bluuebunny/crossref_metadata_2025 huggingface dataset:
Inequalities in access to and outcomes of cardiac surgery in England: retrospective analysis of Hospital Episode Statistics (2010-2019)
Authors: Lai Florence Y , Gibbison Ben , O’Cathain Alicia , Akowuah Enoch , Cleland John , Angelini Gianni D , King Christina , Murphy Gavin J , Pufulete Maria
Published: May 2024

Objectives

To characterise the variation in access to and outcomes of cardiac surgery for people in England.

Methods

We included people >18 years of age with a hospital admission for ischaemic heart disease (IHD) and heart valve disease (HVD) between 2010 and 2019. Within these populations, we identified patients who had coronary artery bypass graft (CABG) and/or valve surgery, respectively. We fitted logistic regression models to examine the effects of age, sex, ethnicity and socio-economic deprivation on having access to surgery and in-hospital mortality, 1-year mortality and hospital readmission.

Results

We included 292,140 people, of whom 28% were women, 11% were from an ethnic minority and 17% were from the most deprived areas. Across all types of surgery, 1 in 5 patients are readmitted to hospital within 1 year, rising to almost 1 in 4 for valve surgery patients. Women, Black people and people living in the most deprived areas were less likely to have access to surgery (CABG: 59%, 32%, 35% less likely; valve: 31%, 33%, 39% less likely, respectively) and more likely to die within 1 year of surgery (CABG: 24%, 85%, 18% more likely, respectively; valve: 19% (women) and 10% (people from most deprived areas) more likely).

Conclusion

Female sex, Black ethnicity, and economic deprivation are independently associated with limited access to cardiac surgery and higher post-surgery mortality. Actions are required to address these inequalities.

WHAT IS ALREADY KNOWN ON THIS TOPIC

There has been a marked improvement in short term (in hospital) outcomes of people having cardiac surgery. It is not clear if this translates to improvement in mid- and long-term outcomes and how these differ by demographic and socio-economic factors.

WHAT THIS STUDY ADDS

Across all types of cardiac surgery, 1 in 5 patients are readmitted to hospital within 1 year of surgery, rising to almost 1 in 4 for valve surgery patients.

While in hospital mortality has decreased markedly since 2010 (by 20%), 1 year mortality and hospital readmission remained largely unchanged.

Women, people of Black ethnicity and people from the most socially deprived areas were less likely to be offered cardiac surgery and more likely to die and be readmitted to hospital in the year after surgery.

HOW THIS STUDY MIGHT AFFECT RESEARCH, PRACTICE OR POLICY

Targeted interventions are required across the cardiovascular medicine pathway to improve mid- and long-term outcome in patients having cardiac surgery, addressing inequalities.
11β-HSD1 inhibitor efficacy in type 2 diabetes is cortisol-dependent
Authors: Wilton-Waddell Atinuke , Farraj Layal Abi , Vasconcelos Elton JR , Byrne Emily , Taylor Angela E , Freeman Adrian , Etal Damla , Stewart Paul M , Arlt Wiebke , Ajjan Ramzi , Tiganescu Ana
Published: May 2024

Cortisol excess drives multiple adverse effects including hypertension, dyslipidemia, and delayed wound healing. Activation of cortisol by the enzyme 11β-hydroxysteroid dehydrogenase type 1 (11β-HSD1) has shown promise as a therapeutic target for these comorbidities but clinical progress has been hampered by variable 11β-HSD1 inhibitor efficacy. Here, transcriptomic profiling of 11β-HSD1 target genes in primary skin fibroblasts as well as skin biopsies from type 2 diabetes individuals treated with the selective 11β-HSD1 inhibitor AZD4017 provide detailed mechanistic insights highlighting new areas of therapeutic potential. We report correlations between changes in 11β-HSD1 target gene expression, blood pressure, lipids, and wound healing with 1) cortisol levels (serum cortisol / dehydroepiandrosterone sulfate) and 2) peripheral 11β-HSD1 activity (serum cortisol / cortisone). Finally, we demonstrate that baseline cortisol levels and changes in placebo group cortisol levels are key determinants of 11β-HSD1 inhibitor efficacy. In conclusion, our findings pave the way for more effective targeting of 11β-HSD1 inhibitor treatment, improving the accuracy of future clinical studies. Larger trials of longer duration are now warranted to fully explore the therapeutic potential of 11β-HSD1 inhibitors across a range of cardiometabolic and age-associated indications.
Laboratory Readiness and genomic surveillance of Covid-19 in the Capital of Brazil
Authors: Cavalcante Fabrício Vieira , Martin Christina Pacheco Santos , Frio Gustavo Saraiva , Stabeli Rodrigo Guerino , Santos Leonor Maria Pacheco
Published: May 2024

Objective

Analyze the diagnostic readiness to Covid-19 and the genomic surveillance of SARS-CoV-2 in Brasília, the capital of Brazil.

Method

Retrospective, cross-sectional study, with data from: cases/deaths - Ministry of Health; RT-PCR analyzes Brasília Central Public Health Laboratory (LACEN); genomics - Global Initiative on Sharing All Influenza Data (GISAID).

Results

In March 2021, with the Gamma variant being predominant, RT-PCR dosages by LACEN reached their peak, followed by a reduction, possibly due to the start of vaccination. New peaks were observed in September 2021 and January 2022. The average time for releasing RT-PCR results was reduced from eight days (July 2020), to around eight hours in 2023. The participation of private laboratories was evident in sequencing the SARS-CoV-2 variants of concern in Brasília (n=1,897). LACEN received 571 samples, sequencing 50%. A decrease in the incidence of cases and deaths due to Covid-19 was noted in the years 2022 to 2023, following the national trend.

Conclusion

LACEN maintained RT-PCR dosages satisfactorily throughout the period. Regarding the genomic surveillance of SARS-CoV-2, the vast majority of samples were sequenced by private laboratories and the sequencing predicted by LACEN was not covered in its entirety.
Highly reduced complementary genomes of dual bacterial symbionts in the mulberry psyllidAnomoneura mori
Authors: Yasuda Yuka , Inoue Hiromitsu , Hirose Yuu , Nakabachi Atsushi
Published: May 2024

The genomes of obligately host-restricted bacteria suffer from accumulating mildly deleterious mutations, resulting in a drastic size reduction. Psyllids (Hemiptera) are phloem sap-sucking insects with a specialized organ called the bacteriome, which typically harbors two vertically transmitted bacterial symbionts: the primary symbiont “CandidatusCarsonella ruddii” (Gammaproteobacteria) and a secondary symbiont phylogenetically diverse among psyllid lineages. Genomes of severalCarsonellalineages were revealed to be drastically reduced (158-174 kb), AT-rich (14.0–17.9% GC), and structurally conserved with similar gene inventories devoted for synthesizing essential amino acids scarce in the phloem sap. However, genomic information for secondary symbionts was limited. Hence, this study analyzed genomes of the bacteriome-associated dual symbionts, Secondary_AM (Gammaproteobacteria) andCarsonella_AM, in the mulberry psyllidAnomoneura mori(Psyllidae). This revealed that the Secondary_AM genome is as small and AT-rich (229,822 bp, 17.3% GC) as those ofCarsonella, includingCarsonella_AM (169,120 bp, 16.2% GC), implying that Secondary_AM is an evolutionarily ancient obligate mutualist likeCarsonella. Phylogenomic analyses demonstrated that Secondary_AM is sister to “CandidatusPsyllophila symbiotica” ofCacopsyllaspp. (Psyllidae), whose genomes (221–237 kb, 17.3–18.6% GC) were recently reported. The Secondary_AM andPsyllophilagenomes showed highly conserved synteny, sharing all genes for complementing the incomplete tryptophan biosynthetic pathway ofCarsonellaand genes for synthesizing B vitamins. However, sulfur assimilation and carotenoid synthesizing genes were retained only in Secondary_AM andPsyllophila, respectively, indicating ongoing gene silencing. Average nucleotide identity, gene ortholog similarity, genome-wide synteny, and substitution rates suggested that the Secondary_AM/Psyllophilagenomes are more labile than theCarsonellagenomes.
Selective regulation of kinesin-5 function by β-tubulin carboxy-terminal tails
Authors: Thomas Ezekiel C. , Moore Jeffrey K.
Published: May 2024

The tubulin code hypothesis predicts that carboxy-terminal tails of tubulins create programs for selective regulation of microtubule-binding proteins, including kinesin motors. However, the molecular mechanisms that determine selective regulation and their relevance in cells are poorly understood. In this work, we report selective regulation of budding yeast kinesin-5 motors, Cin8 and Kip1, by the β-tubulin tail. Cin8, but not Kip1, requires the β-tubulin tail for its recruitment to the mitotic spindle. This creates a balance of both kinesin-5 motors in the spindle, and efficient mitotic progression. We identify a negatively charged patch of acidic amino acids in the β-tubulin tail that mediates the interaction with Cin8in vivo. Usingin vitroreconstitution with genetically modified yeast tubulin, we demonstrate that the charged patch in the β-tubulin tail increases Cin8 plus-end directed velocity and processivity. Finally, we determine that the positively charged amino-terminal extension from the Cin8 motor domain coordinates interactions with the β-tubulin tail. This work provides the first demonstration of a molecular mechanism underlying selective regulation of closely related kinesin motors by tubulin tails, and how this regulation promotes proper function of the mitotic spindle.
Structural insights into GrpEL1-mediated nucleotide and substrate release of human mitochondrial Hsp70
Authors: Morizono Marc A. , McGuire Kelly L. , Birouty Natalie I. , Herzik Mark A.
Published: May 2024

Maintenance of protein homeostasis is necessary for cell viability and depends on a complex network of chaperones and co-chaperones, including the heat-shock protein 70 (Hsp70) system. In human mitochondria, mitochondrial Hsp70 (mortalin) and the nucleotide exchange factor (GrpEL1) work synergistically to stabilize proteins, assemble protein complexes, and facilitate protein import. However, our understanding of the molecular mechanisms guiding these processes is hampered by limited structural information. To elucidate these mechanistic details, we used cryoEM to determine the first structures of full-length human mortalin-GrpEL1 complexes in previously unobserved states. Our structures and molecular dynamics simulations allow us to delineate specific roles for mortalin-GrpEL1 interfaces and to identify steps in GrpEL1-mediated nucleotide and substrate release by mortalin. Subsequent analyses reveal conserved mechanisms across bacteria and mammals and facilitate a complete understanding of sequential nucleotide and substrate release for the Hsp70 chaperone system.
SlSAURs, targeted by SlSTOP1, inhibit SlPP2C.Ds to modulate H+-ATPase and tomato root elongation under aluminum stress
Authors: Dong Danhui , Deng Qilin , Zhang Jialong , Jia Congyang , Zhang Lei , Li Hongxin , Zhang Na , Guo Yang-Dong
Published: May 2024

Aluminum (Al) stress, a prevalent constraint in acid soils, is known to inhibit plant growth by inhibiting root elongation through restricted cell expansion. The molecular mechanisms of Al-induced root inhibition, however, are not fully understood. This study aimed to elucidate the role of SlSAUR (Small auxin up-regulated RNA) proteins, which were downstream of the key Al stress-responsive transcription factor SlSTOP1 and its enhancer SlSZP1, in modulating root elongation under Al stress in tomato (Solanum lycopersicum). Our findings demonstrated that tomato lines withSlSAURsknockout exhibited shorter root lengths when subjected to Al stress. Further investigation into the underlying mechanisms revealed that SlSAURs interact with D-clade type 2C protein phosphatases, specifically SlPP2C.Ds. This interaction was pivotal as it suppresses the phosphatase activity, leading to the derepression of SlPP2C.D’s inhibitory effect on H+-ATPase. Consequently, this promoted cell expansion and root elongation under Al stress conditions. Our research significantly contributes to the current understanding of the molecular mechanisms by which Al ions modulate root elongation. The discovery of the SlSAUR-SlPP2C.D interaction and its impact on H+-ATPase activity provides a novel perspective on the adaptive strategies employed by plants to cope with Al toxicity. This knowledge may pave the way for the development of tomato cultivars with enhanced Al stress tolerance, thereby improving crop productivity in acid soils.
Working memory recovery in adolescents with concussion: Longitudinal fMRI study
Authors: Manelis A. , Lima Santos J.P. , Suss S.J. , Perry C.A. , Hickey R.W. , Collins M.W. , Kontos A.P. , Versace A.
Published: May 2024

Background

Understanding behavioral and neural underpinnings of post-concussion recovery of working memory function is critically important for improving clinical outcomes and adequately planning return-to-activity decisions. Previous studies provided inconsistent results due to small sample sizes and the use of a mixed population of participants who were at different post-injury time points.

Methods

To better understand behavioral and neural correlates of working memory recover during the first 6 months post-concussion, we used functional magnetic resonance imaging (fMRI) to scan 45 concussed adolescents [CONC] at baseline (<10 days post-concussion) and again at 6 months post-concussion. Healthy control [HC] adolescents without a history of concussion were scanned once. During the scans, participants performed 1-back (easy) and 2-back (difficult) working memory tasks with the letters as the stimuli and angry, happy, neutral, and sad faces as distractors.

Results

By the 6-month follow-up, all affected adolescents were asymptomatic and cleared to return-to-activity. Working memory function recovery was reflected by faster and more accurate performance at 6 months vs. baseline (p-values<0.05). It was also characterized by significant difficulty-related activation increases in the left inferior frontal gyrus (LIFG) and the left orbitofrontal cortex (LOFC) at 6 months vs. baseline.

Conclusion

Post-concussion recovery is associated with significant performance improvements in speed and accuracy, as well as normalization of brain responses in the LIFG and LOFC during the n-back task. The observed patterns of LOFC activation might reflect compensatory strategies to distribute neural processing and reduce neural fatigue post-concussion.
Predicting the likelihood of elevated transaminases in lung cancer patients undergoing immune checkpoint blockade
Authors: Shek Dmitrii , Gao Bo , Carlino Matteo S , Nagrial Adnan , Moujaber Tania , Karikios Deme , Pires da Silva Ines , Read Scott A , Ahlenstiel Golo
Published: May 2024

Background

The recent implementation of immune-checkpoint inhibitors (ICIs) has markedly changed the management and clinical outcomes for patients with advanced non-small cell lung cancer (NSCLC). Despite higher efficacy, ICIs are associated with a range of immune-related adverse events (irAEs). This retrospective study aimed to investigate the incidence of ICI-related transaminitis/hepatitis in NSCLC patients as well as to establish if any pre-treatment clinical parameters can predict the onset of liver toxicity.

Methods

We examined medical records of N=420 NSCLC patients treated across two health districts in Sydney, Australia between 2016 to 2020. R packages (corrplot and ggcorrplot) were used to construct correlation matrices and to calculate the correlation p-value using Spearman method. Logistic regression models were used to determine association of clinical parameters with elevated LFTs.

Results

N=185 patients were considered eligible. n=37 (20%) had elevation of liver transaminases at any stage post-ICI commencement, although only n=10 were deemed as those having ICI-related hepatitis. Most of these patients (n=29 [78%]) developed elevated LFTs within 3 months post-therapy initiation. Regression model established that pre-treatment ratio of serum protein (SP) to total bilirubin (TB) showed significant association with the elevated transaminases. Moreover, most of the patients (n=34 [94%]) with elevated LFTs had SP/TB<4. Using a second cohort of melanoma patients, the linear regression model did not establish a significant association between the SP/TB ratio and elevated LFTs. Nonetheless, n=31 (70.5%) patients with immune-mediated transaminitis in the melanoma cohort had SP/TB<4.

Conclusion

Our study has established a clinical risk factor associated with the elevation of LFTs in NSCLC patients, thus potentially enabling their prediction at the pre-treatment stage. However, its predictive accuracy was not confirmed in melanoma patients, stressing that ‘one size does not fit it all’ when developing predictive scores for irAEs in different patient cohorts.
Reliability and competitiveness of a novel balance field test: A cross-sectional pilot study
Authors: Jarnig Gerald , Kerbl Reinhold , van Poppel Mireille N.M.
Published: May 2024

Balancing tests in the field provide important information about the physical fitness and injury risk of athletes. These tests provide useful data on an athlete’s ability to maintain balance in dynamic and unforeseen circumstances, allowing for a more detailed assessment of their athletic performance. We have designed a novel balance test and tested main quality criteria and competitiveness for it. A total of 117 children (girls = 52.1%) aged 10.4 ± 0.5 years participated in the tests. The raw ABC scores show good to excellent test-retest reliability for all participants. Girls show a higher reliability (excellent) than boys (moderate to good). The comparison of raw data of the performance in the ABC and existing balance field tests shows strong correlation of the results. The test duration of the ABC is significantly (p<.001) shorter than that of existing balance field tests. The statistical and graphical analysis of the calculation of the normal distribution shows that the results of the ABC are closer to the normal distribution than those of the existing balance field tests.

The combination of high reliability and competitiveness makes the Austrian Balance Check an extremely attractive option for various areas of application. Overall, the novel designed test is a promising instrument that has the potential to significantly improve the standards of balance testing procedures in the field. The authors recommend a large-scale study to review the test quality criteria of the ABC, including gold standard comparison and development of age- and gender-specific reference values, in order to increase interest in implementing the Austrian Balance Check in international test batteries.
Crosstalk between plasma membrane andStaphylococcusα-hemolysin during oligomerization
Authors: Chatterjee Arnab , Roy Anupam , Sathees Thejas , Chakraborty Debajyoti , Das Partho Pratim , Mondal Bapan , Kishore Prithiv , Ghoshal Bartika , Jhunjhunwala Siddharth , Ganji Mahipal , Dutta Somnath
Published: May 2024

The infectious microbeStaphylococcus aureusreleases an array of cytotoxic pore-forming toxins (PFTs) that severely damage the cell membrane during bacterial infection. However, the interaction interfaces between the host cell and toxin were merely explored. Herein, we monitored the active oligomeric states facilitated membrane disruption processes such as lysis, and protrusion in the plasma membrane and lipid membrane. Furthermore, necrosis was triggered in the neutrophil-like cells upon synergistic binding and oligomerization of the monomeric α-HL. Additionally, we solved RBC membrane stabilized structure of different conformational states of this β-PFT using a single-particle cryo-EM. We further confirmed that internal membrane fluidity was the deterministic factor associated with the formation of intermediate pre-pores, heptameric pore-like, and complete pore species. Together, this is the first study to unveil the structure-function analysis of pre-pore to pore transition of any small β-PFT during its crosstalk with the cell.

Highlights

α-HL promotes necrosis in HL60 cells and lysis of shorter lipid bilayer region.

Cryo-EM of small PFT in the cellular environment.

Structural characterization of heptameric pore, pore-like, and pre-pore complex in the presence of RBCs.

Bilayer phase behavior (Ld/Lo) governs different conformational and geometrical variants of α-HL.
Functional interrogation of cellular Lp(a) uptake by genome-scale CRISPR screening
Authors: Khan Taslima G. , Cunha Juliana Bragazzi , Raut Chinmay , Burroughs Michael , Goonewardena Sascha N. , Smrcka Alan V. , Speliotes Elizabeth K. , Emmer Brian T.
Published: May 2024

An elevated level of lipoprotein(a), or Lp(a), in the bloodstream has been causally linked to the development of atherosclerotic cardiovascular disease and calcific aortic valve stenosis. Steady state levels of circulating lipoproteins are modulated by their rate of clearance, but the identity of the Lp(a) uptake receptor(s) has been controversial. In this study, we performed a genome-scale CRISPR screen to functionally interrogate all potential Lp(a) uptake regulators in HuH7 cells. Strikingly, the top positive and negative regulators of Lp(a) uptake in our screen wereLDLRandMYLIP, encoding the LDL receptor and its ubiquitin ligase IDOL, respectively. We also found a significant correlation for other genes with established roles in LDLR regulation. No other gene products, including those previously proposed as Lp(a) receptors, exhibited a significant effect on Lp(a) uptake in our screen. We validated the functional influence of LDLR expression on HuH7 Lp(a) uptake, confirmedin vitrobinding between the LDLR extracellular domain and purified Lp(a), and detected an association between loss-of-functionLDLRvariants and increased circulating Lp(a) levels in the UK Biobank cohort. Together, our findings support a central role for the LDL receptor in mediating Lp(a) uptake by hepatocytes.
Unraveling the Interplay between Stability and Flexibility in Design of Polyethylene Terephthalate (PET) Hydrolases
Authors: Xu Shiqinrui , Huo Chengze , Chu Xiakun
Published: May 2024

The accumulation of polyethylene terephthalate (PET), a widely used polyester plastic in packaging and textiles, poses a global environmental crisis. Biodegradation presents a promising strategy for PET recycling, with PET hydrolases (PETase) undertaking the task at the molecular level. Unfortunately, due to its low thermostability, PETase can only operate at ambient temperatures with low PET depolymerization efficiency, hindering its practical application in industry. Currently, efforts to engineer PETase have primarily focused on enhancing its thermostability. However, increased stability often reduces the structural dynamics necessary for substrate binding, potentially slowing down the enzymatic activity. To elucidate the delicate balance between stability and flexibility in optimizing PETase catalytic activity, we performed theoretical investigations on both wild-type PETase (WT-PETase) and a thermophilic variant (Thermo-PETase) using molecular dynamics simulations and frustration analysis. Despite being initially designed to stabilize the native structure of enzyme, our findings reveal that Thermo-PETase exhibits an unprecedented increase in structural flexibility at the PET binding and catalytic sites, beneficial for substrate recruitment and product release, compared to WT-PETase. Upon PET binding, we observed that structural dynamics of Thermo-PETase are largely quenched, facilitating subsequent chemical reactions. Compared to WT-PETase, Thermo-PETase forms more extensive interactions with PET, resulting in a higher population of catalytically competent enzyme-substrate states, thus contributing to increased catalytic activity. Our theoretical results are consistent with experimental findings and further suggest that Thermo-PETase exhibits higher catalytic activity than WTPETase across a broad temperature range by leveraging stability and flexibility at high and low temperatures, respectively. Our findings offer valuable insights into how PETase optimizes its enzymatic performance by balancing stability and flexibility, paving the way for future PETase design strategies.
Influence of vine decline disease on the amino acid metabolism of watermelon fruit
Authors: Santo Honoka , Tadano Shota , Inokami Fumika , Nishioka Takuya , Konaka Takafumi , Sakata Motomu , Morimoto Yasufumi , Akashi Kinya
Published: May 2024

Vine decline (VD) is a severe disease of watermelon, melon, and other cucurbits, caused by soil-borne pathogens such as Monosporascus cannonballus and leads to root necrosis and sudden wilting at the later stage of fruit maturation. The present study examined the effects of VD on the metabolism of watermelon fruits. The VD-affected watermelon fruits had significantly lower lycopene and total solid contents. Still, polyphenols content and total antioxidant activities were comparable with the controls, suggesting that VD inhibited the ripening processes but maintained defensive processes in the fruits. The VD fruits showed a lower calcium level than the controls, while the contents of other major nutrition minerals were not significantly altered. The VD fruits had a lower content of total amino acids, and their composition was characterized by an increase in the percentage fractions for several amino acids, including citrulline, which may reflect the physiological response to the VD-related water deficit condition. The PCA plot clearly distinguished amino acid profiles between the VD and control fruits, demonstrating that VD exerted major influences on their amino acid metabolisms. Overall, the present study revealed that VD imposed characteristic impacts on the biochemical behaviors in the watermelon fruits.
Symmetry, gauge freedoms, and the interpretability of sequence-function relationships
Authors: Posfai Anna , McCandlish David M. , Kinney Justin B.
Published: May 2024

Quantitative models that describe how biological sequences encode functional activities are ubiquitous in modern biology. One important aspect of these models is that they commonly exhibit gauge freedoms, i.e., directions in parameter space that do not affect model predictions. In physics, gauge freedoms arise when physical theories are formulated in ways that respect fundamental symmetries. However, the connections that gauge freedoms in models of sequence-function relationships have to the symmetries of sequence space have yet to be systematically studied. Here we study the gauge freedoms of models that respect a specific symmetry of sequence space: the group of position-specific character permutations. We find that gauge freedoms arise when model parameters transform under redundant irreducible matrix representations of this group. Based on this finding, we describe an “embedding distillation” procedure that enables analytic calculation of the number of independent gauge freedoms, as well as efficient computation of a sparse basis for the space of gauge freedoms. We also study how parameter transformation behavior affects parameter interpretability. We find that in many (and possibly all) nontrivial models, the ability to interpret individual model parameters as quantifying intrinsic allelic effects requires that gauge freedoms be present. This finding establishes an incompatibility between two distinct notions of parameter interpretability. Our work thus advances the understanding of symmetries, gauge freedoms, and parameter interpretability in sequence-function relationships.

Significance Statement

Gauge freedoms—diections in parameter space that do not affect model predictions—are ubiquitous in mathematical models of biological sequence-function relationships. But in contrast to theoretical physics, where gauge freedoms play a central role, little is understood about the mathematical properties of gauge freedoms in models of sequence-function relationships. Here we identify a connection between specific symmetries of sequence space and the gauge freedoms present in a large class of commonly used models for sequence-function relationships. We show that this connection can be used to perform useful mathematical computations, and we discuss the impact of model transformation properties on parameter interpretability. The results fill a major gap in the understanding of quantitative sequence-function relationships.
A Survey of Individuals’ Willingness to Share Real-World Data Post-Mortem with Researchers
Authors: Hendricks-Sturrup Rachele M. , Lu Christine Y.
Published: May 2024

Background

Posthumous data use policy within the broader scope of navigating post-mortem data privacy is a procedurally complex landscape for those engaged in data collection and sharing, and data-driven health research.

Objective

To help address some of this complexity by exploring patterns in individuals’ willingness to donate data with health researchers after death and developing practical recommendations.

Methods

An electronic survey was conducted in April 2021 among adults (≥18 years of age) registered in ResearchMatch (www.researchmatch.org), a national health research registry. Descriptive and multinomial logistic regression analyses were conducted at a 95% confidence level to determine the association between willingness to donate data after death overall and across each demographic category (education level, age range, duration of using online medical websites, annual frequency of getting ill) and based on the overall quantity at which individuals expressed willingness to donate data (some, all, none) with researchers.

Results

Of 399 responses, most participants were willing to donate health data (electronic medical record data [67%], prescription history data [63%], genetic data [54%], and fitness tracker data [53%]) after death. We identified that individuals were more likely to donate some data after death (versus no data) if they had longer duration of using online medical websites (relative risk ratio = 1.22, p<0.05, 95% CI: 1.01 to 1.48). No additional significant findings were observed between willingness to donate all, some, or none of their data after death and other demographic factors.

Conclusions

There are opportunities to enhance practices to engage patients in health systems’ online medical websites as one potential mechanism to encourage or inspire individuals in posthumous data donation for health research purposes.
Measurement of electron neutrino and antineutrino cross sections at low momentum transfer
Authors: Henry S. , Su H. , Akhter S. , Ahmad Dar Z. , Ansari V. , Ascencio M. V. , Sajjad Athar M. , Bashyal A. , Betancourt M. , Bonilla J. L. , Bravar A. , Díaz G. A. , Felix J. , Fields L. , Fine R. , Gaur P. K. , Gilligan S. M. , Gran R. , Granados E. , Harris D. A. , Hart A. L. , Kleykamp J. , Klustová A. , Kordosky M. , Last D. , Lozano A. , Lu X.-G. , Manly S. , Mann W. A. , Mauger C. , McFarland K. S. , Mehmood M. , Messerly B. , Morfín J. G. , Naples D. , Nelson J. K. , Nguyen C. , Olivier A. , Paolone V. , Perdue G. N. , Pernas C. , Plows K.-J. , Ramírez M. A. , Ransome R. D. , Roy N. , Ruterbories D. , Schellman H. , Solano Salinas C. J. , Syrotenko V. S. , Valencia E. , Vaughan N. H. , Waldron A. V. , Wret C. , Yaeggy B. , Zazueta L. ,   The MINERvA Collaboration
Published: May 2024

Accelerator based neutrino oscillation experiments seek to measure the relative number of electron and muon (anti)neutrinos at different L/E values. However high statistics studies of neutrino interactions are almost exclusively measured using muon (anti)neutrinos since the dominant flavor of neutrinos produced by accelerator based beams are of the muon type. This work reports new measurements of electron (anti)neutrinos interactions in hydrocarbon, obtained by strongly suppressing backgrounds initiated by muon flavor (anti)neutrinos. Double differential cross sections as a function of visible energy transfer, Eavail, and transverse momentum transfer, pT, or three momentum transfer, q3 are presented.

Published by the American Physical Society
2024
Revisiting
O(N)

σ
model at unphysical pion masses and high temperatures
Authors: Lyu Yuan-Lin , Li Qu-Zhi , Xiao Zhiguang , Zheng Han-Qing
Published: May 2024

Roy-equation analysis on lattice data of ππ scattering phase shifts at mπ=391  MeV reveals that the lowest f0 meson becomes a bound state under this condition. In addition, there is a pair of complex poles below threshold generated by crossing symmetry [X.-H. Cao , ]. We use the N/D method to partially recover crossing symmetry of the O(N) σ model amplitude at leading order of 1/N expansion, and qualitatively reproduce the pole structure and pole trajectories with varying pion masses as revealed by Roy-equation analyses. The σ pole trajectory with varying temperature is also discussed and found to be similar to its properties when varying mπ. As the temperature increases, the complex σ poles firstly move from the second Riemann sheet to the real axis becoming two virtual state poles, and then one virtual state pole moves to the first sheet turning into a bound state pole and finally tends to the pion pole position at high temperature which is as expected from the chiral symmetry restoration. Our results provide further evidence that the lowest f0 state extracted from experiments and lattice data plays the role of the σ meson in the spontaneous breaking of chiral symmetry. Finally, we also briefly discuss the problems of the effective potential in the situation when mπ and the temperature become large.

Published by the American Physical Society
2024
Custodial symmetry breaking and Higgs boson signatures at the LHC
Authors: Butterworth Jon , Debnath Hridoy , Fileviez Pérez Pavel , Mitchell Francis
Published: May 2024

We discuss the simplest model that predicts a tree-level modification of the ρ parameter from a shift in the W-mass without changing the prediction for the Z mass. This model predicts a new neutral Higgs and two charged Higgses, with very similar masses and suppressed couplings to the Standard Model fermions. We discuss the decay properties of these new scalar bosons, and the main signatures at the Large Hadron Collider. Comparing these signatures for the first time to the latest measurements, we show that while masses around 200 GeV are excluded for some scenarios, over a wide range of model parameter space the new bosons can have a mass close to the electroweak scale without violating existing limits from experimental searches or destroying the agreement with measurements. We investigate the scenario where the new neutral Higgs is fermiophobic and has a large branching ratio into W gauge bosons and/or photons, and show that this could lead to a signal in the diphoton mass spectrum at low Higgs masses. We discuss the different signatures that can motivate new measurements and searches at the Large Hadron Collider.

Published by the American Physical Society
2024
Low-scale baryogenesis from three-body decays
Authors: Domínguez F. , Racker J.
Published: May 2024

Baryogenesis at the TeV scale from CP-violating decays of a massive particle requires some way to avoid the washouts from processes closely related to the existence of CP violation. Baryogenesis from three-body decays (instead of two-body decays) has been proposed as a way for TeV scale baryogenesis. In this work we revisit this statement and show that, although three-body-decay models can provide interesting alternatives to address other kind of difficulties faced by low-scale baryogenesis, the generic problem due to the washouts proportional to the CP asymmetry persists. Therefore, as in two-body-decay models, the mass of the decaying particle cannot be below ∼10  TeV unless some mechanism to avoid these kinds of washouts is implemented.

Published by the American Physical Society
2024
Inverse problem in energy-dependent potentials using semiclassical methods
Authors: Albuquerque Saulo , Völkel Sebastian H. , Kokkotas Kostas D.
Published: May 2024

Wave equations with energy-dependent potentials appear in many areas of physics, ranging from nuclear physics to black hole perturbation theory. In this work, we use the semiclassical Wentzel-Kramers-Brillouin (WKB) method to first revisit the computation of bound states of potential wells and reflection/transmission coefficients in terms of the Bohr-Sommerfeld rule and the Gamow formula. We then discuss the inverse problem, in which the latter observables are used as a starting point to reconstruct the properties of the potentials. By extending known inversion techniques to energy-dependent potentials, we demonstrate that so-called width-equivalent or WKB-equivalent potentials are not isospectral anymore. Instead, we explicitly demonstrate that constructing quasi-isospectral potentials with the inverse techniques is still possible. Those reconstructed, energy-independent potentials share key properties with the width-equivalent potentials. We report that including energy-dependent terms allows for a rich phenomenology, particularly for the energy-independent equivalent potentials.

Published by the American Physical Society
2024
Virialized profiles and oscillations of self-interacting fuzzy dark matter solitons
Authors: Indjin Milos , Liu I-Kang , Proukakis Nick P. , Rigopoulos Gerasimos
Published: May 2024

We investigate the effect of self-interactions on the shape and oscillations of the solitonic core profile of condensed fuzzy dark matter systems without the backdrop of a halo, revealing universal features in terms of an appropriately scaled interaction strength characterizing the crossover between the weakly and strongly interacting regimes. Our semianalytical results are further confirmed by spherically symmetric simulations of the Gross-Pitaevskii-Poisson equations. Inverting our obtained relations, we highlight a degeneracy that could significantly affect constraints on the boson mass in the presence of repulsive boson self-interactions and propose the simultaneous extraction of static and dynamical solitonic features as a way to uniquely constrain both the boson mass and self-interactions.

Published by the American Physical Society
2024
Probabilistic model for the gravitational wave signal from merging black holes
Authors: Khan Sebastian
Published: May 2024

Parametrized models that predict the gravitational-wave (GW) signal from merging black holes are used to extract source properties from GW observations. The majority of research in this area has focused on developing methods capable of producing highly accurate, point estimate, predictions for the GW signal. A key element missing from every model used in the analysis of GW data is an estimate for how confident the model is in its prediction. This omission increases the risk of biased parameter estimation of source properties. Current strategies include running analyses with multiple models to measure systematic bias however, this fails to accurately reflect the true uncertainty in the models. In this work we develop a probabilistic extension to the phenomenological modeling workflow for nonspinning black holes and demonstrate that the model not only produces accurate point estimates for the GW signal but can be used to provide well-calibrated local estimates for its uncertainty. Our analysis highlights that there is a lack of numerical relativity (NR) simulations available at multiple resolutions which can be used to estimate their numerical error and implore the NR community to continue to improve their estimates for the error in NR solutions published. Waveform models that are not only accurate in their point-estimate predictions but also in their error estimates are a potential way to mitigate bias in GW parameter estimation of compact binaries due to unconfident waveform model extrapolations.

Published by the American Physical Society
2024
Sonoluminescence: Photon production in time-dependent analog systems
Authors: Karmakar Rajesh , Maity Debaprasad
Published: May 2024

Sonoluminescence is a well-known laboratory phenomenon where an oscillating gas bubble in the appropriate environment periodically emits a flash of light in the visible frequency range. In this work, we study the system in the framework of analog gravity. We model the oscillating bubble in terms of analog geometry and propose a nonminimal coupling prescription of the electromagnetic field with the geometry. The geometry behaves as an analogous oscillating time-dependent background in which repeated flux of photons are produced in a wide frequency range through parametric resonance from quantum vacuum. Due to our numerical limitation, we could reach the frequency up to ∼105  m−1. However, we numerically fit the spectrum in a polynomial form including the observed frequency range around ∼107  m−1. Our current analysis seems to suggest that parametric resonance in analog background may play a fundamental role in explaining such phenomena in the quantum field theory framework.

Published by the American Physical Society
2024
Cell migration dynamics explained by the coupling of mechanics with electrochemistry and pH regulation
Authors: Li Yizeng , Sun Sean X.
Published: May 2024

Anisotropic environmental signals or polarized membrane ion/solute carriers can generate spatially varying intracellular gradients, leading to polarized cell dynamics. For example, the directional migration of neutrophils, galvanotaxis of glioblastoma, and water flux in kidney cells all result from the polarized distribution of membrane ion carriers and other intracellular components. The underlying physical mechanisms behind how polarized ion carriers interact with environmental signals are not well studied. Here, we use a physiology-relevant, physics-based mathematical model to reveal how ion carriers generate intracellular ion and voltage gradients. The model can discern the contribution of individual ion carriers to the intracellular pH gradient, electric potential, and water flux. We discover that an extracellular pH gradient leads to an intracellular pH gradient via chloride-bicarbonate exchangers, whereas an extracellular electric field leads to an intracellular electric potential gradient via passive potassium channels. In addition, mechanical-biochemical coupling can modulate actin distribution and flow, creating a biphasic dependence of cell speed on water flux. Moreover, we find that F-actin interaction with NHE alone can generate cell movement, even when other ion carriers are not polarized. Taken together, the model highlights the importance of cell ion dynamics in modulating cell migration and cytoskeletal dynamics.

Published by the American Physical Society
2024
Composite cores of monopoles and Alice rings in spin-2 Bose-Einstein condensates
Authors: Baio Giuseppe , Borgh Magnus O.
Published: May 2024

We show that energy relaxation causes a point defect in the uniaxial-nematic phase of a spin-2 Bose-Einstein condensate to deform into a spin-Alice ring that exhibits a composite core structure with distinct topology at short and long distances from the singular line. An outer biaxial-nematic core exhibits a spin half-quantum vortex structure with a uniaxial-nematic inner core. By numerical simulation, we demonstrate a dynamical oscillation between the spin-Alice ring and a split-core hedgehog configuration via the appearance of ferromagnetic rings with associated vorticity inside an extended core region. We further show that a similar dynamics is exhibited by a spin-Alice ring surrounding a spin-vortex line resulting from the relaxation of a monopole situated on a spin-vortex line in the biaxial-nematic phase. In the cyclic phase, similar states are shown instead to form extended phase-mixing cores containing rings with fractional mass circulation or cores whose spatial shape reflects the order-parameter symmetry of a cyclic inner core, depending on the initial configuration.

Published by the American Physical Society
2024
Wheeling towards sustainability: the nexus of external pressures, green innovation and circular supply chain excellence
Authors: Singh Rohit Kumar
Published: May 2024

Purpose

The study aims to investigate the firm reaction to external pressures and the subsequent transformation to green innovation (GI) and sustainability, leading to an enhanced circular supply chain performance. The research examined the effect of coercive, normative and mimetic pressures on GI within the Indian tire industry context.

Design/methodology/approach

The authors have designed a self-administered questionnaire and received 283 responses. Nonresponse bias analysis was conducted first before proceeding to other assumptions such as constant variance and normality. The confirmatory factor analysis was used to check the data’s integrity and reliability. The PLS-structural equation modeling (SEM) is used to validate the constructs and test the established hypotheses.

Findings

External regulatory pressures significantly impact the tire industry’s move towards GI. Normative pressures from societal expectations and industry standards, along with mimetic pressures where companies emulate best practices, both drive the industry toward sustainable initiatives. Further, a clear positive relationship emerges between GI and sustainable supply chain practices (SSCP). This shift emphasizes recycling, reusing and reducing waste and showcases the industry’s commitment to minimizing its environmental impact.

Originality/value

Unlike existing literature that predominantly explores SSCP, the study introduces an integrated framework that intertwines institutional pressures (IP), green innovation (GI), and SSCP to elevate circular supply chain practices (CSCP). The current study highlights the relationships and practical implications within the Indian tire industry.
Religiosity and entrepreneurship: women entrepreneurs in Turkiye
Authors: Ozasir Kacar Sibel
Published: May 2024

Purpose

The purpose of this study is to showcase how entrepreneurial opportunities can be contextually formed differently for women entrepreneurs concerning their relationship with religion. This article reveals the multi-level and nuanced relationship between religiosity and entrepreneurship through a contextual lens by studying the interaction in a specific national country, Turkiye.

Design/methodology/approach

The study uses the life stories of 10 Turkish women entrepreneurs operating in Turkiye. Data were selected purposefully to conduct an in-depth analysis. Thematic content analysis with a discursive approach and deductive and inductive coding methods were performed.

Findings

The findings suggest that the relationship between religiosity and entrepreneurial opportunities is highly contextual and nuanced. Religiosity brings trust and provides access to religious networks which can lead to entrepreneurial opportunities, while leaving people outside of this network bereft of these benefits. The creation of a closed circle for its beneficiaries is a feature of a social network, yet the results show that contextual forces of politics and gender can lead women entrepreneurs outside of this religious network to limit their possibilities of accessing public funding and facilities based on their perceptions as well as negative experiences. It is also seen that religiosity at a certain level is necessary to operate in conservative settings and traditionally masculine business environments with patriarchal practices and norms, as well as due to the religious affinity of the ruling political party. However, because of perceptions and discursive meanings attached to religion and religiosity in the country, women entrepreneurs need to be cautious in expressing their religiosity and find a balance so that they are not seen as unprofessional, incompetent and unqualified as well as do not jeopardise their business due to a controversial religious affiliation.

Originality/value

This paper is of value as it studies religiosity from a contextual perspective enabling and constraining women entrepreneurs in their entrepreneurship in relation to gendered and political structures. In this way, it displays the multiple ways of limitation and support that religiosity can bring for them concerning entrepreneurial opportunities. Turkiye provides a rich context with its mixed religious and secular societal norms and values and neo-liberal institutions and policies to examine the so-far underexplored issue of religiosity in the field of entrepreneurship.