bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparison of gallbladder extraction via the subxiphoid port and the supraumbilical port during laparoscopic cholecystectomy: a prospective randomized clinical trial
Authors: Ye Xiwen , Niu Xiaoya , Bai Dan , Cao Yu , Mao Yaling , Liu Huizhen , Luo Yuting , Fuyu-Li  , Cheng Nansheng , You Zhen
Published: July 2024

Background:

Postoperative pain after laparoscopic cholecystectomy (LC) is the most frequent postoperative complaint. To date, gallbladder extraction via the subxiphoid port (SXP) versus the supraumbilical port (SUP) is still controversial. Thus, the authors performed this randomized controlled trial to compare postoperative pain between the SXP and SUP for LC.

Method:

From June 2021 to June 2023, patients who met the inclusion criteria were randomly assigned to two groups. The perioperative data of both groups were recorded and compared.

Results:

A total of 253 patients were enrolled in the analysis. There were 126 in the SXP group and 127 in the SUP group. There was no significant difference between the two groups in terms of the duration of gallbladder extraction, whether the incision was extended, the least rate of pain, the average rate of pain, the right-now rate of pain, postoperative pain on the 5th, 7th, and 14th days, postoperative complications and Vancouver Scar scale. However, the SUP group had a lower the worst rate of pain (4.24±2.45 vs. 4.91±2.45, P=0.031) and 3 days of pain (3.35±1.57 vs. 3.75±1.52, P=0.045) than did the SXP group. The influence of pain on general activity (4.51±2.90 vs. 3.76±2.92, P=0.041), mood (3.62±2.66 vs. 2.92±2.36, P=0.028), walking ability (4.40±3.01 vs. 3.66±2.76, P=0.044), and enjoyment of life (3.19±2.68 vs. 2.32±2.34, P=0.007) in the SXP was more severe than that in the SUP.

Conclusion:

The extraction of the gallbladder via the SUP is superior to that via the SXP because the early postoperative 24 h pain and pain on the third day are mild and do not increase the duration of gallbladder extraction or the risk of infection or hernia.
Dialoxygenation: A Preclinical Trial for Transforming the Artificial Kidney Into an Oxygenator
Authors: Karacanoğlu Dilek , Bedir Esra , Nakip Özlem Saritaş , Kesici Selman , Duran Hatice , Bayrakci Benan
Published: July 2024

Critically ill patients sometimes require tandem application of extracorporeal membrane oxygenation (ECMO) and continuous renal replacement therapy (CRRT) which is easier and cheaper. We aimed to transform the kidney membrane into a lung membrane by adding hydrogen peroxide (H2O2) to the dialysate as the oxygen source. A solution containing H2O2 and a dialysate fluid mixture was used as the final dialysate. Starting with 100% H2O2 solution and gradually reducing the volume of H2O2, respectively: 50%, 10%, 5%, 4%, 3%, 2%, and 1%. PRISMAFLEX system, Prismaflex M60 set and a bag of packed red blood cells (pRBCs) were the prototype. blood flow rate was about 40 ml/minute and the dialysis rate was about 200 ml/m2/minute/1.73 m2. blood sampling times were; at the beginning (T
0), at 15th (T
1), 30th (T
2), 60th (T
3) minutes. Amongst eight attempts H2O2 concentration that increased the partial oxygen pressure (pO2) level significantly in a reasonable period, without any bubbles, was 3%. Methemoglobinemia was not observed in any trial. After the test with 3%, H2O2 in the dialysate fluid decreased progressively without any H2O2 detection at post-membrane blood. Three percent H2O2 solution is sufficient and safe for oxygenation in CRRT systems. With this new oxy-dialysate solution, both pulmonary and renal replacement can be possible via
a single membrane in a simpler manner.
Efficacy and Safety of Endoscopic Through-the-Scope Suture System for Gastrointestinal Defects
Authors: Aziz Muhammad , Haghbin Hossein , Gangwani Manesh Kumar , Beran Azizullah , Dahiya Dushyant Singh , Ali Hassam , Sohail Amir Humza , Lee-Smith Wade , Hamdani Syed Uzair , Kamal Faisal , Adler Douglas G.
Published: July 2024

Objective:

Recently, a through-the-scope suturing (TTSS) system has received FDA approval and has been evaluated for closing mucosal defects postintervention. We hereby performed a systematic review and pooled meta-analysis of available studies to assess the safety and efficacy of this intervention.

Methods:

We queried the following databases through April 26, 2023: Embase, MEDLINE, Cochrane Central Register of Controlled Trials, and Web of Science Core Collection. Endoscopists utilizing TTSS for the following reasons were included: endoscopic mucosal resection, endoscopic submucosal dissection, peroral endoscopic myotomy, perforation, fistula closure, and/or stent fixation. The outcomes assessed were technical success, primary clinical success (closure of defect without additional intervention), and overall clinical success (closure of defect with/without additional intervention). Random effects model with the DerSimonian Laird approach was used to report event rates expressed as proportions with a 95% CI.

Results:

A total of 12 studies with 512 patients (mean age of 61.5 ± 18.4 y, 54.6% females) were included. The technical success rate was 96.0% (CI: 94.3%-97.7%). The primary clinical success rate was 74.8% (CI: 65.5%-84.1%). The overall clinical success rate was 95.4% (CI: 92.6-98.2%). Only 1 mortality case unrelated to intervention was reported.

Conclusion:

The TTSS appears safe and effective for closing mucosal defects after therapeutic endoscopic interventions. Further cost-effective studies should be performed comparing with endoclips for use in clinical settings.
Decreased Completion of Ordered Laboratories and Imaging in Telehealth Compared With In-person Hepatology Encounters
Authors: Henson Jacqueline B. , Patel Yuval A. , Wall April H. , Muir Andrew J.
Published: July 2024

Objective:

To evaluate order completion after telehealth compared with in-person encounters.

Background:

Completion of ordered testing, including laboratories and imaging, is an important aspect of successful outpatient care of patients with liver disease. Whether the completion of orders from telehealth encounters differs from in-person visits is unknown.

Materials and Methods:

Completion of ordered laboratories and imaging from hepatology encounters at our center from 2021 to 2022 were evaluated and compared between video telehealth and in-person visits. Laboratory completion was evaluated at 14 days, 30 days, and 90 days, and imaging completion was assessed at 1 year.

Results:

Telehealth encounters were significantly less likely to have laboratories completed at all evaluated time points (14 d: 40.7% vs 90.9%; 30 d: 50.9% vs 92.2%; 90 d: 63.9% vs 94.3%, P< 0.001 for all). Among telehealth encounters, encounters in patients more remote from the center were less likely to have laboratories completed. Imaging ordered at telehealth encounters was also less likely to be completed within 1 year (62.5% vs 70.1%, P< 0.001), including liver ultrasounds (59.1% vs 67.6%, P= 0.001), which persisted when limited to encounters for cirrhosis (55.8% vs 66.4%, P= 0.01).

Conclusions:

Telehealth encounters were significantly less likely to have ordered laboratories and imaging completed compared with in-person visits, which has important clinical implications for effective outpatient care of patients with liver disease. Further research is needed to better understand the barriers to order completion for telehealth visits and ways to optimize this to improve the effectiveness of this visit modality.
PrEP Use in a US National Sample of Trans Men and Other Transmasculine People Who Have Sex With Men: A Longitudinal Analysis
Authors: Carneiro Pedro B. , Radix Asa E. , Golub Sarit , Grosskopf Nicholas , Grov Christian
Published: July 2024

Introduction:

Efforts to improve pre-exposure prophylaxis (PrEP) uptake among gay men, transgender women, and Black cisgender women are evident across the United States, responding to epidemiologic data showing a disproportionate HIV burden in these communities. However, transgender men and other transmasculine people who have sex with men (TMSM)—those assigned female at birth who identify otherwise and have sex with cisgender men—are often excluded from these statistics. This community has unique vulnerabilities and prevention needs. National HIV prevention and planning has yet to include transgender men as a group with increased vulnerability to HIV seroconversion. This study follows a cohort of TMSM to characterize PrEP use longitudinally.

Methods:

Using data from a prospective US national cohort of TMSM not on PrEP, we analyzed annual PrEP uptake, discontinuation, and other HIV prevention measures over 24 months. We also used generalized estimating equations modeling to assess demographic, healthcare access, gender-affirming, and behavioral factors associated with PrEP uptake over time.

Results:

Our cohort of 196 TMSM was demographic and regionally diverse. 29% of our sample reported uptake of PrEP in 24 months, with about one-third of users discontinuing within 1 year. Health insurance, having had lower surgery, used post-exposure prophylaxis, or recently having a sexually transmitted infection were associated with increased odds of PrEP use.

Conclusion:

We found low uptake of PrEP and high discontinuation rates in a US national sample of TMSM over 24 months, despite significant need for HIV prevention. It is vital to increase efforts and investments to support this neglected community.
Assessment of Nontechnical Skills During Resuscitation
Authors: Milatino Sgambati Michele A. , d'Ercole Adriana , Cascio Michela , Di Viesto Giuseppe , Visicchio Daniele , Boccardo Chiara , Pozzetti Ilaria , Milocco Mimosa , Caporale Mariagiovanna , Poggi Alessandro Delli
Published: July 2024

Summary Statement

Nontechnical skills (hereinafter referred to as NTS), such as task management, leadership, situational awareness, communication, and decision making contribute to safe and efficient team performance. The importance during cardiopulmonary resuscitation is being increasingly emphasized. We carried out the intercultural adaptation of the TEAM score in Italian and to evaluate the reliability and validity of the resulting Italian version (i-TEAM). A forward-backward translation was made with the author called i-TEAM. Psychometric properties of the i-TEAM score were evaluated, including acceptability, construct validity, and interrater reliability. We divided the participants into 3 groups based on their experience, and we verified if there was a correlation between the final score NTS of i-TEAM and the groups. The Cronbach coefficient was 0.91 for the Total i-TEAM score. The descriptive statistics showed that there was no correlation between NTS score and experience (group). Our results show that i-TEAM has psychometric properties similar to the original score.
Variational inequality for a Timoshenko plate contacting at the boundary with an inclined obstacle
Authors: Kovtunenko Victor A. , Lazarev Nyurgun P.
Published: July 2024

A class of variational inequalities describing the equilibrium of elastic Timoshenko plates whose boundary is in contact with the side surface of an inclined obstacle is considered. At the plate boundary, mixed conditions of Dirichlet type and a non-penetration condition of inequality type are imposed on displacements in the mid-plane. The novelty consists of modelling oblique interaction with the inclined obstacle which takes into account shear deformation and rotation of transverse cross-sections in the plate. For proposed problems of equilibrium of the plate contacting the inclined obstacle, the unique solvability of the corresponding variational inequality is proved. Under the assumption that the variational solution is smooth enough, optimality conditions are obtained in the form of equilibrium equations and relations revealing the mechanical properties of integrated stresses, moments and generalized displacements on the contact part of the boundary. Accounting for complementarity type conditions owing to the contact of the plate with the inclined obstacle, a primal-dual variational formulation of the obstacle problem is derived. A semi-smooth Newton method based on a generalized gradient is constructed and performed as a primal-dual active-set algorithm. It is advantageous for efficient numerical solution of the problem, provided by a super-linear estimate for the corresponding iterates in function spaces.

This article is part of the theme issue ‘Non-smooth variational problems with applications in mechanics’.
Exploring the performance of the topological energy method for object and damage detection from noisy and poor databases
Authors: Pena M. , Muñoz S. , Rapún M.-L.
Published: July 2024

In this work, we study the performance of numerical methods based on the computation of topological energies to process data from synthetic and real experiments where only noisy limited-view data corresponding to a few frequencies are available. We show numerical experiments in two problems of practical interest. The first one corresponds to experimental measurements of the electromagnetic scattering produced by different objects extracted from the Fresnel database. The second one is related to synthetic experiments in a simplified model where steel welding joints are acoustically tested to identify possible flaws (air bubbles and inclusions) produced during the welding process.

This article is part of the theme issue ‘Non-smooth variational problems with applications in mechanics’.
Exploration and characterization of a newly isolated bacterium, Enterobacter quasihormaechei strain BDIFST24001, capable of producing rhamnolipids biosurfactant for oil remediation
Authors: Jui Afsana Habib , Bhuiyan Mohammad Nazrul Islam , Bhowmik Banasree , Khatun Nazia , Chowdhury Abhijit , Bhuiyan Riyadh Hossen , Kabir Md. Alamgir , Rashid Md. Mamunur , Bhuiyan Md. Habibur Rahman , Afrin Sadia
Published: July 2024

Biosurfactants are naturally occurring compounds synthesized by microorganisms that increasingly attract attention due to both their living area and application in various industries. In this study, we explore and characterize a novel bacterium, Enterobacter quasihormaechei strain BDIFST24001, isolated for its ability to produce rhamnolipids biosurfactants, with the aim of facilitating oil remediation processes. The isolation of this bacterium was carried out using Luria-Bertani broth (LB) media from environmental samples collected from oil-contaminated sites in Dhaka city. Screening tests, including the oil spreading method and drop collapse assay, were conducted to identify potential biosurfactant-producing strains, leading to the selection of E. quasihormaechei strain BDIFST24001 based on its favorable performance. Subsequent molecular identification revealed a high similarity of the strain's 16S rRNA gene to E. quasihormaechei, which was corroborated through phylogenetic analysis. Further analysis of the biosurfactant produced by this strain indicated its rhamnolipids nature, as confirmed by FT-IR spectroscopy. The rhamnolipids exhibited promising surface-active properties, including a significant reduction in surface tension and emulsification activity, as evidenced by surface tension measurements and emulsification index assays. Optimization studies revealed that the optimal conditions for rhamnolipids production by E. quasihormaechei strain BDIFST24001 were a temperature of 37°C, pH 10.0, and salinity of 4%. The rhamnolipids produced by this strain demonstrated effective oil remediation capabilities, as observed through controlled experiments using petrol oil. The rhamnolipids effectively reduced the surface tension of the oil-water interface, facilitating the dispersion and emulsification of the oil phase in water. Overall, our findings highlight the potential of E. quasihormaechei strain BDIFST24001 as a promising candidate for biosurfactant-mediated oil spill cleanup and environmental remediation efforts.
FUSION: A web-based application for in-depth exploration of multi-omics data with brightfield histology
Authors: Border Samuel , Melo Ferreira Ricardo , Lucarelli Nicholas , Manthey David , Kumar Suhas , Paul Anindya , Mimar Sayat , Naglah Ahmed , Cheng Ying-Hua , Barisoni Laura , Ray Jessica , Strekalova Yulia , Rosenberg Avi Z , Tomaszewski John E , Hodgin Jeffrey B ,   HuBMAP consortium, El-Achkar Tarek M , Jain Sanjay , Eadon Michael T , Sarder Pinaki
Published: July 2024

Spatial -OMICS technologies facilitate the interrogation of molecular profiles in the context of the underlying histopathology and tissue microenvironment. Paired analysis of histopathology and molecular data can provide pathologists with otherwise unobtainable insights into biological mechanisms. To connect the disparate molecular and histopathologic features into a single workspace, we developed FUSION (Functional Unit State IdentificatiON in WSIs [Whole Slide Images]), a web-based tool that provides users with a broad array of visualization and analytical tools including deep learning-based algorithms for in-depth interrogation of spatial -OMICS datasets and their associated high-resolution histology images. FUSION enables end-to-end analysis of functional tissue units (FTUs), automatically aggregating underlying molecular data to provide a histopathology-based medium for analyzing healthy and altered cell states and driving new discoveries using "pathomic" features. We demonstrate FUSION using 10x Visium spatial transcriptomics (ST) data from both formalin-fixed paraffin embedded (FFPE) and frozen prepared datasets consisting of healthy and diseased tissue. Through several use-cases, we demonstrate how users can identify spatial linkages between quantitative pathomics, qualitative image characteristics, and spatial --omics
NF-κB Epigenetic Attractor Landscape Drives Breast Cancer Heterogeneity
Authors: Lopes Francisco , Pires Bruno R. B. , Lima Alexandre A. B. , Binato Renata , Abdelhay Eliana
Published: July 2024

Heterogeneity in breast cancer (BC) subtypes within a tumor contributes to therapy resistance and cancer recurrence. Development of subtype heterogeneity results from stochastic transitions between cell types as the tumor evolves over time. Here, we sought to characterize how NF-κB contributes to the progression of the human epidermal growth factor receptor 2-positive (HER2+) breast cancer subtype. Initially, we used RNA to determine the expression levels of NF-κB, TWIST1, SIP1, and SLUG in two breast cancer (BC) cell lines, HCC-1954 and MDA-MB-231, classified as HER2+and triple-negative breast cancer (TNBC) subtypes, respectively. Then, we built and calibrated a Gene Regulatory Network (GRN) model reproducing the transcriptional regulation between these genes. For validation, we used DHMEQ-treated cells, along with published patient data and in vitro results. The model epigenetic landscape exhibits two attractor basins corresponding to both HER2+and TNBC subtypes, separated by an unstable stationary state. Stochastic fluctuations in the NF-κB levels induce spontaneous irreversible transition from HER2+to TNBC attractor basins at different times, contributing to subtype heterogeneity. The unstable state mediates this transition by providing a slow route between subtypes in the phase space that is susceptible to dynamic fluctuations. Mutations or drugs that change the availability of NF-κB alters the size of the subtype basins, changing the transition probabilities. Together, our findings enhance the established attractor landscape formulation and deepen understanding of BC heterogeneity, leading to more precise classification, prognosis, and targeted strategies for BC progression.
SAMA: a contig assembler with correctness guarantee
Authors: Salmela Leena
Published: July 2024

In genome assembly the task is to reconstruct a genome based on sequencing reads. Current practical methods are based on heuristics which are hard to analyse and thus such analysis is not readily available. We present a model for estimating the probability of misassembly at each position of a de Bruijn graph based assembly. Unlike previous work, our model also takes into account missing data. We apply our model to produce contigs with correctness guarantee. Our model may have further applications in downstream analysis of contigs or in any analysis working directly on the de Bruijn graph. Our experiments show that when the coverage ofk-mers is high enough, our method produces contigs with similar contiguity characteristics as state-of-the-art assemblers which are based on heuristic correction of the de Bruijn graph.
Strawberry COP9 signalosome FvCSN5A regulates plant development and fruit ripening by facilitating polyamine oxidase FvPAO5 degradation to control polyamine and H2O2homeostasis
Authors: Huang Yun , Gao Jiahui , Ji Guiming , Li Wenjing , Wang Jiaxue , Wang Qinghua , Shen Yuanyue , Guo Jiaxuan , Gao Fan
Published: July 2024

Polyamines (PAs), mainly including putrescine, spermidine, and spermine, are essential for plant growth and development. However, the post-translational regulation of PA metabolism remains unknown. Here, we report the COP9 signalosome subunit 5A (FvCSN5A)-mediated degradation of the PA oxidase FvPAO5, which catalyzes the conversion of spermidine/spermine to produce H2O2. FvCSN5A is localized in the cytoplasm and nucleus, ubiquitously expressed in strawberry plants, and rapidly increases during fruit ripening.FvCSN5ARNA interference (RNAi) transgenic strawberries exhibit pleiotropic effects on plant development, fertility, and fruit ripening by regulating PA and H2O2homeostasis, similar toFvPAO5overexpression transgenic lines. FvCSN5A interacts with FvPAO5 in vitro and in vivo. The ubiquitination and degradation of FvPAO5 are impaired inFvCSN5ARNAi lines. Additionally, FvCSN5A interacts with cullin 1 (FvCUL1), a core component of the E3 ubiquitin-protein ligase complex. Transient genetic analysis in cultivated strawberry fruits showed that inhibitingFaPAO5expression could partially rescue the ripening phenotype ofFaCSN5ARNAi fruits. Collectively, the CSN5A-CUL1-PAO5 signaling pathway responsible for PA and H2O2homeostasis is crucial to strawberry vegetative and reproductive growth and, final to fruit ripening. Our findings may open a promising avenue for improving crop yield and quality by manipulating the CSN5-PAO5 pair.
In search for multifunctional lncRNAs
Authors: Iyengar Bharat Ravi
Published: July 2024

Long non-coding RNAs (lncRNAs) were so named because at the time of their discovery, no corresponding protein products were known. Despite the lack of evidence for translation, many lncRNAs perform essential cellular functions such as regulation of gene expression. Recent studies show that many lncRNAs, including those with known regulatory functions, bind to ribosomes and are translated, suggesting that RNAs can perform two different kinds of functions (a phenomenon known in proteins, called moonlighting). Using a formal mathematical model, I show that execution of one function limits that of the other. However, an RNA can transition from one function to the other, simply by a spatiotemporal regulation of its interacting partners. I further studied the properties of proteins encoded in functional human lncRNAs and found that many of them have complex sequences, and some of them can even adopt stable 3D structures. These findings may encourage further exploration of moonlighting lncRNAs, their regulation, and their role in the evolution of new protein coding genes.
Radiobiological meta-analysis of the response of prostate cancer to high dose rate brachytherapy
Authors: Kölmel Eva G , Pombar Miguel , Pardo-Montero Juan
Published: July 2024

Background and purpose

Clinical studies have shown a marked reduction in tumor control in prostate cancer treated with radically hypofractionated high-dose-rate brachytherapy (HDR-BT). The purpose of this study was to analyze the dose-response of prostate cancer treated with HDR-BT, specifically aiming at investigating the potential failure of the linear-quadratic (LQ) model to describe the response at large dosesper-fraction.

Materials and methods

We collated a dataset of dose-response to HDR-BT (3258 patients). The analysis was conducted separately for low and intermediate risk, resulting in 21 schedules (1643 patients) and 22 schedules (1615 patients), respectively. Data were fitted to tumor control probability models based on the LQ model, the linear-quadratic-linear (LQL), and a modification of the LQ model to include the effect of reoxygenation during treatment.

Results

The LQ cannot fit the data unless the α/β is allowed to be very high (∼[20-100] Gy, 95% confidence interval). If the α/β is constrained to be low (< 8 Gy) the LQ model cannot reproduce the clinical results, and the LQL model, which includes a moderation of radiation damage with increasing dose, significantly improves the fitting. On the other hand, the reoxygenation model does not match the results obtained with the LQL.

Conclusion

The clinically observed reduction in tumor control in prostate cancer treated with radical HDR-BT is better described by the LQL model. Using the best-fitting parameters, the BED for a 20 Gy × 1 treatment (95 Gy) is far less than that of a conventional 2 Gy × 37 fractionation (184 Gy). These results may assist in the design of radical HDR-BT treatment.
Unremodeled plasma membrane GPI-anchored proteins trigger aberrant clathrin-mediated endocytosis
Authors: Chen Li , Banfield David K.
Published: July 2024

The plasma membrane has a complex organization that includes the polarized distribution of membrane proteins as well as lipids. Glycosylphosphatidylinositol-anchored proteins (GPI-AP) are ubiquitously expressed in eukaryotes and represent a functionally diverse group of proteins some of which are critical for the organization and function of the plasma membrane. Here we investigated how the plasma membrane of yeast cells responded to the accumulation of GPI-APs in which phosphoethanolamine (EtNP) had not been removed from mannose 2 (Man2) of the GPI moiety. The persistence of EtNP on Man2 prevented cleavage of a subset of GPI-APs, but the proteins were not endocytosed. Man2 unremodeled GPI-APs increased lipid disorder and generated a stress response whereby abnormal ubiquitin- and clathrin-dependent endocytosis was triggered. The resulting stress-induced endocytosis disrupted the trafficking repertoire of a subset of plasma membrane proteins. These proteins were redirected, via the multivesicular body, to numerous small vacuoles for degradation. Our findings highlight the critical importance GPI-AP Man2 remodeling for maintaining the integrity and homeostasis of the plasma membrane.
Investigating the structure of Schizotypy through the “Multidimensional Schizotypy Scale” and “Oxford-Liverpool Inventory”: an Exploratory network analysis approach in the healthy population
Authors: Sarti Pierfrancesco , Surbeck Werner , Cecere Giacomo , Dannecker Noemi , Horisberger Rahel , Kallen Nils , Omlor Wolfgang , Steiner Anna , Palpella Dario , Langer Nicolas , Blom Johanna M.C. , Homan Philipp
Published: July 2024

Background

Schizophrenia spectrum disorders and schizotypy share traits across positive, negative, and disorganized domains. Instruments like MSS and O-LIFE provide insights into these dimensions. Despite challenges posed by cultural variations and measurement methodologies, these instruments offer nuanced perspectives on the spectrum of schizotypy, spanning from its expression as a personality trait to its potential implications in clinical settings.

Methods

Through an Exploratory Graph Analysis (EGA) applied to a sample of 1059 healthy subjects, we compare the resulting networks with the original factorial structure of the two questionnaires and explore how each one conceptualizes schizotypy. Comparing both models quantitatively and qualitatively these models, we seek to elucidate the unique insights provided by each instrument regarding the spectrum of schizotypy as a personality trait.

Results

EGA analyses unveiled a three-dimensional structure plus an additional one consisting of items related to the concept of “Disconnection”. Confirmatory factor analysis showed this four-dimensional model outperformed others. High reliability and strong factor saturation were observed for all four factors.

O-LIFE’s EGA revealed a complex structure, refined to four factors removing items with low fitting indices from the scale. Confirmatory analysis validated a final model with robust reliability and well-defined factor structures across the new “Cognitive and Behavioural Disorganization”, “Introversion”, “Unusual Experiences”, and “Environmental Pressure” factors.

Conclusions

This study improves the understanding of schizotypy by proposing new MSS and O-LIFE factor structures via EGA. Both scales uniquely contribute to schizotypy assessment in healthy populations, warranting further research to validate and refine these new domains across diverse populations.
Detecting HRD in whole-genome and whole-exome sequenced breast and ovarian cancers
Authors: Abbasi Ammal , Steele Christopher D. , Bergstrom Erik N. , Khandekar Azhar , Farswan Akanksha , Mckay Rana R. , Pillay Nischalan , Alexandrov Ludmil B.
Published: July 2024

Breast and ovarian cancers harboring homologous recombination deficiency (HRD) are sensitive to PARP inhibitors and platinum chemotherapy. Conventionally, detecting HRD involves screening for defects inBRCA1,BRCA2, and other relevant genes. Recent analyses have shown that HRD cancers exhibit characteristic mutational patterns due to the activities of HRD-associated mutational signatures. At least three machine learning tools exist for detecting HRD based on mutational patterns. Here, using sequencing data from 1,043 breast and 182 ovarian cancers, we trained Homologous Recombination Proficiency Profiler (HRProfiler), a machine learning method for detecting HRD using six mutational features. HRProfiler’s performance is assessed against prior approaches using additional independent datasets of 417 breast and 115 ovarian cancers, including retrospective data from a clinical trial involving patients treated with PARP inhibitors. Our results demonstrate that HRProfiler is the only tool that robustly and consistently predicts clinical response from whole-exome sequenced breast and ovarian cancers.

SIGNIFICANCE

HRProfiler is a novel machine learning approach that harnesses only six mutational features to detect clinically useful HRD from both whole-genome and whole-exome sequenced breast and ovarian cancers. Our results provide a practical way for detecting HRD and caution against using individual HRD-associated mutational signatures as clinical biomarkers.
Social Determinants of Health and Healthcare Utilization Disparities among Older Adults with and Without Cognitive Impairment
Authors: Rahemi Zahra , Shalhout Sophia Z. , Bacsu Juanita-Dawne R. , Petrovsky Darina V. , Zanwar Preeti Pushpalata , Adams Swann Arp
Published: July 2024

The purpose of this study was to determine the healthcare utilization patterns in a national sample of older adults across several social determinants of health factors (ethnicity, gender, race, education) with normal and dementia/impaired cognition. We used datasets from the Health and Retirement Study (HRS, 2018) to evaluate healthcare utilization, including metrics such as hospital and nursing home stays, hospice care, and number of visits to the doctor. Logistic models were used to predict healthcare utilization separately in those with normal cognition and dementia. Our final sample comprised 15,607 adults (mean age: 65.2 normal cognition, mean age 71.5 dementia). Hispanics with normal cognition were less likely to stay in a hospital than non-Hispanic respondents (OR: 0.52-0.71, p<0.01). Being female was associated with a higher risk for shorter nursing home days (OR: 1.41, p<0.01) and doctor visits (OR: 1.63-2, p<0.01) in cognitively normal older adults. Being female was associated with a lower risk for hospital stay in those with dementia (OR: 0.50-0.78, p<0.01). Respondents identifying as Black or other races with dementia were less likely to experience nursing home days (OR: 0.42, p<0.04). Black respondents with normal cognition were less likely to experience doctor visits (OR: 0.32-0.37, p<0.01). Those with more than a high school education in both groups were more likely to experience doctors’ visits. The study points to the continued disparities in healthcare utilization linked to participants’ social determinants of health factors and cognition.
VIRAL METAGENOMIC SURVEY OF CASPIAN SEALS
Authors: Karamendin K , Goodman SJ , Kasymbekov Y , Kumar M , Nuralibekov  , Kydyrmanov A
Published: July 2024

Viral diseases of pinnipeds cause substantial mortality and morbidity and can influence population demography. Viral metagenomic studies can therefore play an important role in pinniped health assessments and disease surveillance relevant to both individual species and in a ‘One Health’ context. This study used a metagenomic approach with high throughput sequencing to make the first assessment of viral diversity in Caspian seals (Pusa caspica), the only marine mammal species endemic to the Caspian Sea. Sequencing libraries from 35 seals sampled 2009-2020 were analysed, finding sequences from the viral familiesPicornaviridae, Adenoviridae, Circoviridae, Herpesviridae, Papillomaviridae, Caliciviridae, Orthomyxoviridae, Anelloviridae, Smacoviridae, CruciviridaeandParvoviridae. The similarity of viral contigs from Caspian seal to sequences to those recovered from other pinnipeds ranged from 63.74% (San Miguel sea lion calicivirus) to 78.79% (Seal anellovirus 4). Some may represent novel viral species, but overall, the viral repertoire of Caspian seals is similar to available viromes from other pinnipeds. Among the sequences recovered were partial contigs for influenza B, representing only the second such molecular identification in marine mammals. This work provides a foundation for further studies of viral communities in Caspian seals, the diversity of viromes in pinnipeds more generally, and contributes data relevant for disease risk assessments in marine mammals.
A new pathway in central metabolism mediates nutrient control of development and antibiotic production byStreptomyces
Authors: Li Chao , Urem Mia , Kotsogianni Ioli , Lau Josephine , Elsayed Somayah S. , Martin Nathaniel I. , McNae Iain W. , Voskamp Patrick , Mayer Christoph , Rigali Sébastien , Pannu Navraj , Abrahams Jan Pieter , Schada von Borzyskowski Lennart , van Wezel Gilles P.
Published: July 2024

The amino sugarN-acetylglucosamine (GlcNAc) plays a central role in primary metabolism and is a key signaling molecule for the onset of morphological and chemical differentiation ofStreptomyces. The global nutrient-sensory regulator DasR acts as the gatekeeper of development in streptomycetes, and its activity is modulated by aminosugar phosphates. Here, we report the discovery of a novel pathway in aminosugar metabolism that governs GlcNAc sensing. GlcNAc-6P is converted into a toxic metabolite via two new enzyme functions, namely dehydration ofN-acetylglucosamine-6-phosphate by NagS to form 6P-Chromogen I, a reaction that has not yet been described in the textbooks, and its subsequent deacetylation by NagA producing a cytotoxic structural analogue of ribose. The latter reveals an unexpected promiscuous activity for GlcNAc-6P deacetylase NagA. The crystal structures of NagS apoenzyme and NagS in complex with its substrate GlcNAc-6P or its inhibitor 6-phosphogluconate were resolved at 2.3 Å, 2.6 Å, and 1.7 Å resolution, respectively. Detailedin vivoandin vitrostudies resolved the key residues of the NagS catalytic site. Thus, we have uncovered a novel pathway in aminosugar metabolism that sheds new light on nutrient-mediated control of development and antibiotic production inStreptomyces.
Generation of 1.6 GeV single-particle proton beams
Authors: Zhou Kai , Han Yanliang , Li Zhiping , Jing Hantao , Yu Yongji
Published: July 2024

We present a scattering slow extraction method employing a rotating foil in the Rapid Cycling Synchrotron (RCS) to produce a stable 1.6 GeV single-particle proton beam at CSNS. The foil scatters particles on the beam’s edge over multiple turns, with those at large scattering angles being separated and extracted through a Lambertson magnet. By adjusting the scatter foil’s rotational speed and position, we can precisely control the intensity and repetition rate of the extracted beam. This approach enables the efficient extraction of extremely low-intensity proton beams from CSNS-II/RCS. By setting single-particle collimators in the downstream beamline, a single-particle proton beam is achieved. Using 4y, we simulated the scattering slow extraction process in detail, confirming that a stable 1.6 GeV single-particle proton beam can be extracted, the beam energy can be adjusted from 0.8 to 1.6 GeV using the degrader, the time interval between adjacent single protons can be adjusted from hundreds of nanoseconds to tens of microseconds, to meet the needs of different experiments. Both the beam loss and the residual radiation doses are kept at low levels.

Published by the American Physical Society
2024
Direct production of light scalars in the type-I two-Higgs-doublet model at the lifetime frontier of the LHC
Authors: Liu Wei , Wang Lei , Zhang Yu
Published: July 2024

A light pseudoscalar A in the sufficient large tanβ region of type-I two-Higgs-doublet model can be naturally a long-lived particle. We focus on H±A, HA, and AA pair productions via the electroweak processes mediated by the bosons at the LHC, including pp→W±/Z→H±/HA and pp→h→AA at the 14 TeV LHC. The possibility of probing A as a LLP at the FASER-2, FACET, MoEDAL-MAPP-2, and MATHUSLA is discussed. We find that FASER-2 fails to probe any parameter space within 0.2  GeV<mA<10  GeV for all the considered processes. For 130<mH±=mH<400  GeV, FACET, MoEDAL-MAPP-2, and MATHUSLA can probe tanβ≲104−6 for mA≲3  GeV, and tanβ≲106−8 for 3  GeV≲mA<10  GeV from pp→W±/Z→H±/ZA processes. And pp→h→AA process covers similar parameter space. All processes can surpass the current limits.

Published by the American Physical Society
2024
Causality criteria from stability analysis at ultrahigh boost
Authors: Roy Shuvayu , Mitra Sukanya
Published: July 2024

In this work, we have exclusively employed the linear stability analysis at ultrahigh boost on two well-known stable-causal theories—second-order Müller-Israel-Stewart and first-order Bemfica-Disconzi-Noronha-Kovtun, to identify the region of parameter space over which they are frame-invariantly stable and obey causal signal propagation. It has been shown for these two theories that at near-luminal boost, stability criteria alone can provide the causality constraints on transport coefficients, which are identical to the asymptotic causality conditions, without actually going to the asymptotic limit of the theories. The analysis indicates an alternative approach to derive the causality constraints, which is more appropriate for low-energy effective theories like relativistic hydrodynamics.

Published by the American Physical Society
2024
Exact evaluation of large-charge correlation functions in nonrelativistic conformal field theory
Authors: Beane Silas R. , Orlando Domenico , Reffert Susanne
Published: July 2024

The large-charge master field which generates all n-point correlation functions with an insertion of large charge Q in nonrelativistic conformal field theory is obtained. This field is used to compute Schrödinger-invariant n-point correlation functions of large-charge operators via a direct evaluation of the path integral. Conformal dimensions are found to agree with calculations based on the state-operator correspondence. The master field solution exhibits an emergent harmonic trap whose frequency is a function of the Euclidean time. The large-charge effective action with operator insertions describes a droplet of superfluid matter whose spatial size scales with the time separation of sources. The solution is used to compute Schrödinger symmetry breaking corrections in the large-charge effective field theory (EFT) due to a finite scattering length in the fundamental theory of fermions near unitarity. The scaling of these effects in the large-charge power counting scheme is established, and the size of the effects is quantified using input from quantum Monte Carlo simulations of the near-unitary gas, as well as from the large-N expansion at large charge.

Published by the American Physical Society
2024
Dynamics and resonance fluorescence from a superconducting artificial atom doubly driven by quantized and classical fields
Authors: Ruan Xinhui , Wang Jia-Heng , He Dong , Song Pengtao , Li Shengyong , Zhao Qianchuan , Kuang L. M. , Tsai Jaw-Shen , Zou Chang-Ling , Zhang Jing , Zheng Dongning , Astafiev O. V. , Liu Yu-xi , Peng Zhihui
Published: July 2024

We report an experimental demonstration of resonance fluorescence in a two-level superconducting artificial atom under two driving fields coupled to a detuned cavity. One of the fields is classical and the other is varied from quantum (vacuum fluctuations) to classical by controlling the photon number inside the cavity. The device consists of a transmon qubit strongly coupled to a one-dimensional transmission line and a coplanar waveguide resonator. We observe a sideband anticrossing and asymmetry in the emission spectra of the system through a one-dimensional transmission line, which is fundamentally different from the weak-coupling case. By changing the photon number inside the cavity, the emission spectrum of our doubly driven system approaches the case when the atom is driven by two classical bichromatic fields. We also measure the dynamical evolution of the system through the transmission line and study the properties of the first-order correlation function, Rabi oscillations, and energy relaxation in the system. The study of resonance fluorescence from an atom driven by two fields promotes understanding decoherence in superconducting quantum circuits and may find applications in superconducting quantum computing and quantum networks.

Published by the American Physical Society
2024
Chaotic edge regimes in magnetohydrodynamic channel flow: An alternative path towards the tipping point
Authors: Brynjell-Rahkola Mattias , Duguet Yohann , Boeck Thomas
Published: July 2024

The effect of an imposed magnetic field on the flow of an electrically conducting fluid in a channel geometry is investigated numerically using high-performance temporal simulations. For the strongest spanwise magnetic fields considered, the turbulent state appears metastable, which makes the determination of the associated tipping point arduous. As an alternative, edge states, i.e., unstable states located on the state space boundary between the laminar and the turbulent basin of attraction, are investigated in detail. Their continuation smoothly leads to the tipping point where they are expected to collide with the turbulent dynamics. As the magnetic field intensity is raised, edge states become, on average, more energetic and more unstable, while their fluctuations become more chaotic, less predictable, and less symmetric. Nevertheless, their continuation allows one to accurately determine the value of the tipping point beyond which the laminar state becomes the only attractor.

Published by the American Physical Society
2024
Quantifying the U
5f
covalence and degree of localization in U intermetallics
Authors: Marino Andrea , Christovam Denise S. , Takegami Daisuke , Falke Johannes , Carvalho Miguel M. F. , Okauchi Takaki , Chang Chun-Fu , Altendorf Simone G. , Amorese Andrea , Sundermann Martin , Gloskovskii Andrei , Gretarsson Hlynur , Keimer Bernhard , Andreev Alexandr V. , Havela Ladislav , Leithe-Jasper Andreas , Severing Andrea , Kuneš Jan , Tjeng Liu Hao , Hariki Atsushi
Published: July 2024

A procedure for quantifying the U 5f electronic covalency and degree of localization in U intermetallic compounds is presented. To this end, bulk sensitive hard and soft x-ray photoelectron spectroscopy were utilized in combination with density-functional theory (DFT) plus dynamical mean-field theory (DMFT) calculations. The energy dependence of the photoionization cross sections allows the disentanglement of the U 5f contribution to the valence band from the various other atomic subshells so the computational parameters in the DFT+DMFT can be reliably determined. Applying this method to UGa2 and UB2 as model compounds from opposite ends of the (de)localization range, we have achieved excellent simulations of the valence band and core-level spectra. The width in the distribution of atomic U 5f configurations contributing to the ground state, as obtained from the calculations, quantifies the correlated nature and degree of localization of the U 5f. The findings permit answering the longstanding question why different spectroscopic techniques give seemingly different numbers for the U 5f valence in intermetallic U compounds.

Published by the American Physical Society
2024
Error mitigation in variational quantum eigensolvers using tailored probabilistic machine learning
Authors: Jiang Tao , Rogers John , Frank Marius S. , Christiansen Ove , Yao Yong-Xin , Lanatà Nicola
Published: July 2024

Quantum computing technology has the potential to revolutionize the simulation of materials and molecules in the near future. A primary challenge in achieving near-term quantum advantage is effectively mitigating the noise effects inherent in current quantum processing units (QPUs). This challenge is also decisive in the context of quantum-classical hybrid schemes employing variational quantum eigensolvers (VQEs) that have attracted significant interest in recent years. In this paper, we present a method that employs parametric Gaussian process regression (GPR) within an active learning framework to mitigate noise in quantum computations, focusing on VQEs. Our approach, grounded in probabilistic machine learning, exploits a custom prior based on the VQE ansatz to capture the underlying correlations between VQE outputs for different variational parameters, thereby enhancing both accuracy and efficiency. We demonstrate the effectiveness of our method on a two-site Anderson impurity model and a eight-site Heisenberg model, using the IBM open-source quantum computing framework, Qiskit, showcasing substantial improvements in the accuracy of VQE outputs while reducing the number of direct QPU energy evaluations. This paper contributes to the ongoing efforts in quantum-error mitigation and optimization, bringing us a step closer to realizing the potential of quantum computing in quantum matter simulations.

Published by the American Physical Society
2024