-species synthetic community (SynCom) in which individual members are sensitive towards key P. protegens antimicrobial metabolites (DAPG, pyoluteorin, and orfamide A) to determine how antibiotic production contributes to P. protegens community invasion and to identify community traits that counteract the antimicrobial effects. We show that P. protegens readily invades and alters the SynCom composition over time, and that P. protegens establishment requires production of DAPG and pyoluteorin. An orfamide A-deficient mutant of P. protegens invades the community as efficiently as wildtype, and both cause similar perturbations to community composition. Here, we identify the microbial interactions underlying the absence of an orfamide A mediated impact on the otherwise antibiotic-sensitive SynCom member, and show that the cyclic lipopeptide is inactivated and degraded by the combined action of Rhodococcus globerulus D757 and Stenotrophomonas indicatrix D763. Altogether, the demonstration that the synthetic community constrains P. protegens invasion by detoxifying its antibiotics may provide a mechanistic explanation to inconsistencies in biocontrol effectiveness in situ.
In vitro activity of ozenoxacin against Staphylococcus aureus and Streptococcus pyogenes clinical isolates recovered in a worldwide multicentre study (2020–2022)
Authors: García-Castillo María , Hernández-García Marta , Correa Adriana , Coppi Marco , Griener Thomas , Fritsche Thomas , Pitart Cristina , Sampaio Jorge , Seifert Harald , Wake Karen , Wootton Mandy , Vila Jordi , Cantón Rafael 
Published: June 2024

Abstract

Objectives
We performed a multicentre study (2020–2022) to compare the in vitro activity of ozenoxacin and comparator agents against Staphylococcus aureus and Streptococcus pyogenes clinical isolates from skin and soft-tissue infections (SSTI).

Methods
A total of 1725 isolates (1454 S. aureus and 271 S. pyogenes) were collected in 10 centres from eight countries between January 2020 and December 2022. Antimicrobial susceptibility testing was determined (microdilution-SENSITITRE). Results were interpreted following European Committee on Antimicrobial Susceptibility Testing (EUCAST) 2023 (clinical breakpoints, ECOFF) and CLSI criteria.

Results
Ozenoxacin exhibited high in vitro activity against S. aureus (MIC50/90 = 0.002/0.12 mg/L) and S. pyogenes (MIC50/90 = 0.015/0.03 mg/L), inhibiting 99% of the isolates at MIC ≤ 0.5 mg/L and at MIC ≤ 0.06, respectively. The most active comparators against S. aureus were retapamulin (MIC90 = 0.12 mg/L), fusidic acid (MIC90 = 0.25 mg/L) and mupirocin (MIC90 = 0.5 mg/L); and against S. pyogenes were retapamulin (MIC90 = 0.03 mg/L), clindamycin (MIC90 = 0.12 mg/L) and mupirocin (MIC90 = 0.25 mg/L). Ciprofloxacin and methicillin resistant rates for S. aureus were 31.3% (455/1454) and 41% (598/1454), respectively. Additionally, 62% (373/598) of the MRSA were also ciprofloxacin non-susceptible, whereas only 10% (23/271) of the MSSA were ciprofloxacin resistant. Ozenoxacin was more active against ciprofloxacin-susceptible S. aureus than against ciprofloxacin-resistant isolates, and showed a slightly higher MIC in MRSA isolates than in MSSA. However, ozenoxacin activity was comparable in both ciprofloxacin-resistant MSSA and MRSA subsets. On the other hand, ozenoxacin had similar activity in ciprofloxacin-susceptible and resistant S. pyogenes isolates.

Conclusions
Ozenoxacin is a potent antimicrobial agent of topic use against Gram-positive bacteria causing SSTI, including MRSA isolates non-susceptible to ciprofloxacin.
Two-phase biomarker studies for disease progression with multiple registries
Authors: Mao Fangya , Cook Richard J 
Published: June 2024

Abstract
We consider the design and analysis of two-phase studies of the association between an expensive biomarker and disease progression when phase I data are obtained by pooling registries having different outcome-dependent recruitment schemes. We utilize two analysis methods, namely maximum-likelihood and inverse probability weighting (IPW), to handle missing covariates arising from a two-phase design. In the likelihood framework, we derive a class of residual-dependent designs for phase II sub-sampling from an observed data likelihood accounting for the phase I sampling plans used by the different registries. In the IPW approach, we derive and evaluate optimal stratified designs that approximate Neyman allocation. Simulation studies and an application to a motivating example demonstrate the finite sample improvements from the proposed designs over simple random sampling and standard stratified sampling schemes.
(421) SYSTEMATIC REVIEW OF PROSTATIC AND PELVIC IMAGING PARAMETERS TO PREDICT POST RADICAL PROSTATECTOMY ERECTILE DYSFUNCTION
Authors: Al-Mitwalli Dr Abdullah , Wani Dr Mudassir , Lee Dr Wai Gin , Tandogdu Dr Zafer , Ralph Prof David 
Published: June 2024

Abstract

Objectives
With surgery for prostate cancer there remains significant long-term post operative sequalae; these are, urinary incontinence and erectile dysfunction (ED). Certain mpMRI parameters such as membranous-urethral-length, have been shown to correlate with post-operative recovery of urinary continence. We are carrying out a comprehensive systematic review to identify imaging parameters that predict the recovery of erectile function after laparoscopic or robotic prostatectomy.

Methods
A systematic search was performed including Pubmed, Embase and Cochrane reviews from January 2000 up to August 2022. A protocol of this study was registered preliminarily in the International Prospective Register of Systematic Reviews (PROSPERO; Registrations ID CRD 42022359557). The review considered studies utilising an imaging parameter or technique obtained by any form of imaging modality and in any operative phase to correlate with validated erectile function assessment after robotic or laparoscopic radical prostatectomy.

Results
A total of 8 studies met our inclusion criteria. We categorised the studies based on the imaging modality into three groups: MRI (n=4), diffusion tensor imaging (DTI) (n=2) and intraoperative ultrasonography (n=2). Parameters with significant correlation to erectile function identified on pre-operative MRI were dynamic contrast enhancement of prostatic tissue and area of neurovascular bundle (NVB). The number of periprostatic nerve fibres on DTI had significant correlation erectile function post-operatively. Ultrasonography studies identified used pulsatile arterial flow and the number of visible blood vessels on simultaneous transrectal ultrasound during laparoscopic prostatectomy and also ultrasound doppler used as a laparoscopic probe to identify arterial flow intra-operatively.

Conclusions
Our systematic review revealed possible imaging parameters of anatomical and functional features that could be linked out erectile function after minimally invasive radical prostatectomy. Small sample studies, lack of heterogeneity makes pooling of results challenging. More research is needed to establish these parameters to predict and mitigate risk of erectile function post prostatectomy.

Conflicts of Interest
None.