bluuebunny/crossref_metadata_2025 huggingface dataset:
Signature of Superconductivity in Pressurized Trilayer-Nickelate Pr4Ni3O10–δ
Authors: Huang 黄 Xing 星 , Zhang 张 Hengyuan 恒源 , Li 李 Jingyuan 婧嫄 , Huo 霍 Mengwu 梦五 , Chen 陈 Junfeng 俊峰 , Qiu 邱 Zhengyang 钲阳 , Ma 马 Peiyue 培跃 , Huang 黄 Chaoxin 潮欣 , Sun 孙 Hualei 华蕾 , Wang 王 Meng 猛
Published: December 2024

The discovery of high-temperature superconductivity in La3Ni2O7 and La4Ni3O10 under pressure has garnered extensive attention. Herein, we report systematic investigations on the structure, magnetism, and electrical resistance evolutions of Pr4Ni3O10–δ
polycrystalline samples under various pressures. Pr4Ni3O10–δ
exhibits density wave transitions on Ni and Pr sublattices at approximately 157.6 and 4.3 K, respectively. The density wave can be progressively suppressed by pressure. A structural transformation from the monoclinic P21/a space group to the tetragonal I4/mmm occurs around 20 GPa. An apparent drop in resistance with an evident magnetic field dependence is observed at pressures above 20 GPa, indicating the emergence of superconductivity. The discovery of superconductivity in Pr4Ni3O10–δ
broadens the family of nickelate superconductors. Pr4Ni3O10–δ
provides a new platform for investigation of the mechanisms of superconductivity in the Ruddlesden–Popper phases of nickelates.
A new search for the variation of fundamental constants using the rovibrational levels and isotope effects of the magnesium fluoride molecule
Authors: Wu 吴 Di 迪 , Wei 魏 Jin 晋 , Dong 董 Taojing 涛晶 , Zu 祖 Chenyu 晨宇 , Xia 夏 Yong 勇 , Yin 印 Jianping 建平
Published: December 2024

The recently demonstrated methods for cooling and trapping diatomic molecules offer new possibilities for precision searches in fundamental physical theories. Here, we propose to study the variations of the fine-structure constant (α = e
2/(ℏc)) and the proton-to-electron mass ratio (μ = m
p/m
e) with time by taking advantage of the nearly degenerate rovibrational levels in the electronic states of the magnesium fluoride (MgF) molecule. Specifically, due to the cancellation between the fine-structure splitting and the rovibrational intervals in the different MgF natural isotopes, a degeneracy occurs for A2 Π3/2 (v′ = 0, J′ = 18.5, −) and A2Π1/2 (v″ = 0, J″ = 20.5, −). We find that using the nearly degenerate energy level of such states can be 104 times more sensitive than using a pure rotational transition to measure the variations of α and μ. To quantify the small gap between A2Π3/2 (v′ = 0, J′ = 18.5, −) and A2 Π1/2 (v″ = 0, J″ = 20.5, −), special transitions of choice are feasible:

X
2

Σ

1
/
2

+

(v = 0, J = 19.5, +) to A2Π3/2 (v′ = 0, J′ = 18.5, −) and

X
2

Σ

1
/
2

+

(v = 0, J = 19.5, +) to A2Π1/2 (v″ = 0, J″ = 20.5, −). In addition, we estimate the frequency uncertainties caused by the narrow linewidth, Zeeman shift, Stark shift, Doppler broadening and blackbody radiation.
When neuromodulation met control theory
Authors: Guidotti Roberto , Basti Alessio , Pieramico Giulia , D’Andrea Antea , Makkinayeri Saeed , Pettorruso Mauro , Roine Timo , Ziemann Ulf , Ilmoniemi Risto J , Luca Romani Gian , Pizzella Vittorio , Marzetti Laura
Published: December 2024

The brain is a highly complex physical system made of assemblies of neurons that work together to accomplish elaborate tasks such as motor control, memory and perception. How these parts work together has been studied for decades by neuroscientists using neuroimaging, psychological manipulations, and neurostimulation. Neurostimulation has gained particular interest, given the possibility to perturb the brain and elicit a specific response. This response depends on different parameters such as the intensity, the location and the timing of the stimulation. However, most of the studies performed so far used previously established protocols without considering the ongoing brain activity and, thus, without adaptively targeting the stimulation. In control theory, this approach is called open-loop control, and it is always paired with a different form of control called closed-loop, in which the current activity of the brain is used to establish the next stimulation. Recently, neuroscientists are beginning to shift from classical fixed neuromodulation studies to closed-loop experiments. This new approach allows the control of brain activity based on responses to stimulation and thus to personalize individual treatment in clinical conditions. Here, we review this new approach by introducing control theory and focusing on how these aspects are applied in brain studies. We also present the different stimulation techniques and the control approaches used to steer the brain. Finally, we explore how the closed-loop framework will revolutionize the way the human brain can be studied, including a discussion on open questions and an outlook on future advances.
Optimal convergence of arbitrary Lagrangian–Eulerian finite element methods for the Stokes equations in an evolving domain
Authors: Rao Qiqi , Wang Jilu , Xie Yupei
Published: December 2024

The numerical solution of the Stokes equations in an evolving domain with a moving boundary is studied based on the arbitrary Lagrangian–Eulerian finite element method along the trajectories of the evolving mesh, where the Taylor–Hood finite elements of degree $r\ge 2$ is employed for spatial discretization. The error of the semidiscrete arbitrary Lagrangian–Eulerian method is proved to be $O(h^{r+1})$ for velocity approximation in $ L^{\infty }(0,T;L^{2}) $ norm and $ O (h^{r}) $ for pressure approximation in $ L^{2}(0,T;L^{2}) $ norm, respectively. The analyses are based on a Nitsche’s duality argument adapted to an evolving mesh, by proving that the material derivative and the Stokes–Ritz projection commute up to terms that have optimal-order convergence in the $L^{2}$ norm. Numerical examples are provided to support the theoretical analysis.
Using Generative Artificial Intelligence in Medical Education
Authors: Rodman Adam , Mark Nicholas M. , Artino Anthony R. , Lessing Juan N.
Published: December 2024

Large Language Models (LLMs) are a type of generative artificial intelligence (AI) that produce realistic-sounding language in response to text prompts, giving AI the capability to simulate human discourse in various domains, including medical education.1 The pace of technological advancement is staggering, which comes with promise and peril. This Last Page summarizes some potential LLM uses in medical education.2 However, AI is rapidly advancing, and these uses will likely evolve as well.
Using a Popular Video Platform to Assess Patient Perceptions of Clubfoot Deformity
Authors: Al Ramlawi Akram , Over Daniel J. , Assayag Michael , McClure Philip
Published: December 2024

Background:

In today’s world, individuals receive much of their medical information from the Internet, including social media platforms such as the increasingly popular TikTok, a video-sharing site. This study’s purpose was to better understand the content popular online regarding clubfoot deformity.

Methods:

The 50 most viewed, English language videos on TikTok with the tags #clubfootjourney, #talipes, #clubfootcast, #clubfoottreatment, and #clubfoot were identified and independently evaluated by 2 separate reviewers for creator demographics, video type, and prominent themes. Videos were also assessed for medical accuracy and given a score for understandability and actionability based on the Patient Education Materials Assessment Tool (PEMAT).

Results:

In total, the videos had 87.7 million views, 3.8 million “likes”, and 42.1 thousand comments. Health care professionals created 10% of the videos, and only 1 video was made by an orthopaedic surgeon. Of all the videos, including those created by non-health-care professionals, 82% included medically substantiated and accurate claims. A majority of the videos were primarily educational (70%), with the remainder primarily motivational (30%). Tone varied between positive (74%), and neutral (26%) with no negative tone although most watched videos accounting for 30 million views were primarily motivational. Prominent themes included casting journey (32%), medical education/demonstration (22%), and adults with clubfoot deformity (12%). Ideas such as fear, pain, and discomfort (55%), the importance of family support (25%), and hygiene (20%) were also represented. None of the videos exhibited themes of race in medicine or socioeconomic barriers. All videos were also found to have an average understandability of 74.3% and an average actionability of 36.3%, according to the PEMAT.

Conclusions:

The substantial number of views and “likes” accumulated by these videos highlights the breadth of content and utilization of social media by the public. This study reveals an opportunity for health care professionals to reach patients with accurate information, identify areas of fear/distrust, and address negative or incorrect perceptions that pervades a variety of interventions with regards to clubfoot deformity management and treatment.
The Impact of Prior Hip or Knee Arthroplasty on Oswestry Disability Index Two Years after Elective Lumbar Surgery
Authors: Hambrecht Jan , Köhli Paul , Chiapparelli Erika , Amoroso Krizia , Duculan Roland , Zhu Jiaqi , Guven Ali E. , Evangelisti Gisberto , Burkhard Marco D. , Tsuchiya Koki , Shue Jennifer , Sama Andrew A. , Cammisa Frank P. , Girardi Federico P. , Mancuso Carol A. , Hughes Alexander P.
Published: December 2024

Study Design.

Secondary analysis of prospective study.

Objective.

To analyze the impact of prior total knee arthroplasty (TKA), total hip arthroplasty (THA), or both on the Oswestry Disability Index (ODI) two years after elective lumbar surgery.

Background.

Degenerative conditions that cause pain and mobility loss significantly reduce quality of life. The rising prevalence of total joint arthroplasties (TJA) and spinal surgeries complicates treatment and may result in persistent postoperative symptoms. Understanding how these surgeries interact and how surgical history and underlying conditions influence postoperative outcomes is crucial.

Methods.

A secondary analysis was performed on a prospective study of patients undergoing lumbar surgery for degenerative conditions. Patients with a two-year ODI follow-up were included. ODI was prospectively assessed pre- and postoperatively. Patients without ODI-assessment were excluded. Differences in pre- and postoperative ODI were evaluated, and patients were categorized based on ODI-improvement. Statistical analyses included Mann-Whitney-U-test, univariable logistic regression, and multivariable logistic regression adjusted for age, sex, and BMI.

Results.

Overall, 385 patients (57% female, 65±10 y) were included. 46 patients (12%) had prior THA, 34 (9%) patients had prior TKA, and 11 (3%) patients had both. ODI-improvement was achieved in 91%. After adjusting for covariates, combined TKA and THA was significantly associated with postoperative ODI non-improvement (OR9.96, 95%CI 2.53-38.3, P=0.001). Prior TKA also tended to be a risk factor for ODI non-improvement, although not statistically significant (P=0.052) after adjusting for covariates.

Conclusion.

Patients with prior concomitant TKA and THA have higher odds of ODI non-improvement two years postoperatively, suggesting that concurrent musculoskeletal degeneration of the spine and lower extremities may negatively impact improvement after lumbar surgery. These results highlight the connection not only between the hip but also the knee and spine.
Sex Disparity in Extracorporeal Membrane Oxygenation Clinical Trial Enrollment
Authors: Damuth Emily , Baldwin Caitlin , Schmalbach Nicole , Green Adam , Puri Nitin , Jones Christopher W.
Published: December 2024

OBJECTIVES:

Multiple studies have shown that extracorporeal membrane oxygenation (ECMO) is used clinically more often in men than women. Because clinical trials provide the basis for identifying patients who are likely to benefit from medical therapies, we hypothesized that sex-based imbalances in ECMO trial enrollment may both reflect and perpetuate these observed disparities. Our objective was to determine whether sex-based enrollment imbalances exist within the published ECMO clinical trial literature.

DESIGN:

Cross-sectional analysis.

SETTING:

Randomized controlled trials published between 2003 and 2023 that either tested ECMO as a treatment modality or tested another intervention among patients receiving ECMO.

PATIENTS:

Not applicable

INTERVENTIONS:

None.

MEASUREMENTS AND MAIN RESULTS:

We used the Cochrane Highly Sensitive Search Strategy to search PubMed for eligible trials. Data on participant demographics, trial characteristics, and journal information were abstracted for each publication. The primary outcome of interest was the proportion of male and female participants in each published trial. The initial literature search identified 774 articles. Of these, 31 were eligible for inclusion, and 28 provided data on the sex of study participants. Twenty-six of these 28 trials (93%) enrolled more men than women, and in aggregate women comprised 28% (95% CI, 26–30%) of all trial participants (551/1956 subjects). Trials involving extracorporeal cardiopulmonary resuscitation (ECPR) exhibited the largest sex-based enrollment differences (83% men) followed by venoarterial ECMO for cardiogenic shock (73% men). Among trials published in journals with impact factors of ten or higher 74% (95% CI, 72–76%) of participants were men. Only two trials (7%) provided data on the race or ethnicity of study participants.

CONCLUSIONS:

Substantial sex-based disparity exists in published ECMO clinical trials. Underrepresentation of women relative to disease prevalence is most significant among trials utilizing venoarterial ECMO for cardiogenic shock and ECPR for cardiac arrest, limiting the applicability of findings from these trials for women.
Leishmaniasis Diagnosed in the United States Successfully Treated With Miltefosine
Authors: LaRocque Autumn , Zheng Vicky , Khambaty Mariam , Pfau Richard , Wheat Chikoti
Published: December 2024

Leishmaniasis is an infectious disease caused by the parasitic protozoa species Leishmania and is most often transmitted to humans through the bite of a sandfly. The most common manifestation is a cutaneous lesion. Leishmaniasis is endemic to many countries throughout the world but rarely diagnosed in the United States. Here, we report a 64-year-old man with initially undisclosed recent travel to Sudan, an endemic country, who returned to the United States with cutaneous lesions on his forehead and dorsal hand. After failing initial therapy, a biopsy showed amastigotes (the tissue stage of the parasite), chronic inflammation with numerous plasma cells, granulomatous features, focal necrobiosis, and neutrophilic debris, consistent with leishmaniasis. The lesions did not significantly improve with fluconazole, but miltefosine (100–200 mg daily) resulted in remission over an 8-week course. The purpose of this case report is to highlight the importance of including rare infectious organisms in the differential and briefly discuss diagnostic and treatment methods.
Angiosome-Guided Revascularization in Local Flap Reconstruction of the Foot and Ankle
Authors: Rohrich Rachel N. , Li Karen R. , Lava Christian X. , Akbari Cameron M. , Attinger Christopher E.
Published: December 2024

Background

Among patients with critical limb ischemia and tissue loss, revascularization is an essential component for limb salvage. Local flaps of the foot and ankle remain a versatile tool in reconstructive limb salvage but is dependent on adequate arterial flow. In patients with arterial occlusive disease requiring revascularization, there is a lack of evidence in the current literature investigating on the necessity of direct arterial flow to the respective angiosome for local flaps reconstruction. Our study thereby compares the outcomes of direct (DR) and indirect (IR) revascularization for local flap success.

Methods

Patients who received endovascular revascularization (ER) prior to local flap reconstruction for chronic wounds in the foot and ankle were retrospectively reviewed. IR was performed in patients where DR could not be performed. DR was defined as an intervention on the same pedicle used for the local flap. IR was defined as an intervention performed on a different angiosome than the pedicle used for the local flap. Patient demographics, Charlson Comorbidity Index (CCI), angiographic details, postoperative complications, and long-term outcomes were collected.

Results

A total of 33 patients underwent 43 local flap reconstruction with preoperative ER: 58.1% (n = 25) received DR and 41.2% (n = 18) received IR. Patients had a mean CCI of 6.7 ± 1.8, with a high prevalence of diabetes mellitus (93.9%), peripheral arterial disease (90.9%), and end-stage renal disease (33.3%) with no significant differences between groups. In the immediate postoperative period (postoperative day 0 to 12), there were no significant differences in immediate flap success (DR: 100% vs IR: 88.9%, P = 0.169) or partial flap necrosis between (DR: 0.0% vs IR: 16.7%, P = 0.066). Rates of major complications from infection (DR: 28.2% vs IR: 22.2%, P = 0.736), ischemia (DR: 4.0% vs IR: 11.1%, P = 0.562), or dehiscence (DR: 8.0% vs IR: 16.7%, P = 0.634) requiring reoperation were similar between 2 groups. Overall limb salvage rate was 84.9%, and comparable between groups (DR: 78.6% vs IR: 89.5%, P = 0.628).

Conclusions

DR and IR achieve similar rates of limb salvage and flap success after local flap reconstruction. A multidisciplinary vasculo-plastic approach that incorporates preoperative arteriogram and revascularization should be utilized for this highly comorbid patient population to achieve optimal success and limb salvage.
An Epidemiological Survey of Hand Burn Injuries Admitted to a Large Burn Center in the New York City Metropolitan Area
Authors: Salingaros Sophia , Chang Philip H. , Houng Abraham P. , Jacoby Adam
Published: December 2024

Background

Hand form and function play a vital role in daily living, and even minor trauma can significantly impair quality of life. There is a current paucity of data regarding hand burn patient and injury characteristics, particularly in urban areas in the United States. As the field of hand surgery expands, a demographic understanding of patients with severe injury potentially requiring surgical management is imperative. The aim of this study was to define the epidemiological characteristics of burn injuries involving the hand that were admitted to a large New York City burn center.

Methods

A retrospective review of the electronic health record was conducted to identify all patients admitted to our burn center with burn injury involving the hand from August 2020 to December 2023. Patient demographics, injury etiology and characteristics, and hospital course details were recorded and analyzed.

Results

We identified 96 admitted patients with 140 hand burn injuries, with a patient median age of 38 years. Female patients presented to the hospital significantly later after initial injury than male patients and were more likely to suffer from flame-related injury. The median length of stay for initial admission was 17.5 days, with longer length of stay associated with hypertension comorbidity. Patients experiencing homelessness demonstrated higher rates of psychiatric disorder, substance use, and current smoking. Length of follow-up was positively correlated with estimated household income. Compared to the general city population, the patient cohort was made up of a lower percentage of “White alone” and “Asian alone” race categories and higher percentage of persons experiencing homelessness.

Conclusions

We report the clinical and social characteristics of burn patients with hand involvement admitted to a large urban burn center. Hand burn injuries have distinct risk factors and morbidity implications, and consideration for higher-risk groups is imperative for optimal prevention, acute management, and long-term support.
Application of TFPI2 in Sepsis Severity Prediction
Authors: Song Kaiyuan , Wu Yongbin , Song Ruoyu , Zhou Jiankang , Tan Sichuang , Xiao Lan , Zhang Huali , Tan Sipin
Published: December 2024

Introduction

Infection and coagulation dysfunction are two major features of sepsis, and TFPI2 exhibits both antimicrobial and anticoagulant properties. This study aims to evaluate whether TFPI2 is associated with the severity of sepsis, thereby determining its potential value in sepsis diagnosis and prognosis.

Methods

Serum TFPI2 concentrations were measured and compared among 32 healthy controls, 16 ICU non-sepsis patients, and 106 ICU sepsis patients. Correlation analysis was performed between various indicators and TFPI2 levels in sepsis patients. Logistic regression analysis and ROC curves were used to assess the value of TFPI2 in predicting 28-day mortality in sepsis.

Results

Sepsis patients exhibited markedly elevated serum TFPI2 levels compared to both healthy individuals and ICU patients without sepsis. Serum TFPI2 levels were significantly correlated with sepsis severity indicators such as SOFA, APACHE II, Lac, coagulation markers including ISTH-DIC and SIC scores, and platelet count. Univariate and multivariate logistic regression analyses revealed that TFPI2 is an independent risk factor for 28-day mortality in sepsis. The ROC curve showed that TFPI2 has a significant predictive value for 28-day mortality in sepsis, with an AUC of 0.832 and an optimal cutoff value of 8.316.

Conclusions

This study indicates that serum TFPI2 levels hold promise as a biomarker for predicting the severity of sepsis.
FUNCTIONAL IMMUNOPHENOTYPING FOR PRECISION THERAPIES IN SEPSIS
Authors: Rao Mahil , McGonagill Patrick W. , Brackenridge Scott , Remy Kenneth E. , Caldwell Charles C. , Hotchkiss Richard S. , Moldawer Lyle L. , Griffith Thomas S. , Badovinac Vladimir P.
Published: December 2024

Sepsis remains a significant cause of morbidity and mortality worldwide. Although many more patients are surviving the acute event, a substantial number enters a state of persistent inflammation and immunosuppression, rendering them more vulnerable to infections. Modulating the host immune response has been a focus of sepsis research for the past 50 years, yet novel therapies have been few and far between. Although many septic patients have similar clinical phenotypes, pathways affected by the septic event differ not only between individuals but also within an individual over the course of illness. These differences ultimately impact overall immune function and response to treatment. Defining the immune state, or endotype, of an individual is critical to understanding which patients will respond to a particular therapy. In this review, we highlight current approaches to define the immune endotype and propose that these technologies may be used to “prescreen” individuals to determine which therapies are most likely to be beneficial.
Exploring the Potential of BEND7 as an Immunomodulatory Biomarker in Sepsis through Integrative Genomic and Transcriptomic Analysis
Authors: Ren Chao , Liu Yuyang , Ding Zhangna , Yang Zhanyu , Wan Tao , Zhang Ning , Chen Junyi , Feng Hui , Liu Qi
Published: December 2024

Background

Sepsis is a life-threatening condition driven by a dysregulated immune response to infection. Identifying the genetic factors underlying sepsis pathogenesis remains a major challenge in developing effective treatments.

Methods

The Summary-data-based Mendelian Randomization method was used to integrate genome-wide association study and expression quantitative trait loci data to identify sepsis-related genes. These genes were intersected with prognostic gene sets from Gene Expression Omnibus transcriptomic datasets and validated using an independent dataset. Comprehensive single-cell RNA sequencing analysis, including cell clustering, differential expression analysis, cell-cell communication mapping, and pseudotime trajectory analysis, was performed to explore the roles of the identified genes within the sepsis microenvironment.

Results

Intersection of Summary-data-based Mendelian Randomization and Gene Expression Omnibus gene sets, followed by validation, identified two risk genes and five protective genes as significantly differentially expressed. The risk gene BEND7, predominantly expressed in platelets, was further analyzed using single-cell RNA sequencing, revealing strong interactions with immune cells, particularly monocytes and neutrophils, via the intercellular adhesion molecule signaling pathway. Functional enrichment analysis suggested that BEND7-positive platelets play a role in immune modulation and platelet activation.

Conclusion

BEND7 was identified as a platelet-specific gene involved in immune regulation during sepsis. Targeting BEND7-positive platelets may present new therapeutic opportunities in sepsis management.
Long-term functional recovery after rib fractures: The impact of frailty
Authors: Rafaqat Wardah , Panossian Vahe S. , Yi Alisha , Heindel Patrick , Abiad May , Ilkhani Saba , Heyman Annie , Garvey Shannon , Anderson Geoffrey A. , Sanchez Sabrina E. , Herrera-Escobar Juan P. , Hwabejire John O.
Published: December 2024

BACKGROUND

Previous studies have shown that patients with rib fractures experience long-term functional limitations. However, the specific predictors of these worse long-term functional limitations remain under-characterized.

METHODS

We conducted a prospective cohort study including patients ≥18 years with an injury severity score ≥9 and isolated chest injury. Patients included had ≥1 rib fracture and were admitted between July 2015 and May 2019 at one of three Level I trauma centers present in our region. We performed stepwise regression analysis to identify predictors of new functional limitations, i.e., limitations that patients developed postinjury in an activity of daily living. Patients were contacted between 5 and 12 months postinjury to inquire about functional limitations. We assessed frailty using the mFI-5 tool, and a score of 1 was considered moderate frailty, while >1 was considered severe frailty.

RESULTS

Among 279 included patients, 74 (26.5%) developed new functional limitations. The majority of patients had a displaced fracture [118 (42.3%)] and ≥3 rib fractures [237 (84.9%)]. A proportion of patients had superior rib fractures [105 (37.6%)], concomitant clavicular, scapular, or sternal fractures [64 (22.9%)], flail chest [37 (13.3%)], moderate frailty [106 (38.0%)], and severe frailty [57 (20.4%)]. Severe frailty and discharge to a skilled nursing facility, rehabilitation facility, or other location as opposed to home were predictors of new functional limitations.

CONCLUSION

In our population, frailty, not injury characteristics, predicted new long-term functional limitations in patients with rib fractures. Frail patients may benefit from additional inpatient and discharge resources for improved long-term outcomes.

LEVEL OF EVIDENCE

Therapeutic/Care Management; Level III.
Properties of tsunami-generated electromagnetic variation observed on islands
Authors: Minami Takuto
Published: December 2024

Electrically conductive seawater, moving in an ambient magnetic field, generates electromagnetic (EM) variations. Tsunamis are significant contributors to this phenomenon, inducing observable electric and magnetic fluctuations at seafloor and coastal observatories. While understanding of these occurrences in open oceans is robust, knowledge regarding their observation on islands remains limited. This article seeks, through the use of numerical experimentation, to enhance our understanding of tsunami-generated EM (TGEM) variations observed on islands. Utilizing simulations involving conical islands, we identify three key insights regarding EM intensity normalized by the height of incident tsunamis: (i) increased ocean depth surrounding the island amplifies tsunami EM signals, particularly for periods shorter than 20 min; (ii) magnetic field strength at the island is approximately comparable to that observed at the seafloor in the absence of the island when the island radius is smaller than 6 km; and (iii) electric field intensity at the island notably surpasses that observed at the seafloor, especially with smaller island radii (

≤

6 km). Additionally, we establish that employing the ratio of island radius to tsunami wavelength near the island coast facilitates the derivation of empirical functions for this phenomenon.

This article is part of the theme issue ‘Magnetometric remote sensing of Earth and planetary oceans’.
Comparative molecular diagnosis of GeneXpert to gold standard RT-PCR for SARS-CoV-2: A retrospective study
Authors: William Ashish , Rai Yogita , Rawat Deepti , Gogoi Sanjib , Dhakad Megh Singh , Jais Manoj , Kaur Ravinder
Published: December 2024

Background
The novel coronavirus disease (COVID-19) has highlighted vulnerabilities in healthcare systems and has single-handedly brought the world to a standstill. Diagnostic testing for COVID-19 is critical for understanding epidemiology, contact-tracing, case management, and to control the transmission of the SARS-CoV-2. rRT-PCR test, the gold standard test, involves fairly complex steps and take nearly 24–48 h for generating the results. GeneXpert is a rapid nucleic-acid-detection-based test approved by ICMR (Indian Council of Medical Research), which can shorten the turnaround time significantly.
Aim
The aim of the study was to compare the performance of GeneXpert against the gold standard rRT-PCR for SARS-CoV-2.
Materials and methods
This retrospective study was conducted at a tertiary care centre from 25th March 2020 to 8th December 2020. The Nasopharyngeal/Oropharyngeal swabs that were sent to the VRDL (Viral Research and Diagnostic laboratory) for testing of SARS-CoV-2 by GeneXpert (CBNAAT) were included for the study. A total of 270 samples (220 samples positive and 50 samples negative for SARS-CoV-2 by GeneXpert) were simultaneously tested for rRT-PCR. rRT-PCR was considered as gold standard test (reference) for calculating the sensitivity and specificity of GeneXpert (CBNAAT) test.
Results
Out of 220 samples positive for COVID-19 by GeneXpert, 118 (53.64%) were also positive by rRT-PCR while 102 (46.36%) showed negative results by rRT-PCR. However, 50 GeneXpert negative samples showed 100% agreement with rRT-PCR i.e. they were also negative by rRT-PCR. The GeneXpert sensitivity and specificity for COVID-19 was seen to be 100% (95% CI: 96.92 to 100%) and 32.89% (95% CI: 25.50 to 40.97%) respectively as compared to gold standard rRT-PCR test. The positive predictive value (PPV) and negative predictive value (NPV) of GeneXpert for COVID-19 was found to be 53.64% and 100% respectively.
Conclusion
This study highlights that the GeneXpert test is highly sensitive and found to be helpful in emergency and challenging situations in releasing the negative reports, whereas due to low specificity of GeneXpert the positivity has to be confirmed with rRT-PCR. Therefore, it can be useful in the early diagnosis and management of COVID-19 infection and thus, prevention of morbidity and mortality.
PANGENOMES AID ACCURATE DETECTION OF LARGE INSERTION AND DELETIONS FROM GENE PANEL DATA: THE CASE OF CARDIOMYOPATHIES
Authors: Mazzarotto Francesco , Kalay Özem , Arslan Elif , Cinquina Valeria , Turgut Deniz , Buchan Rachel J , Allouba Mona , Bertini Valeria , Halawa Sarah , Theotokis Pantazis , Budak Gungor , Girolami Francesca , Peldova Petra , Bonaventura Jiri , Aguib Yasmine , Colombi Marina , Olivotto Iacopo , Gennarelli Massimo , Macek Milan , Pelo Elisabetta , Ritelli Marco , Yacoub Magdi , Barton Paul JR , Tetikol H Serhat , Walsh Roddy , Ware James S , Jain Amit
Published: December 2024

Gene panels represent a widely used strategy for genetic testing in a vast range of Mendelian disorders. While this approach aids reliable bioinformatic detection of short coding variants, it fails to detect most larger variants. Recent studies have recommended the adoption of pangenomes to augment detection of large variants from targeted sequencing, potentially providing diagnostic laboratories with the possibility to streamline diagnostic work-ups and reduce costs.

Here, we analyze a large-scale cohort comprising 1,952 cardiomyopathy cases and 1,805 technically matched controls and show that a pangenome-based workflow, GRAF, conjugates higher precision and recall (F1 score 0.86) compared with conventional orthogonal methods (F1 0-0.57) in detecting potentially pathogenic ≥20bp variants from short-read panel data.

Our results indicate that pangenome-based workflows aid precise and cost-effective detection of large variants from targeted sequencing data in the clinical context. This will be particularly relevant for conditions in which these variants explain a high proportion of the disease burden.
Association of Polygenic Risk Scores for Neurodevelopmental Traits and Psychiatric Conditions with Incontinence and Constipation in Children and Young People
Authors: Bastiani Oliver , Dardani Christina , Burrows Kimberley , Christensen Jane Hvarregaard , Joinson Carol
Published: December 2024

Observational studies report prospective associations of neurodevelopmental and psychiatric traits with paediatric incontinence and constipation, but unmeasured and residual confounding may limit observational measures. Here, we use a prospective birth cohort study to investigate whether common variant genetic liability for a range of neurodevelopmental and psychiatric conditions are associated with paediatric incontinence and constipation. We used data from 7,857 participants from the Avon Longitudinal Study of Parents and Children (ALSPAC) with data on genotype, incontinence, and constipation, and calculated Polygenic risk scores (PRS) for neurodevelopmental traits (ADHD, autism, intelligence) and psychiatric conditions (anxiety, depression, and OCD). Incontinence subtypes (daytime urinary incontinence [DUI], enuresis [any bedwetting and enuresis subtypes: monosymptomatic, non-monosymptomatic], faecal incontinence), and constipation, were assessed by parental reports at age 9 years and self-reports at age 14. PRS for ADHD (OR=1.14, 95% CI, 1.01-1.29, unadjustedp=0.040) and depression (OR=1.09, 95% CI, 1.00–1.20, unadjustedp=0.063) were associated with DUI at age 9. PRS for autism (OR=1.19, 95% CI, 1.02-1.41, unadjustedp=0.032) and intelligence (OR=1.17, 95%, 0.99-1.38, unadjustedp=.06l) were associated with DUI at age 14. PRS for ADHD (OR=1.13, 95% CI, 1.03-1.24, unadjustedp=0.008) were associated with constipation at age 9. Within enuresis subtypes, PRS for autism were associated with MNE at age 9 (OR=1.15, 95% CI, 1.03–1.28, unadjustedp=0.012), but not NMNE (OR=0.93, 95% CI, 0.79–1.18, unadjustedp=0.335). No associations survived false discovery rate adjustment. The findings add to existing evidence that common variant genetic liability for neurodevelopmental traits and psychiatric conditions could be associated with paediatric incontinence and constipation.

Key points

Question

Are common variant genetic liabilities for neurodevelopmental and psychiatric conditions associated with paediatric incontinence and constipation in a population-based cohort?

Findings

We found some evidence that polygenic risk scores (PRS) for ADHD, autism, intelligence, and depression may be associated with daytime urinary incontinence. PRS for ADHD were also associated with constipation and enuresis and PRS for autism and depression were weakly associated with constipation. None of the associations survived adjustment for false discovery rate.

Meaning

Common variant genetic liabilities for ADHD, autism, intelligence, and depression could be risk factors for developing paediatric incontinence and constipation.
Unbiased learning of protein conformational representation via unsupervised random forest
Authors: Sahil Mohammad , Ahalawat Navjeet , Mondal Jagannath
Published: December 2024

Accurate data representation is paramount in biophysics to capture the functionally relevant motions of biomolecules. Traditional feature selection methods, while effective, often rely on labeled data based on prior knowledge and user-supervision, limiting their applicability to novel systems. Here, we presentunsupervised random forest(URF), a self-supervised adaptation of traditional random forests that identifies functionally critical features of biomolecules without requiring prior labels. By devising a memory-efficient implementation, we first demonstrate URF’s capability to learn important sets of inter-residue features of a protein and subsequently to resolve its complex conformational landscape, performing at par or surpassing its traditional supervised counterpart and 15 other leading baseline methods. Crucially, URF is supplemented by an internal metric, thelearning coefficient, which automates the process of hyper-parameter optimization, making the method robust and user-friendly. URF’s remarkable ability to learn important protein features in an unbiased fashion was validated against 10 independent protein systems including both both folded and intrinsically disordered states. In particular, benchmarking investigations showed that the protein representations identified by URF are functionally meaningful in comparison to current state-of-the-art deep learning methods. As an application, we show that URF can be seamlessly integrated with downstream analyses pipeline such as Markov state models to attain better resolved outputs. The investigation presented here establishes URF as a leading tool for unsupervised representation learning in protein biophysics.
Thermal-density-functional-theory approach to quantum thermodynamics
Authors: Palamara Antonio , Plastina Francesco , Sindona Antonello , D'Amico Irene
Published: December 2024

Understanding the thermodynamic properties of many-body quantum systems and their emergence from microscopic laws is a topic of great significance due to its profound fundamental implications and extensive practical applications. Recent advances in experimental techniques for controlling and preparing these systems have increased interest in this area, as they have the potential to drive the development of quantum technologies. In this study, we present a density-functional-theory approach to extract detailed information about the statistics of work and the irreversible entropy associated with quantum quenches at finite temperature. Specifically, we demonstrate that these quantities can be expressed as functionals of thermal and out-of-equilibrium densities, which may serve as fundamental variables for understanding finite-temperature many-body processes. We, then, apply our method to the case of the inhomogeneous Hubbard model, showing that our density-functional-theory-based approach can be usefully employed to unveil the distinctive roles of interaction and external potential on the thermodynamic properties of such a system.

Published by the American Physical Society
2024
Fine structure of the doublet
P
levels of boron
Authors: Nasiri Saeed , Tumakov Dmitry , Stanke Monika , Kędziorski Andrzej , Adamowicz Ludwik , Bubin Sergiy
Published: December 2024

We report high-accuracy calculations of the ground and the lowest eight excited Po2 states of the two stable isotopes of the boron atom, B10 and B11, as well as of the boron atom with an infinite nuclear mass ∞B. The nonrelativistic wave function of each of the states is generated in an independent variational calculation by expanding it in terms of a large number, 12000–17000, of all-electron explicitly correlated Gaussian (ECG) functions whose nonlinear parameters are extensively optimized with a procedure that employs analytic energy gradient determined with respect to these parameters. These highly accurate wave functions are used to compute the fine-structure splittings using the first order of the perturbation theory (∼α2), where α is the fine-structure constant, which are then corrected for the electron magnetic moment anomaly (∼α3). As the nonrelativistic Hamiltonian explicitly depends on the mass of the nucleus, the recoil corrections up to the order of α2 are automatically accounted for in the fine-structure calculations. Furthermore, the off-diagonal corrections to the fine structure (∼α4) are estimated using the multireference methods based on one-electron Gaussian orbitals. The results obtained in this paper are considerably more accurate than those available in the literature. Moreover, we report accurate splittings for a number of excited

P

o

2

states, for which there have been no reliable experimental or theoretical data at all. The calculated values presented in this paper may serve as a valuable guide for future experimental measurements of the fine structure of the boron atom. As the fine structure of an atom provides a spectral signature that can facilitate atom's detection, our data can also aid the search for trace amounts of boron in the interstellar medium.

Published by the American Physical Society
2024
Long-range four-body interactions in structured nonlinear photonic waveguides
Authors: Wang Xin , Li Jia-Qi , Liu Tao , Miranowicz Adam , Nori Franco
Published: December 2024

Multiphoton dynamics beyond linear optical materials are of significant fundamental and technological importance in quantum information processing. However, it remains largely unexplored in nonlinear waveguide QED. In this work, we theoretically propose a structured nonlinear waveguide in the presence of staggered photon-photon interactions, which supports two branches of gaped bands for doublons (i.e., spatially bound-photon-pair states). In contrast to linear waveguide QED systems, we identify two important contributions to its dynamical evolution, i.e., single-photon bound states (SPBSs) and doublon bound states (DBSs). Most remarkably, the nonlinear waveguide can mediate the long-range four-body interactions between two emitter pairs, even in the presence of disturbance from SPBSs. By appropriately designing system's parameters, we can achieve high-fidelity four-body Rabi oscillations mediated only by virtual doublons in DBSs. Our findings pave the way for applying structured nonlinear waveguide QED in multi-body quantum information processing and quantum simulations among remote sites.

Published by the American Physical Society
2024
Fixing detailed balance in ancilla-based dissipative state engineering
Authors: Lambert Neill , Cirio Mauro , Lin Jhen-Dong , Menczel Paul , Liang Pengfei , Nori Franco
Published: December 2024

Dissipative state engineering is a general term for a protocol which prepares the ground state of a complex many-body Hamiltonian using engineered dissipation or engineered environments. Recently, it was shown that a version of this protocol, where the engineered environment consists of one or more dissipative qubit ancillas tuned to be resonant with the low-energy transitions of a many-body system, resulted in the combined system evolving to reasonable approximation to the ground state. This potentially broadens the applicability of the method beyond nonfrustrated systems, to which it was previously restricted. Here we argue that this approach has an intrinsic limitation because the ancillas, seen as an effective bath by the system in the weak-coupling limit, do not give the detailed balance expected for a true zero-temperature environment. Our argument is based on the study of a similar approach employing linear coupling to bosonic ancillas. We explore overcoming this limitation using a recently developed open quantum systems technique called pseudomodes. With a simple example model of a one-dimensional quantum Ising chain, we show that detailed balance can be fixed, and a more accurate estimation of the ground state obtained, at the cost of two additional unphysical dissipative modes and the extrapolation error of implementing those modes in physical systems.

Published by the American Physical Society
2024
Exploring novel compact quasi-axisymmetric stellarators
Authors: Schuett T. M. , Henneberg S. A.
Published: December 2024

The new class of compact quasi-axisymmetric stellarators with a wide range of field periods offers the unique potential to combine the advantages of the two leading magnetic confinement fusion devices, tokamaks and stellarators. Here, we present the numerical optimization of this class which has so far only been obtained analytically. Our approach finds significantly improved quasi-axisymmetric equilibria at aspect ratio <2.5, resulting in no losses of alpha particles at reactor volume while also satisfying improved magnetohydrodynamic stability and a self-consistent plasma current.

Published by the American Physical Society
2024
Strategies of perceived justice for added value in public–private partnership (PPP) projects
Authors: Cheng Mengyuan , Chong Heap-Yih , Liu Guoliang , Li Qian
Published: December 2024

Purpose

Perceived justice is crucial to achieving public–private partnership (PPP) projects’ goals, but little is known about the transmission mechanism of perceived justice that affects added value in PPP projects. Therefore, this research intends to investigate the link between perceived justice and PPP projects’ added value and their underlying mechanism by analysing the mediating role of cooperative behaviour.

Design/methodology/approach

Based on 246 valid survey data collected from the Chinese PPP professionals, structural equation modelling was adopted to analyse and test the proposed hypotheses.

Findings

The results show all three dimensions of perceived justice positively correlated with PPP projects’ added value. The influence effect from high to low was determined to be as follows: interactive, distributive and procedural justice. Moreover, both perfunctory and consummate performance were found to be positively correlated with and thus of great importance to PPP projects’ added value, but perfunctory performance was found to have a greater influence coefficient. The relationship between perceived justice and PPP projects’ added value is mediated by perfunctory and consummate performance. Therefore, the strategies of perceived justice in improving added value are verified in the context of Chinese PPP projects.

Research limitations/implications

The findings of this study can help realise added value in three ways. Firstly, new perspectives for PPP project added value should be proposed by combining the improvement of project basic objectives and the realisation of the participants’ implicit demands. Secondly, the effects of different perceived justice on added value should be analysed instead of a single dimension of perceived justice. Thirdly, the mediating effects of different types of cooperative behaviour that may influence the relationship between perceived justice and added value should be evaluated.

Practical implications

This study contributes to a better understanding of the relationship between perceived justice and PPP projects’ added value and provides a reliable reference for project managers to achieve added value outcomes in PPP projects. In addition, this study reveals the impact of perceived justice on PPP projects’ added value and the path of perceived justice transformation. This provides a useful reference for project managers to take advantage of the positive effects of distributive, interactive and procedural justice to enhance inter-organizational cooperative behaviour. This study thus helps improve the practice and value of PPP projects by using the right strategy of perceived justice.

Originality/value

The research clarifies the impacts of multidimensional perceived justice for added value of PPP projects throughout the implementation process. It offers a new perspective on PPP projects’ added value by combining the improvement of the realisation of participants’ implicit claims.