bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of dark matter spikes on the merger rates of Primordial Black Holes
Authors: Jangra Pratibha , Kavanagh Bradley J. , Diego J.M. 
Published: November 2023

Abstract
Mergers of Primordial Black Holes (PBHs) may contribute to the gravitational wave mergers detected by the LIGO-Virgo-KAGRA (LVK) Collaboration. We study the dynamics of PBH binaries dressed with dark matter (DM) spikes, for PBHs with extended mass functions. We analyze the impact of DM spikes on the orbital parameters of the PBH binaries formed in the early Universe and calculate their merger rates at the age of the Universe today. We consider two possible scenarios for the dynamics of the dressed binaries: assuming that either the DM spikes are completely evaporated from the binaries before merger or they remain static until the merger. Contrary to previous studies, we find that the presence of spikes may increase or decrease the present-day PBH merger rates, in some cases dramatically. Comparing with merger rates reported by the LVK Collaboration in the third Gravitational Wave Transient Catalog (GWTC-3), we derive approximate constraints on the fraction of Solar-mass PBHs in cold dark matter as f
pbh ≤ 𝒪(10-5–10-3), depending on the mass function. Our calculations are valid only for the idealized scenarios in which the DM spikes are either evaporated or static. However, they suggest that the impact of DM spikes on PBH merger rates may be more complicated than previously thought and motivate the development of a more general description of the merger dynamics, including feedback of the DM spikes in highly eccentric PBH binaries.
Spectral analysis of deviations from key comparison reference values
Authors: Maham Kinza , Kosonen Vili , Peltoniemi Juha , Kärhä Petri , Ikonen Erkki 
Published: November 2023

Abstract
When studying the results of the key comparisons of spectral quantities, it appears that in many cases participants’ results systematically deviate from the key comparison reference values over a limited spectral range. We carried out spectral analysis of such deviations in seven key comparisons of optical radiometry. The results reveal an approximate outcome that, on the average, each harmonic amplitude is inversely proportional to the order of the harmonic in all studied key comparisons. This new finding gives important information on the characteristics of spectral correlations. The result can be used in the uncertainty evaluation of spectral integrals, where the effect of unknown spectral correlations has earlier been challenging to assess quantitatively.
3D numerical study of neutral gas dynamics in the DTT particle exhaust using the DSMC method
Authors: Tantos C. , Varoutis S. , Hauer V. , Day C. , Innocente P. 
Published: November 2023

Abstract
Recently the design of the divertor tokamak test (DTT) Facility divertor has been modified and consolidated. The new divertor design presents significant geometrical differences compared to the previous ITER-like one, including the presence of a more flattened dome shape. This paper presents a complete 3D numerical analysis of the neutral gas dynamics inside the DTT subdivertor area for the latest divertor design. The analysis has been performed based on the direct simulation Monte Carlo method by applying the DIVGAS simulator code. SOLEDGE2D-EIRENE plasma simulations have been performed for a deuterium plasma scenario at the maximum additional power in partially detached condition achieved by neon impurity seeding and the extracted information about the neutral particles has been imposed as incoming boundary conditions. The pumping efficiency of the DTT divertor is examined by considering various cases with respect to the pumping probability and the effect of the toroidal and poloidal leakages is quantified. The results show that a significant percentage of the incoming flux of neutrals returns back to the plasma site through the entry gaps (60% for deuterium and 40% for neon), and, consequentially, only a small percentage (∼2%–15%) of the incoming flux can be pumped out from the system. The toroidal leakages affect significantly the pumping performance of the divertor causing a significant decrease in the pumped flux (and also in the pressure at the pumping opening) about 37%–47% and 43%–56% for deuterium and neon respectively. It is discussed how many pumping ports are needed depending on the achievable pumping performance per port. The number can be reduced by closing the toroidal gaps. The analysis shows that enlarging the poloidal gaps by a factor of two causes a significant increase in the poloidal flux losses by a factor 1.7. It is also illustrated how the presence of the cooling pipes leads to conductance losses.
Real-world data analysis of post-COVID-19 condition risk in older patients
Authors: Liu Ting-Hui , Huang Po-Yu , Wu Jheng-Yan , Chuang Min-Hsiang , Hsu Wan-Hsuan , Tsai Ya-Wen , Tsai Meng-Hsiu , Lai Chih-Cheng 
Published: November 2023

Abstract
This study investigated the risk of post-COVID-19 conditions in older patients with COVID-19 compared to those with influenza, and how age impacts this relationship. Patients aged ≥65 years with COVID-19 or influenza were identified using the TriNetX network. The risk of post-COVID-19 conditions was compared between survivors of COVID-19 and influenza, followed by a comparison of post-COVID-19 conditions risk between patients aged 65–74 years and those aged over 75 years. Compared with influenza survivors, post-COVID-19 conditions were significantly more prevalent in patients with COVID-19 (hazard ratio [HR], 1.534; 95% confidence interval [CI]: 1.405–1.675). Specifically, COVID-19 survivors have a significantly higher risk of experiencing abnormal breathing (HR, 2.052; 95% CI: 1.757–2.397), fatigue (HR, 1.587; 95% CI: 1.322–1.905), anxiety/depression (HR, 1.587; 95% CI: 1.322–1.905), cognitive symptoms (HR, 1.667; 95% CI: 1.295–2.146) and cough (HR, 1.250; 95% CI: 1.006–1.553) compared with the influenza group. Contrastingly, no significant difference was observed in the risk of any post-COVID-19 condition between COVID-19 survivors aged 65–74 years and those aged over 75 years (HR, 0.994; 95% CI: 0.920–1.073). However, a lower incidence of cognitive symptoms was observed in patients aged 65–74 years compared to those aged ≥75 years (HR, 0.543; 95% CI: 0.445–0.661). In conclusion, compared with influenza, older patients have a higher risk of developing post-COVID-19 conditions after SARS-CoV-2 infection, and those aged over ≥75 years may have an increased risk of developing cognitive symptoms compared to those aged 65–74 years.
Women physicians in academic pathology leadership
Authors: Brown Miriam R , Tay Cindy , Jacobs Jeremy W , Booth Garrett S 
Published: November 2023

Abstract

Objectives
To evaluate the gender composition of departmental chairs and program leadership of Accreditation Council for Graduate Medical Education–accredited pathology residencies and American Board of Pathology–certified subspecialty fellowships across the United States.

Methods
In this cross-sectional analysis, we examined the gender of individuals holding leadership positions in academic pathology in the United States. Using publicly available online data, 2 authors independently coded perceived gender (ie, man/woman/other) with 100% concordance.

Results
In 144 pathology residency programs, more women hold residency program director positions (52.1% [75/144]). Among 11 pathology subspecialties, women overall hold fewer fellowship program director positions (45.0% [212/471]). Among the residency-associated pathology department chair positions identified, women hold fewer positions (31.8% [42/132]). There is some geographic variation in pathology leadership gender composition when stratified using US Census regions.

Conclusions
Women in academic pathology departments are well represented in residency and overall fellowship program leadership but are underrepresented in department chair and certain pathology subspecialty leadership positions. The disproportionate number of women in department chair positions is observed across medical specialties, highlighting the need for improved gender equity among high-level academic medicine positions.
A retrospective cohort analysis of treatment outcomes of patients with tuberculosis who used substances in Tel Aviv, Israel
Authors: Kaliner Ehud , Bornstein Sandy , Kabha Doaa , Lidji Moshe , Sheffer Rivka , Mor Zohar 
Published: November 2023

Abstract

Aims
To outline the demographic, clinical, laboratory characteristics, and treatment outcomes of tuberculosis (TB) patients who used substances.

Methods
This retrospective cohort study compared 50 TB patients who used substances with a matched random sample of 100 TB patients who did not use substances between 2007 and 2017. Treatment failure was defined as a sputum smear or culture that tested positive after 5 months of treatment, loss to follow-up, unevaluated patients, or death.

Results
TB patients who used substances were typically younger, experienced homelessness, smokers, and had fewer chronic diseases than those who did not use substances. They also were hospitalized for longer periods, their treatment durations were longer, had higher rates of multidrug resistant strains, increased rates of treatment failure, and higher mortality. Individuals whose treatment failed predominantly originated from the former Soviet Union, experienced homelessness, and had chronic diseases compared with those whose treatment was successful. In the multivariate analysis, homelessness [odds ratios (OR) = 6.7], chronic diseases (OR = 12.4), and substance use (OR = 4.0) were predictors of treatment failures.

Conclusions
TB patients who used substances were more likely to have treatment failure. Targeted interventions, including early diagnosis and enhanced support during treatment, are essential to achieve treatment success in this vulnerable population, in addition to TB-alcohol/drug collaborative activities.
Prejuvenation: What Social Media Tells Us About the Rising Trend
Authors: Rothchild Evan , Jung Geena , Wang Fei , Ricci Joseph A 
Published: November 2023

Abstract

Background
“Prejuvenation,” a practice gaining enormous popularity among younger adults, can largely attribute its explosive growth to TikTok, the platform on which many first encounter this trend. Despite the rising usage of prejuvenation, however, there is a lack of clarity regarding its clinical practice and efficacy.

Objectives
To investigate the understandability, reliability, and actionability of prejuvenation-related TikTok content.

Methods
TikTok was queried using 13 hashtags consisting of popular colloquial terms associated with prejuvenation treatments, and the top 25 videos meeting inclusion criteria for each hashtag were analyzed. For each video, poster credentials and video type were determined. Videos considered “educational” were analyzed using the validated modified DISCERN score and the Patient Education Materials Assessment Tool scales. Creator's prejuvenation recommendations were recorded. Univariate and linear regression models were utilized for analysis.

Results
A total of 303 videos amassed over 61,000,000 million views, 3,957,091 likes, 24,455 comments, and 71,697 shares. Nonphysicians posted the most videos (n = 257, 84.8%) and had significantly higher median views, likes, comments, and engagement than physician videos. Analysis of “educational” videos showed that most videos (50, 67%) supported the use of prejuvenation treatments, 18 (24%) were neutral, and 6 (8%) were opposed.

Conclusions
Prejuvenation content on TikTok varies widely in terms of quality and recommendations, calling for more standardization regarding the practice. Physician-generated prejuvenation content was more reliable, but distinguishing it from nonphysician content was challenging, underscoring the need for platform-specific verification tools.
Sexually attractive traits predict predation-threat sensitivity of male alternative mating tactics
Authors: Godin Jean-Guy J , McDonough Heather E , Houslay Thomas M 
Published: November 2023

Abstract
Although visual sexual signals, such as ornamental colors and courtship displays, and large body size in males are attractive to females in numerous species, they may also inadvertently attract the attention of eavesdropping predators and thus may be costly in terms of increasing individual risk of mortality to predation. Theoretically, more color ornamented and larger males should be more predation threat sensitive and suppress their sexual signaling and(or) mating effort relatively more than their less color ornamented and smaller counterparts when under predation hazard. Here, we experimentally tested this hypothesis by quantifying concurrently the rates of alternative mating tactics (courtship displays, sneak mating attempts) expressed by male Trinidadian guppies (Poecilia reticulata) varying in color ornamentation and body size under a staged immediate threat of predation. Males suppressed their overall mating effort in response to the perceived predation threat, decreasing the frequency of their (presumably more conspicuous) courtship displays significantly more on average than the frequency of their sneak mating behavior. Statistically controlling for body length, more color-ornamented males were more threat sensitive in their courtship displays, but not sneak mating attempts, under predation hazard than drabber males. Controlling for body coloration, larger males exhibited lower courtship and sneak mating efforts than smaller males in both predation treatments, but body length only influenced threat sensitivity in sneak mating behavior. These results are consistent with both the threat sensitive hypothesis and asset protection principle and highlight the phenotype dependency and adaptive plasticity of alternative mating tactics in male guppies under varying predation risk.
EMVC-2: an efficient single-nucleotide variant caller based on expectation maximization
Authors: Dufort y Álvarez Guillermo , Xargay-Ferrer Martí , Pagès-Zamora Alba , Ochoa Idoia 
Published: November 2023

AbstractMotivationSingle-nucleotide variants (SNVs) are the most common type of genetic variation in the human genome. Accurate and efficient detection of SNVs from next-generation sequencing (NGS) data is essential for various applications in genomics and personalized medicine. However, SNV calling methods usually suffer from high computational complexity and limited accuracy. In this context, there is a need for new methods that overcome these limitations and provide fast reliable results.ResultsWe present EMVC-2, a novel method for SNV calling from NGS data. EMVC-2 uses a multi-class ensemble classification approach based on the expectation–maximization algorithm that infers at each locus the most likely genotype from multiple labels provided by different learners. The inferred variants are then validated by a decision tree that filters out unlikely ones. We evaluate EMVC-2 on several publicly available real human NGS data for which the set of SNVs is available, and demonstrate that it outperforms state-of-the-art variant callers in terms of accuracy and speed, on average.Availability and implementationEMVC-2 is coded in C and Python, and is freely available for download at: https://github.com/guilledufort/EMVC-2. EMVC-2 is also available in Bioconda.
Nunchaku: optimally partitioning data into piece-wise contiguous segments
Authors: Huo Yu , Li Hongpei , Wang Xiao , Du Xiaochen , Swain Peter S 
Published: November 2023

Abstract

Motivation
When analyzing 1D time series, scientists are often interested in identifying regions where one variable depends linearly on the other. Typically, they use an ad hoc and therefore often subjective method to do so.

Results
Here, we develop a statistically rigorous, Bayesian approach to infer the optimal partitioning of a dataset not only into contiguous piece-wise linear segments, but also into contiguous segments described by linear combinations of arbitrary basis functions. We therefore present a general solution to the problem of identifying discontinuous change points. Focusing on microbial growth, we use the algorithm to find the range of optical density where this density is linearly proportional to the number of cells and to automatically find the regions of exponential growth for both Escherichia coli and Saccharomyces cerevisiae. For budding yeast, we consequently are able to infer the Monod constant for growth on fructose. Our algorithm lends itself to automation and high throughput studies, increases reproducibility, and should facilitate data analyses for a broad range of scientists.

Availability and implementation
The corresponding Python package, entitled Nunchaku, is available at PyPI: https://pypi.org/project/nunchaku.
Experimental evidence of mate choice as the driving mechanism behind negative assortative mating for shell colour in a marine snail
Authors: Gefaell Juan , Vigo Ramón , Galindo Juan , Rolán-Alvarez Emilio 
Published: November 2023

Abstract
How colour polymorphisms are maintained in natural populations constitutes a key subject of study for evolutionary ecologists. One of the mechanisms that has been put forward to explain this phenomenon is negative frequency-dependent selection, which can be caused by different mechanisms. Among these mechanisms is mate choice, or the selection as a potential mate of the rare or dissimilar colour morph by the choosy sex of a given species. In the context of colour polymorphism, mate choice predicts the occurrence of a negative assortative mating pattern, whereby different colour morphs mate more often than expected by chance alone. However, negative assortative mating can also result from other mechanisms, making it, at best, a fallible indicator of a mate choice-driven negative frequency-dependent selection. For this reason, experimental evidence explicitly connecting such a mating pattern to mate choice is necessary to claim that a particular colour polymorphism is being maintained by negative frequency-dependent selection. Here we present experimental evidence backing this relationship for the colour polymorphic marine gastropod Littorina saxatilis from the Ría de Vigo (NW Iberian Peninsula), although how specifically these organisms choose their mates remains unclear. This calls for further experimental efforts to clarify this issue and its relationship to the maintenance of colour polymorphism in L. saxatilis.
Association of women-specific size threshold and mortality in elective abdominal aortic aneurysm repair
Authors: Talvitie Mareia , Jonsson Magnus , Roy Joy , Hultgren Rebecka 
Published: November 2023

Abstract

Background
It is unclear whether women derive mortality benefit from early repair of abdominal aortic aneurysms (AAA). The aim of this study was to compare short- and mid-term mortality for women treated at small versus large diameters.

Method
Women receiving elective repair of AAA at small (49–54 mm) and large (≥55 mm) diameters from 2008 to 2022 were extracted from the Swedish National Registry for Vascular Surgery (n = 1642 women). The effect of diameter on 90-day, 1- and 3-year mortality was studied in logistic regression and propensity score models. Age, co-morbidities, smoking and repair modality were considered as confounders. Men (n = 9047) were analysed in parallel.

Results
Some 1642 women were analysed, of whom 34% underwent repair at small diameters (versus 52% of men). Women with small (versus large) AAAs were younger (73 versus 75 years, P &lt; 0.001), and 63% of women in both size groups had endovascular repairs (P = 0.120). Mortality was 3.5% (90 days), 7.1% (1 year) and 15.8% (3 years), with no differences between the size strata. There was no consistent association between AAA size and mortality in multivariable models. Sex differences in mortality were almost entirely due to mortality in younger-than-average women versus men (3-year mortality: small AAAs 11.1% versus 7.3%, P &lt; 0.030, or large 14.4% versus 10.7%, P &lt; 0.038).

Conclusion
Mortality in women is high and unaffected by AAA size at repair. The optimal threshold for women remains undefined. The higher rupture risk in women should not automatically translate into a lower, women-specific threshold.
Impact of Prior Tuberculosis Treatment With New/Companion Drugs on Clinical Outcomes in Patients Receiving Concomitant Bedaquiline and Delamanid for Multidrug- and Rifampicin-Resistant Tuberculosis
Authors: Mikiashvili L , Kempker R R , Chakhaia T S , Bablishvili N , Avaliani Z , Lomtadze N , Schechter M C , Kipiani M 
Published: November 2023

Abstract

Background
There are scarce data on the clinical outcomes of persons retreated with new/companion anti-tuberculosis (TB) drugs for multidrug- and rifampicin-resistant tuberculosis (MDR/RR-TB). We sought to evaluate the efficacy and safety of bedaquiline and delamanid containing regimens among patients with and without prior exposure to the new/companion drugs (bedaquiline, delamanid, linezolid, clofazimine, and fluoroquinolones).

Methods
We conducted a retrospective cohort study among patients with pulmonary MDR/RR-TB in Georgia who received bedaquiline and delamanid combination as a part of a salvage regimen from November 2017 to December 2020 in a programmatic setting.

Results
Among 106 persons with a median age of 39.5 years, 44 (41.5%) were previously treated with new/companion TB drugs. Patients with prior exposure to new/companion drugs had higher rates of baseline resistance compared to those without exposure to new/companion TB drugs (bedaquiline 15.2% vs 1.8%, linezolid 22.2% vs 16.7%). Sputum culture conversion rates among patients exposed and not exposed to new/companion drugs were 65.9% vs 98.0%, respectively (P &lt; .001). Among patients with and without prior new/companion TB drug use, favorable outcome rates were 41.0% and 82.3%, respectively (P &lt; .001). Treatment adherence in 32 (30.2%) patients was ≤80%. Five of 21 patients (23.8%) who had a baseline and repeat susceptibility test had acquired bedaquiline resistance. QTC/F prolongation (&gt;500 ms) was rare (2.8%).

Conclusions
Prior exposure to new/companion TB drugs was associated with poor clinical outcomes and acquired drug resistance. Tailoring the TB regimen to each patient's drug susceptibility test results and burden of disease and enhancing adherence support may improve outcomes.