bluuebunny/crossref_metadata_2025 huggingface dataset:
Noncausal relationship between body weight and breast cancer based on bidirectional Mendelian randomization evidence
Authors: Li Qiuhua , Wang Ying , Ren Lu , Liu Zhaozhe
Published: August 2024

Background

Some observational associations between body weight and breast cancer have attracted attention. However, the causal relationship between these 2 factors remains unclear, and more clinical outcomes are needed for its validation.

Methods

Based on statistical data from a Genome Wide Association Study, we performed a bidirectional Mendelian randomization analysis to assess the bidirectional causal relationship between body weight and breast cancer using 4 methods, with inverse variance weighting as the primary method. To verify the robustness and reliability of the causal relationship, we performed a sensitivity analysis using horizontal pleiotropy, outlier, and one-by-one elimination tests.

Results

The inverse variance weighting results revealed no significant positive causal relationship between body weight and breast cancer. Similarly, the reverse analysis revealed no causal effect of breast cancer on body weight.

Conclusions

The relationship between body weight and breast cancer may be attributed to confounding factors.
Impact of Varying Pre-exposure Prophylaxis Programs on HIV and Neisseria gonorrhoeae Transmission Among MSM in the Netherlands: A Modeling Study
Authors: Reitsema Maarten , Wallinga Jacco , van Sighem Ard I. , Bezemer Daniela , van der Valk Marc , van Aar Fleur , Heijne Janneke Cornelia Maria , Hoornenborg Elske , Rozhnova Ganna , van Benthem Birgit , Xiridou Maria
Published: August 2024

Background:

In 2019, a 5-year pre-exposure prophylaxis (PrEP) program started in the Netherlands, in which up to 8500 men who have sex with men (MSM) can obtain PrEP and 3-monthly consultations with HIV/STI testing.

Setting:

We assessed the impact of the PrEP program on transmission of HIV and Neisseria gonorrhea (NG) among MSM in the Netherlands and examined prospective variations of the program after 2024.

Methods:

We used an agent-based model to estimate the effect of the PrEP program. For hypothetical prospective PrEP programs starting in 2024, we varied the capacity (8,500; 12,000; 16,000 participants) and consultation frequency (3-monthly; 6-monthly; 70% 3-monthly and 30% 6-monthly).

Results:

At a capacity of 8,500 participants and 3-monthly consultations, the PrEP program could lead to 3,140 [95% credible interval (95% CrI): 1,780–4,780] and 27,930 (95% CrI: 14,560–46,280) averted HIV and NG infections, requiring 316,050 (95% CrI: 314,120–317,580) consultations. At a capacity of 16,000 participants, the programs with 3-monthly consultations and 6-monthly consultations could lead to comparable number of averted HIV [3,940 (95% CrI: 2,420–5,460), and 3,900 (2,320–5,630) respectively] and NG infections [29,970 (95% CrI: 15,490–50,350), and 29,960 (95% CrI: 13,610–50,620) respectively], while requiring substantially different number of consultations: 589,330 (95% CrI: 586,240–591,160) and 272,590 (95% CrI: 271,770–273,290), respectively.

Conclusions:

Continuation of a PrEP program could lead to a substantial reduction in HIV and NG transmission. More infections could be averted if the number of participants is increased. In turn, the consultation frequency could be reduced without reducing the number of averted infections if capacity is increased.
Determinants of Potential HIV Vaccine Uptake Among Young Sexual Minoritized Men 17–24 Year Old
Authors: John Steven A. , Walsh Jennifer L. , Doherty Ryan M. , Rine Sarah R. , O'Neil Andrew M. , Dang Madeline , Quinn Katherine G.
Published: August 2024

Background:

Failures in prior rollout of HIV prevention efforts have widened disparities in HIV incidence by race/ethnicity among young sexual minoritized men (YSMM). We hypothesized greater perceptions of medical mistrust would be associated with lower willingness to get an HIV vaccine, mediating the relationship between race/ethnicity and willingness to accept a future HIV vaccine.

Methods:

HIV-negative and unknown-status YSMM 17–24 years old (n = 229) recruited through social media and men-for-men networking apps completed online surveys from September 2021 to March 2022. Participants were asked about demographics, medical mistrust (health care-related sexual orientation stigma, health care-related race stigma, global medical mistrust, and trust in health care providers), and willingness to accept a future HIV vaccine.

Results:

Vaccine willingness was highest among White YSMM (96.0%) and lower among Black (71.0%), Latino (83.6%), and multiracial or another race/ethnicity YSMM (80.0%). Even after accounting for medical mistrust constructs as mediators, compared with White participants, Black participants had lower odds of being willing to accept a future HIV vaccine. Participants with greater trust in health care providers had higher odds of willingness to accept a future HIV vaccine.

Discussion:

Gaps in willingness to get an HIV vaccine are evident among YSMM by race/ethnicity, indicating potential further widening of disparities in HIV incidence when a vaccine becomes available without intervention.
Maxillofacial Symptoms and Diagnosis Criteria Concerning Chronic Recurrent Multifocal Osteomyelitis: A Systematic Literature Review
Authors: El Hamid Sami , Barry Florent , Nobile Mathieu , Ferri Joël
Published: August 2024

Introduction:

Chronic recurrent multifocal osteomyelitis (CRMO) is a rare autoinflammatory disease characterized by sterile inflammation of bony tissue. Although it has distinct clinical and radiologic features, it is often misdiagnosed, leading to inappropriate and delayed treatment. Indeed, at the origin the disease can have an exclusive maxillofacial location and so be, at least clinically, difficult to prove.

Objective:

The aim of this study was to summarize through a systematic literature review the clinical, laboratory, and imaging data regarding maxillofacial manifestations of CRMO.

Methods:

The present systematic review of the literature was designed following the standard PROSPERO eligibility criteria. Three electronic databases were searched to find clinical studies describing cases of patients diagnosed with CRMO of the orofacial area. Relevant clinical, radiographic, and laboratory results were extracted.

Results:

The search strategy retrieved 95 articles. Assessment of the full text was done for 47 articles among them, 30 were included. The total patients included was 82, mean age was 8.2 years. Pain and swelling association was present in 94% of the cases, mandible was involved in 96.3% of the cases. Sclerosis, lytic lesion, and periostal reaction were the most frequent radiologic findings.

Conclusion:

Chronic recurrent multifocal osteomyelitis is often misdiagnosed as infectious osteomyelitis, practitioners should therefore be familiar of its distinct clinical course and paraclinical features. Further investigations would be beneficial to assess the extraosseous manifestations and the long-term outcome of CRMO.
Virtual Surgical Planning and Customized Subperiosteal Implant for Reconstruction of Maxillary Defect After Oncological Resection
Authors: Kundakçioğlu Abdulsamet , Bilazeroğlu Eda , Emes Yusuf , Aybar Büket
Published: August 2024

Reconstructing defects after jaw tumor removal is difficult because of the complex facial skeleton, which affects patient nutrition and self-confidence. Traditional methods like iliac bone or fibula grafts take a long time and may raise aesthetic issues. Advancements in computer-aided three-dimensional (3D) modeling allow precise surgical planning, leading to more symmetrical reconstructions. Moreover, the application of custom-designed prostheses, similar to joint prostheses used in joint surgery, offers promising outcomes, particularly in cases involving the removal of the ramus and temporomandibular joint. A 28-year-old female had a maxillectomy for maxillary myxoma, using 3D-printed implants for reconstruction and dental rehabilitation. “Computer-Aided Design” software optimized implant coordination, reducing soft tissue pressure. Postoperative permanent dentures were successful with few complications. Compared with traditional methods, 3D-printed titanium plates improve patient satisfaction and reduce treatment time, particularly with sufficient soft tissue thickness, offering aesthetic benefits and eliminating extra surgeries for effective defect treatment.
Effect of Delayed Parathyroidectomy on Risk of Future Cardiovascular and Nephrolithiasis Interventions in Adults with Primary Hyperparathyroidism [Original Study]
Authors: Ramonell Kimberly M. , Liou Rachel , Zheng Xinyan , Song Zhixing , Lee James A. , Sedrakyan Art , Chen Herbert
Published: August 2024

Objective:

To determine whether the timing of parathyroid surgery impacts the risk of renal stone retreatment and cardiovascular interventions.

Summary Background Data:

Long-term, untreated primary hyperparathyroidism is associated with significant morbidity including nephrolithiasis and cardiovascular disease.

Methods:

We conducted a Population-based Cohort study of New York and California state-wide data from 2000-2020. Adult patients who underwent renal stone treatment and subsequently diagnosed with primary hyperparathyroidism (pHPT) and underwent parathyroidectomy (PTX) were included. Patients were excluded if PTX was prior to index stone procedure, they underwent second stone treatment within 6 months, with stage V CKD, with secondary or tertiary hyperparathyroidism, with prior kidney transplant or hemodialysis, or with prior cancer diagnosis. Rate of renal stone retreatment and cardiovascular interventions after PTX in pHPT patients with nephrolithiasis who underwent parathyroid surgery at ≤ 2 years and >2 years after index stone procedure was measured.

Results:

We identified 2,093 patients who underwent first-time stone treatment and subsequent PTX. The median time to PTX was 560 days (IQR 187-1477) and follow-up was 7.4 years (IQR 4.5-13.1). Delaying PTX for more than 2 years increased the risk of renal stone retreatment by 59% (HR 1.59; P<0.001), increased the risk of experiencing coronary disease or associated interventions by 118% (HR=2.18; P=0.01), and increased the risk of experiencing an overall cardiovascular event by 52% (HR 1.52; P<0.01).

Conclusions and Relevance:

In symptomatic pHPT, delaying PTX significantly increases the risk of requiring future stone retreatment and cardiac/vascular surgical interventions. This highlights the importance of early surgical referral and multidisciplinary approaches to optimize outcomes and resource utilization in pHPT.
Promoting sleep and rest in hospitalized children: a best practice implementation project
Authors: Lechosa-Muñiz Carolina , Ruiz-Azcona Laura , Pérez Belmonte Elena , Gallego-Jiménez Marina , Cabero-Pérez María Jesús
Published: August 2024

Objective:

The objective of this project was to implement scientific evidence to promote sleep and rest in pediatric patients during hospitalization.

Introduction:

Hospitals are not conducive to quality sleep, as external factors such as light, noise, and interruptions from health care staff can disturb patients. Being hospitalized has a detrimental impact on children's sleep because it reduces how much sleep they get and the quality of that sleep. It has been reported that up to 20% to 30% of hospitalized children experience sleep problems.

Methods:

This project was conducted at the Marqués de Valdecilla University Hospital in Cantabria, northern Spain. The project used the JBI Evidence Implementation Framework, which is grounded in an audit, feedback, and re-audit process, together with a structured approach to identifying and managing barriers to change. The study subjects were 100 children aged 2 to 16 years, who were admitted to the hospital's pediatric unit from November to December 2021, and 27 multi-disciplinary health care staff.

Results:

Implementing the evidence-based strategies improved our care practices, with the follow-up audit results showing a marked improvement in compliance. Thus, training health care staff on pediatric sleep increased from 4% to 80%; using a multi-faceted approach to sleep promotion increased from 21% to 87%; and promoting relaxation techniques to promote sleep increased from 0% to 80%.

Conclusions:

The project met its objectives. Areas for improving children's sleep and rest during hospitalization were identified. To avoid resistance to change, it was necessary to involve the entire team and maintain training. We recommend follow-up audits once a year, to ensure the sustainability of the project.

Spanish abstract:

http://links.lww.com/IJEBH/A252
Sir David R. Cox. 15 July 1924—18 January 2022
Authors: Reid FRS Nancy
Published: August 2024

David Cox was the leading statistical scientist of his generation and had an extraordinary influence on the field. His research career spanned some 75 years and 386 published works, with several drafts in preparation at the time of his death. He was held in extremely high regard by the community of scholars for his seminal contributions to scholarship, his enthusiasm for science and his generosity of intellect. One obituary called him a ‘rock star’ of the statistical world, and in spite of the hyperbole the description is apt. His work was very broad; he made influential contributions to the fields of experimental design, stochastic processes, statistical methodology, foundations of inference, statistics in medicine and public health, and more. His 23 published books continue to be key references for students and researchers. His most widely cited paper (
J. R. Stat. Soc. B
34
, 187–220 (1972)) introduced what is now called the Cox model for the analysis of survival data; this was included in
Nature
’s list of the top 100 cited scientific papers of all time. He received many accolades, including the Copley Medal (2010) and the inaugural International Prize in Statistics (2016).
Punctuated virus-driven succession generates dynamical alternations in CRISPR-mediated microbe-virus coevolution
Authors: Liaghat Armun , Yang Jiayue , Whitaker Rachel , Pascual Mercedes
Published: August 2024

The coevolutionary dynamics of lytic viruses and microbes with CRISPR-Cas immunity exhibit alternations between sustained host control of viral proliferation and major viral epidemics in previous computational models. These
alternating
dynamics have yet to be observed in other host–pathogen systems. Here, we address the breakdown of control and transition to large outbreaks with a stochastic eco-evolutionary model. We establish the role of host density-dependent competition in punctuated virus-driven succession and associated diversity trends that concentrate escape pathways during control phases. Using infection and escape networks, we derive the viral emergence probability whose fluctuations of increasing size and frequency characterize the approach to large outbreaks. We explore alternation probabilities as a function of non-dimensional parameters related to the probability of viral escape and host competition. Our results demonstrate how emergent feedbacks between host competition and viral diversification render the host immune structure fragile, potentiating a dynamical transition to large epidemics.
Evidence of HARKing in mouse behavioural tests of anxiety
Authors: Rosso Marianna , Herrera Adrian , Würbel Hanno , Voelkl Bernhard
Published: August 2024

Over the last decades, behavioural tests in animals, especially rodents, have been a standard screening method to determine the mechanisms of action and efficacy of psychopharmacological compounds. Yet, recently the reproducibility of some of these tests has been questioned. Based on a systematic review of the sensitivity of mouse behavioural tests to anxiolytic drugs, we analysed behavioural outcomes extracted from 206 studies testing the effect of diazepam in either the open-field test or the hole-board test. Surprisingly, we found that both the rationale given for using the test, whether to detect anxiolytic or sedative effects, and the predicted effect of diazepam, anxiolytic or sedative, strongly depended on the reported test results. The most likely explanation for such strong dependency is post hoc reasoning, also called hypothesizing after the results are known (HARKing). HARKing can invalidate study outcomes and hampers evidence synthesis by inflating effect sizes. It may also lead researchers into blind alleys, and waste animals, time and resources for inconclusive research.
Solitary humpback whales manufacture bubble-nets as tools to increase prey intake
Authors: Szabo A. , Bejder L. , Warick H. , van Aswegen M. , Friedlaender A. S. , Goldbogen J. , Kendall-Bar J. M. , Leunissen E. M. , Angot M. , Gough W. T.
Published: August 2024

Several animal species use tools for foraging; however, very few manufacture and/or modify those tools. Humpback whales, which manufacture bubble-net tools while foraging, are among these rare species. Using animal-borne tag and unoccupied aerial system technologies, we examine bubble-nets manufactured by solitary humpback whales (
Megaptera novaeangliae
) in Southeast Alaska while feeding on krill. We demonstrate that the nets consist of internally tangential rings and suggest that whales actively control the number of rings in a net, net size and depth and the horizontal spacing between neighbouring bubbles. We argue that whales regulate these net structural elements to increase per-lunge prey intake by, on average, sevenfold. We measured breath rate and swimming and lunge kinematics to show that the resulting increase in prey density does not increase energetic expenditure. Our results provide a novel insight into how bubble-net tools manufactured by solitary foraging humpback whales act to increase foraging efficiency.
Metallic aluminium in municipal solid waste incineration fly ash as a blowing agent for porous alkali-activated granules
Authors: Luukkonen Tero , Yu Yangmei , Adhikary Suman Kumar , Kauppinen Sami , Finnilä Mikko , Perumal Priyadharshini
Published: August 2024

Porous alkali-activated materials are synthetic aluminosilicates that should be often produced as granules for practical applications. In the present study, municipal solid waste incineration fly ash with ~1.2 wt% of metallic aluminium was used as a novel blowing agent for metakaolin (their ratio ranged from 0% to 100%) with an aqueous sodium silicate solution as the alkali-activator and granulation fluid in high-shear granulation. The compressive strength of all granules was sufficient (≥2 MPa). Water absorption indicated an increase in porosity as the fly ash content increased. However, X-ray microtomography imaging showed no clear correlation between the fly ash content and porosity. The granules exceeded the leaching limits for earth construction materials for antimony, vanadium, chloride and sulphate. Of those, antimony, chloride and sulphate could be controlled by decreasing the ash content, but the source of vanadium was identified as metakaolin. The increase in the fly ash content decreased the cation exchange capacity of the granules. In conclusion, the recommended fly ash content is equivalent to 0.3 wt% of Al
0
and the developed granules could be best suited as light-weight artificial aggregates in concrete where the additional binder would provide stabilization to decrease the leaching.
A large-scale study and six-month follow-up of an intervention to reduce causal illusions in high school students
Authors: Martínez Naroa , Matute Helena , Blanco Fernando , Barberia Itxaso
Published: August 2024

Causal illusions consist of believing that there is a causal relationship between events that are actually unrelated. This bias is associated with pseudoscience, stereotypes and other unjustified beliefs. Thus, it seems important to develop educational interventions to reduce them. To our knowledge, the only debiasing intervention designed to be used at schools was developed by Barberia
et al.
(Barberia
et al.
2013
PLoS One
8
, e71303 (doi:
10.1371/journal.pone.0071303
)), focusing on base rates, control conditions and confounding variables. Their assessment used an active causal illusion task where participants could manipulate the candidate cause. The intervention reduced causal illusions in adolescents but was only tested in a small experimental project. The present research evaluated it in a large-scale project through a collaboration with the Spanish Foundation for Science and Technology (FECYT), and was conducted in schools to make it ecologically valid. It included a pilot study (
n
= 287), a large-scale implementation (
n
= 1668; 40 schools) and a six-month follow-up (
n
= 353). Results showed medium-to-large and long-lasting effects on the reduction of causal illusions. To our knowledge, this is the first research showing the efficacy and long-term effects of a debiasing intervention against causal illusions that can be used on a large scale through the educational system.
Functional response metrics explain and predict high but differing ecological impacts of juvenile and adult lionfish
Authors: McCard Monica , McCard Nathan , Coughlan Neil E. , South Josie , Kregting Louise , Dick Jaimie T. A.
Published: August 2024

Recent accumulation of evidence across taxa indicates that the ecological impacts of invasive alien species are predictable from their functional response (FR; e.g. the maximum feeding rate) and functional response ratio (FRR; the FR attack rate divided by handling time). Here, we experimentally derive these metrics to predict the ecological impacts of both juvenile and adult lionfish (
Pterois volitans
), one of the world’s most damaging invaders, across representative and likely future prey types. Potentially prey-population destabilizing Type II FRs were exhibited by both life stages of lionfish towards four prey species:
Artemia salina
,
Gammarus oceanicus
,
Palaemonetes varians
and
Nephrops norvegicus
. FR magnitudes revealed ontogenetic shifts in lionfish impacts where juvenile lionfish displayed similar if not higher consumption rates than adult lionfish towards prey, apart from
N. norvegicus
, where adult consumption rate was considerably higher. Additionally, lionfish FRR values were very substantially higher than mean FRR values across known damaging invasive taxa. Thus, both life stages of lionfish are predicted to contribute to differing but high ecological impacts across prey communities, including commercially important species. With lionfish invasion ranges currently expanding across multiple regions globally, efforts to reduce lionfish numbers and population size structure, with provision of prey refugia through habitat complexity, might curtail their impacts. Nevertheless, the present study indicates that management programmes to support early detection and complete eradication of lionfish individuals when discovered in new regions are advised.
Complete genome of the Medicago anthracnose fungus, Colletotrichum destructivum, reveals a mini-chromosome-like region within a core chromosome
Authors: Lapalu Nicolas , Simon Adeline , Lu Antoine , Plaumann Peter-Louis , Amselem Joëlle , Pigné Sandrine , Auger Annie , Koch Christian , Dallery Jean-Félix , O'Connell Richard J.
Published: August 2024

Colletotrichum destructivum (Cd) is a phytopathogenic fungus causing significant economic losses on forage legume crops (Medicago and Trifolium species) worldwide. To gain insights into the genetic basis of fungal virulence and host specificity, we sequenced the genome of an isolate from Medicago sativa using long-read (PacBio) technology. The resulting genome assembly has a total length of 51.7 Mb and comprises ten core chromosomes and two accessory chromosomes, all of which were sequenced from telomere to telomere. A total of 15, 631 gene models were predicted, including genes encoding potentially pathogenicity-related proteins such as candidate-secreted effectors (484), secondary metabolism key enzymes (110) and carbohydrate-active enzymes (619). Synteny analysis revealed extensive structural rearrangements in the genome of Cd relative to the closely related Brassicaceae pathogen, Colletotrichum higginsianum. In addition, a 1.2 Mb species-specific region was detected within the largest core chromosome of Cd that has all the characteristics of fungal accessory chromosomes (transposon-rich, gene-poor, distinct codon usage), providing evidence for exchange between these two genomic compartments. This region was also unique in having undergone extensive intra-chromosomal segmental duplications. Our findings provide insights into the evolution of accessory regions and possible mechanisms for generating genetic diversity in this asexual fungal pathogen.
Phylogenetic diversity of putative nickel-containing carbon monoxide dehydrogenase-encoding prokaryotes in the human gut microbiome
Authors: Katayama Yuka Adachi , Kamikawa Ryoma , Yoshida Takashi
Published: August 2024

Although the production of carbon monoxide (CO) within the human body has been detected, only two CO-utilizing prokaryotes (CO utilizers) have been reported in the human gut. Therefore, the phylogenetic diversity of the human gut CO-utilizing prokaryotes remains unclear. Here, we unveiled more than a thousand representative genomes containing genes for putative nickel-containing CO dehydrogenase (pCODH), an essential enzyme for CO utilization. The taxonomy of genomes encoding pCODH was expanded to include 8 phyla, comprising 82 genera and 248 species. In contrast, putative molybdenum-containing CODH genes were not detected in the human gut microbial genomes. pCODH transcripts were detected in 97.3 % (n=110) of public metatranscriptome datasets derived from healthy human faeces, suggesting the ubiquitous presence of prokaryotes bearing transcriptionally active pCODH genes in the human gut. More than half of the pCODH-encoding genomes contain a set of genes for the autotrophic Wood–Ljungdahl pathway (WLP). However, 79 % of these genomes commonly lack a key gene for the WLP, which encodes the enzyme that synthesizes formate from CO2, suggesting that potential human gut CO-utilizing prokaryotes share a degenerated gene set for WLP. In the other half of the pCODH-encoding genomes, seven genes, including putative genes for flavin adenine dinucleotide-dependent NAD(P) oxidoreductase (FNOR), ABC transporter and Fe-hydrogenase, were found adjacent to the pCODH gene. None of the putative genes associated with CO-oxidizing respiratory machinery, such as energy-converting hydrogenase genes, were found in pCODH-encoding genomes. This suggests that the human gut CO utilization is not for CO removal, but potentially for fixation and/or biosynthesis, consistent with the harmless yet continuous production of CO in the human gut. Our findings reveal the diversity and distribution of prokaryotes with pCODH in the human gut microbiome, suggesting their potential contribution to microbial ecosystems in human gut environments.
Synergy between Group 2 capsules and lipopolysaccharide underpins serum resistance in extra-intestinal pathogenic Escherichia coli
Authors: McGarry Naoise , Roe Domhnall , Smith Stephen G. J.
Published: August 2024

Escherichia coli (E. coli) is a major cause of urinary tract infections, bacteraemia, and sepsis. CFT073 is a prototypic, urosepsis isolate of sequence type (ST) 73. This laboratory, among others, has shown that strain CFT073 is resistant to serum, with capsule and other extracellular polysaccharides imparting resistance. The interplay of such polysaccharides remains under-explored. This study has shown that CFT073 mutants deficient in lipopolysaccharide (LPS) O-antigen and capsule display exquisite serum sensitivity. Additionally, O-antigen and LPS outer core mutants displayed significantly decreased surface K2 capsule, coupled with increased unbound K2 capsule being detected in the supernatant. The R1 core and O6 antigen are involved in the tethering of K2 capsule to the CFT073 cell surface, highlighting the importance of the R1 core in serum resistance. The dependence of capsule on LPS was shown to be post-transcriptional and related to changes in cell surface hydrophobicity. Furthermore, immunofluorescence microscopy suggested that the surface pattern of capsule is altered in such LPS core mutants, which display a punctate capsule pattern. Finally, targeting LPS biosynthesis using sub-inhibitory concentrations of a WaaG inhibitor resulted in increased serum sensitivity and decreased capsule in CFT073. Interestingly, the dependency of capsule on LPS has been observed previously in other Enterobacteria, indicating that the synergy between these polysaccharides is not just strain, serotype or species-specific but may be conserved across several pathogenic Gram-negative species. Therefore, using WaaG inhibitor derivatives to target LPS is a promising therapeutic strategy to reduce morbidity and mortality by reducing or eliminating surface capsule.
ChatGPT as a bioinformatic partner
Authors: Mondillo Gianluca , Perrotta Alessandra , Colosimo Simone , Frattolillo Vittoria
Published: August 2024

The advanced Large Language Model ChatGPT4o, developed by OpenAI, can be used in the field of bioinformatics to analyze and understand cross-reactive allergic reactions. This study explores the use of ChatGPT4o to support research on allergens, particularly in the cross-reactivity syndrome between cat and pork. Using a hypothetical clinical case of a child with a confirmed allergy to Fel d 2 (cat albumin) and Sus s 1 (pork albumin), the model guided data collection, protein sequence analysis, and three-dimensional structure visualization. Through the use of bioinformatics tools like SDAP 2.0 and BepiPRED, the epitope regions of the allergenic proteins were predicted, confirming their accessibility to immunoglobulin E (IgE) and probability of cross-reactivity. The results show that regions with high epitope probability exhibit high surface accessibility and predominantly coil and helical structures. The construction of a phylogenetic tree further supported the evolutionary relationships among the studied allergens. ChatGPT4o has demonstrated its usefulness in guiding non-specialist researchers through complex bioinformatics processes, making advanced science accessible and improving analytical and innovation capabilities.
Epithelial-mesenchymal boundary guides cell shapes and axis elongation in embryonic explants
Authors: Barrett Katia , Anand Shalabh , Thome Virginie , Lenne Pierre-François , Merkel Matthias
Published: August 2024

The spatial arrangement of tissues during development establishes regions of tissue-tissue interactions. While such interactions are prominent during gastrulation and organogenesis, how they guide morphogenesis remains unclear. Here, using Xenopus animal cap explants, we show that the coupling between epithelial and mesenchymal tissues is instrumental in robust axis elongation. We find that mesenchymal and epithelial tissues drive elongation hierarchically - the epithelium can elongate independently, while the mesenchyme requires the initial presence of the epithelium. The epithelial-mesenchymal boundary defines the direction of cell shape alignment and the axis of tissue elongation. Prior to explant elongation, epithelial cells align and elongate, a process that propagates into the underlying mesenchyme. These findings reveal how tissue boundaries can organize coherent axis elongation without external patterning cues, providing insights into the self-organization principles that guide embryonic morphogenesis.
Chiral properties of the nucleon interpolating current and
θ
-dependent observables
Authors: Ema Yohei , Gao Ting , Pospelov Maxim , Ritz Adam
Published: August 2024

We revisit the chiral properties of nucleon interpolating currents, and show that of the two leading order currents j1 and j2, only two linear combinations j1±j2 transform covariantly under the anomalous U(1)A symmetry. As a result, calculations of quantities which vanish by symmetry in the chiral limit may produce unphysical results if carried out with different linear combinations of the currents. This includes observables such as electric dipole moments, induced by the quantum chromodynamics (QCD) parameter θ, and the θ-dependence of the nucleon mass. For completeness, we also exhibit the leading order results for nucleon electric dipole moments (dn,p) induced by θ, and the nucleon magnetic moments (μn,p), when calculated using QCD sum rules for both the covariant choices of the nucleon interpolating current. The results in each channel, conveniently expressed as the ratios, dn,p/μn,p, are numerically consistent, and reflect the required physical dependence on θ.

Published by the American Physical Society
2024
Exact quantization conditions and full transseries structures for
PT
symmetric anharmonic oscillators
Authors: Kamata Syo
Published: August 2024

We study exact Wentzel–Kramers–Brillouin analysis (EWKB) for a PT symmetric quantum mechanics (QM) defined by the potential VPT(x)=ω2x2+gx2K(ix)ϵ with ω∈R≥0,

g

∈

R

>

0

and K,ϵ∈N to clarify its perturbative/nonperturbative structure. In our analysis, we mainly consider the massless cases, i.e., ω=0, and derive the exact quantization conditions (QCs) for arbitrary (K,ϵ) including all perturbative/nonperturbative corrections. From the exact QCs, we clarify full transseries structure of the energy spectra with respect to the inverse energy level expansion, and then formulate the Gutzwiller trace formula, the spectral summation form, and the Euclidean path integral. For the massive cases, i.e., ω>0, we show the fact that, by requiring the existence of the solution of the exact QCs, the path of analytic continuation in EWKB is uniquely determined for a given N=2K+ϵ, and in consequence the exact QCs, the energy spectra, and the three formulas are all perturbative. Similarities to Hermitian QMs and resurgence are also discussed as additional remarks.

Published by the American Physical Society
2024
Non-Markovian enhancement of nonequilibrium quantum thermometry
Authors: Aiache Y. , Seida C. , El Anouz K. , El Allati A.
Published: August 2024

Accurate measurement at low temperatures is essential for both gaining a fundamental understanding of physical processes and developing technological applications. In this paper, we propose a theoretical framework for quantum temperature sensing in a composite environment with non-Markovian dynamics. Our suggested system uses a single qubit as a temperature sensor to test its sensitivity in calculating the temperature of a composite environment. We show that the temperature sensor's sensitivity can saturate the quantum Cramér-Rao bound by measuring the σ̂z observable of the probe qubit. Temperature sensing performance is measured using the quantum signal-to-noise ratio. We underline how non-Markovianity can enhance the performance of our thermometers. Furthermore, we emphasize that nonequilibrium conditions do not always result in the best sensitivities in temperature estimation.

Published by the American Physical Society
2024
Exact solution for the collective non-Markovian decay of two fully excited quantum emitters
Authors: Lanuza Alfonso , Schneble Dominik
Published: August 2024

Waveguide quantum electrodynamics constitutes a modern paradigm for the interaction of light and matter, in which strong coupling, bath structure, and propagation delays can break the radiative conditions that quantum emitters typically encounter in free space. These characteristics intertwine the excitations of quantum emitters and guided radiation modes to form complex multiphoton dynamics. So far, combining the collective decay of the emitters with the non-Markovian effects induced by the modes has escaped a full solution and the detailed physics behind these systems remains unknown. Here we analyze such a collective non-Markovian decay in a minimal system of two excited emitters coupled to a one-dimensional single-band waveguide. We develop an exact solution for this system in terms of elementary functions that unveils hidden symmetries and predicts new forms of spontaneous decay. The collective non-Markovian dynamics, which are strongly dependent on the vacuum coupling and the detuning from the center of the band, show exotic features that can be characterized with a simple and readily available criterion. Our analytic methods shed light on the complexity of collective light-matter interactions and open up a pathway for understanding multiparticle open quantum systems.

Published by the American Physical Society
2024
Quantum inception score
Authors: Sone Akira , Tanji Akira , Yamamoto Naoki
Published: August 2024

Motivated by the great success of classical generative models in machine learning, enthusiastic exploration of their quantum version has recently started. To depart on this journey, it is important to develop a relevant metric to evaluate the quality of quantum generative models; in the classical case, one such example is the (classical) inception score (cIS). In this paper, as a natural extension of cIS, we propose the quantum inception score (qIS) for quantum generators. Importantly, qIS relates the quality to the Holevo information of the quantum channel that classifies a given dataset. In this context, we show several properties of qIS. First, qIS is greater than or equal to the corresponding cIS, which is defined through projection measurements on the system output. Second, the difference between qIS and cIS arises from the presence of quantum coherence, as characterized by the resource theory of asymmetry. Third, when a set of entangled generators is prepared, there exists a classifying process leading to the further enhancement of qIS. Fourth, we harness the quantum fluctuation theorem to characterize the physical limitation of qIS. Finally, we apply qIS to assess the quality of the one-dimensional spin chain model as a quantum generative model, with the quantum convolutional neural network as a quantum classifier, for the phase classification problem in the quantum many-body physics.

Published by the American Physical Society
2024
Fluctuation-dominated quantum oscillations in excitonic insulators
Authors: Allocca Andrew A. , Cooper Nigel R.
Published: August 2024

The realization of excitonic insulators in transition metal dichalcogenide systems has opened the door to explorations of the exotic properties that such a state exhibits. We study theoretically the potential for excitonic insulators to show an anomalous form of quantum oscillations: the de Haas–van Alphen effect in an insulating system. We focus on the role of the interactions that generate the energy gap and show that it is crucial to consider quantum fluctuations that go beyond the mean-field treatment. Remarkably, quantum fluctuations can be dominant and lead to quantum oscillations that are significantly larger than those predicted using mean-field theory. Indeed, in experimentally accessible parameter regimes these fluctuation-generated quantum oscillations can even be larger than what would be found for the corresponding gapless system.

Published by the American Physical Society
2024
Two atoms in a harmonic trap with spin-orbital-angular-momentum coupling
Authors: Chen Xiao-Long , Chen Aixi , Peng Shi-Guo
Published: August 2024

We study the problem of two harmonically trapped atoms in the presence of spin-orbital-angular-momentum (SOAM) coupling. The two-body energy spectrum is numerically calculated by utilizing the exact diagonalization method. We analyze how the degeneracy of energy levels is lifted under the interplay between the interatomic interaction and SOAM coupling. The exact numerical results show excellent agreement with that of perturbation theory in the weak-interaction limit as well as that in the absence of SOAM coupling. The properties of correlations between the two atoms are also discussed with respect to the interaction strength. The findings in this paper may provide valuable insights into few-body physics subjected to SOAM coupling and the possible experimental detection of spectrum functions in many-body systems, such as radiofrequency spectroscopy.

Published by the American Physical Society
2024
Emergence and growth dynamics of wetting-induced phase separation on soft solids
Authors: Qian Wenjie , Zhao Weiwei , Qian Tiezheng , Xu Qin
Published: August 2024

Liquid droplets on soft solids, such as soft polymeric gels, can induce substantial surface deformations, leading to the formation of wetting ridges at contact points. While these contact ridges have been shown to govern the rich surface mechanics on compliant substrates, the inherently divergent characteristics of contact points and the multiphase nature of soft reticulated gels pose great challenges for continuum mechanical theories in modeling soft wetting phenomena. In this study, we report experimental characterizations of the emergence and growth dynamics of the wetting-induced phase separation. The measurements demonstrate how the migration of free chains prevents the stress singularities at contact points. Based on the Onsager variational principle, we present a phenomenological model that effectively captures the extraction process of free chains, including a crossover from a short-term diffusive state to a long-term equilibrium state. By comparing model predictions with experimental results for varied crosslinking densities, we reveal how the intrinsic material parameters of soft gels dictate phase-separation dynamics.

Published by the American Physical Society
2024
Orientation-dependent yield and Bauschinger effects in two-dimensional Yukawa solids
Authors: Lu Shaoyu , Huang Dong , Liang Chen , Feng Yan
Published: August 2024

Langevin dynamics simulations of two-dimensional (2D) Yukawa solids are performed to investigate the orientation-dependent yield and Bauschinger effects in solid 2D dusty plasmas. The yield stress of 2D Yukawa solids under different conditions is determined from the corresponding stress-strain response curve, defect fraction, and deviation from the affine displacement. It is discovered that both the shear modulus and yield stress are orientation dependent, exhibiting the significant anisotropic behaviors. It is found that the dependence of the calculated atomic elastic constant on the lattice orientation completely agrees with those of the shear modulus and yield stress. It is also found that, for different initial lattice orientations, the Yukawa solid exhibits the significant regular or reverse Bauschinger effects, or even non-Bauschinger effect.

Published by the American Physical Society
2024
Sodium chloride induced nitrogen salt with cyclo-
N5
anions at high pressure
Authors: Zhang Bi , Xu Meiling , Xin Yu , Lin Shuyi , Hao Jian , Wang Yanchao , Li Yinwei
Published: August 2024

The energy landscape of sodium chloride-nitrogen mixtures has been comprehensively explored to examine the ability of the formation of unknown compounds under pressures of up to 100 GPa, using swarm-intelligence structure prediction methodology and first-principles calculations. We identified a thermodynamically stable NaN5ClN5 compound containing two cyclo-N5 species under pressures exceeding 53 GPa, representing milder conditions in comparison to those requisite for pure solid nitrogen. In NaN5ClN5, the high electron affinity of the cyclo-N5 motif allows it to oxidize the chlorine atoms, resulting in the formation of two cyclo-N5 anions. Additionally, the weak covalent interactions between Cl and nearby N atoms plays a key role in stabilization of structure. It has been demonstrated that simple NaN5 salt was a suitable precursor for the synthesis of NaN5ClN5 at high pressure. molecular dynamics simulations demonstrated the recoverability of NaN5ClN5 as a metastable phase at ambient pressure-temperature conditions. Additionally, NaN5ClN5 exhibits a higher energy density of 3.86 kJ/g and a lower mass density of 1.67 g/cm3 in comparison to metal pentazolate salts, highlighting its potential as a high energy-density material.

Published by the American Physical Society
2024
Impossibility of adversarial self-testing and secure sampling
Authors: Bansal Akshay , Arora Atul Singh , Van Himbeeck Thomas , Sikora Jamie
Published: August 2024

Self-testing is the task where spatially separated Alice and Bob cooperate to deduce the inner workings of untrusted quantum devices by interacting with them in a classical manner. We examine the task above where Alice and Bob do not trust each other which we call adversarial self-testing. We show that adversarial self-testing implies secure sampling—a simpler task that we introduce where distrustful Alice and Bob wish to sample from a joint probability distribution with the guarantee that an honest party's marginal is not biased. By extending impossibility results in two-party quantum cryptography, we give a simple proof that both of these tasks are impossible in all but trivial settings.

Published by the American Physical Society
2024
Quantum soliton-trains of strongly correlated impurities in Bose-Einstein condensates
Authors: Hiyane Hoshu , Busch Thomas , Fogarty Thomás
Published: August 2024

Strongly correlated impurities immersed in a Bose-Einstein condensate (BEC) can form a periodic structure of tightly localized single atoms due to competing inter and intraspecies interactions, leading to a self-organized pinned state. In this work, we show numerically that the impurities in the self-pinned state form a soliton-train, as a consequence of a BEC-mediated attractive self-interaction and ordering due to the exclusion principle. The dynamics of the impurities possess the characteristics of bright matter-wave soliton trains as often seen in classical fields; however, in the few impurities cases, the detailed nature of collisions is determined by their quantum statistics.

Published by the American Physical Society
2024
Robust Estimation of the Quantum Fisher Information on a Quantum Processor
Authors: Vitale Vittorio , Rath Aniket , Jurcevic Petar , Elben Andreas , Branciard Cyril , Vermersch Benoît
Published: August 2024

We present the experimental measurement, on a quantum processor, of a series of polynomial lower bounds that to the quantum Fisher information (QFI), a fundamental quantity for certifying multipartite entanglement that is useful for metrological applications. We combine advanced methods of the randomized measurement toolbox to obtain estimators that are robust regarding drifting errors caused uniquely during the randomized measurement protocol. We estimate the QFI for Greenberger-Horne-Zeilinger states, observing genuine multipartite entanglement. Then we prepare the ground state of the transverse-field Ising model at the critical point using a variational circuit. We estimate its QFI and investigate the interplay between state optimization and noise induced by our increasing the circuit depth.

Published by the American Physical Society
2024