bluuebunny/crossref_metadata_2025 huggingface dataset:
Personalized CZA‐ATM dosing against an XDR E. coli in liver transplant patients; the application of the in vitro hollow fiber system
Authors: Sadouki Zahra , Wey Emmanuel Q. , Iype Satheesh , Nasralla David , Potts Jonathan , Spiro Mike , Williams Alan , McHugh Timothy D. , Kloprogge Frank
Published: November 2024

Background

A patient with an extensively drug‐resistant (XDR) New Delhi metallo‐β‐lactamase (NDM) and oxacillinase (OXA‐48) producing Escherichia coli (E. coli) infection was awaiting orthotopic liver transplant. There is no standardized antibiotic prophylaxis regimen; however, in line with the Infectious Diseases Society of America guidance, an antibiotic prophylactic regimen of ceftazidime‐avibactam 2.5 g TDS with aztreonam 2 g three times a day (TDS) IV was proposed.

Methods

The hollow fiber system (HFS) was applied to inform the individualized pharmacodynamic outcome likelihood prior to prophylaxis.

Results

A 4‐log reduction in CFU/mL in the first 10 h of the regimen exposure was observed; however, the killing dynamics were slow and six 8‐hourly infusions were required to reduce bacterial cells to below the limit of quantification. Thus, the HFS supported the use of the regimen for infection clearance; however, it highlighted the need for several infusions. Standard local practice is to administer prophylaxis antibiotics at induction of orthotopic liver transplantation (OLT); however, the HFS provided data to rationalize earlier dosing. Therefore, the patient was dosed at 24 h prior to their OLT induction and subsequently discharged 8 days after surgery.

Conclusion

The HFS provides a dynamic culture solution for informing individualized medicine by testing antibiotic combinations and exposures against the bacterial isolates cultured from the patient's infection.

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The dynamic N1‐methyladenosine RNA methylation provides insights into the tomato fruit ripening
Authors: Ma Lili , Zuo Jinhua , Bai Chunmei , Fu Anzhen , Wang Qing , Zhou Zhongjing , Deng Zhiping , Tan Jinjuan , Bouzayen Mondher , Zheng Yanyan
Published: November 2024

N1‐methyladenosine (m1A) methylation is an essential mechanism of gene regulation known to impact several biological processes in living organisms. However, little is known about the abundance, distribution, and functional significance of mRNA m1A modification during fruit ripening of tomato the main model species for fleshy fruits. Our study shows that m1A modifications are prevalent in tomato mRNA and are detected in lncRNA and circRNA. The distribution of m1A peaks in mRNA segments indicates that m1A is mainly enriched at the start codon and CDS regions. Assessing changes in global RNA methylation during fruit ripening in wild‐type tomatoes and in the ripening‐impaired Nr mutant affected in the ethylene receptor gene (SlETR3) revealed a decrease in the overall methylation levels from mature green (MG) stage to 6 days postbreaker (Br + 6). Nr mutant fruits show significantly lower methylation levels than Ailsa Craig (AC) fruits. Notably, differences in m1A methylation are well correlated to the expression levels of a number of key ripening‐related genes. The integration of RNA‐seq and MeRIP‐seq data suggests a potential positive impact of m1A modifications on gene expression. In comparison to the AC fruits, the hypomethylation and reduced expression of ethylene‐related genes, ACO3, EBF1, and ERF.D6, in the Nr mutants likely underpin the distinct phenotypic traits observed between the two fruit genotypes at the Br6 stage. Overall, our study brings further arguments supporting the potential significance of m1A methylation modifications in fruit ripening, a developmental process that is instrumental to plant reproduction and to fruit sensory and nutritional qualities.
A plastidial lipoyl synthase LIP1p plays a crucial role in phosphate homeostasis in Arabidopsis
Authors: Ge Shenghong , Xiao Xinlong , Zhang Ke , Yang Changhong , Dong Jinsong , Chen Keying , Lv Qiuyu , Satheesh Viswanathan , Lei Mingguang
Published: November 2024

Phosphate (Pi) homeostasis is important for plant growth and adaptation to the dynamic environment, which requires the precise regulation of phosphate transporter (PHT) trafficking from the endoplasmic reticulum to the plasma membrane. LIPOYL SYNTHASE 1p (LIP1p) is known as a key enzyme in plastids to catalyze lipoylation of pyruvate dehydrogenase complex for de novo fatty acid synthesis. It is unknown whether this process is involved in regulating Pi homeostasis. Here, we demonstrate a new role of LIP1p in controlling Pi homeostasis by regulating PHT1 trafficking. We recovered a weak mutant allele of LIP1p in Arabidopsis that accumulates much less Pi and has enhanced expression of phosphate starvation‐induced genes. LIP1p mutation alters the lipid profile and compromises vesicle trafficking of PHT1 to the plasma membrane to impair Pi uptake. Beside phosphorus, the homeostasis of a series of mineral nutrients was also perturbed in lip1p mutant. Our findings provide powerful genetic evidence to support the linkage between lipoylation and ion homeostasis in plants.
ABI3 regulates ABI1 function to control cell length in primary root elongation zone
Authors: Datta Saptarshi , Mandal Drishti , Mitra Sicon , Chakraborty Swarnavo , Nag Chaudhuri Ronita
Published: November 2024

Post‐embryonic primary root growth is effectively an interplay of several hormone signalling pathways. Here, we show that the ABA‐responsive transcription factor ABI3 controls primary root growth through the regulation of JA signalling molecule JAZ1 along with ABA‐responsive factor ABI1. In the absence of ABI3, the primary root elongation zone is shortened with significantly reduced cell length. Expression analyses and ChIP‐based assays indicate that ABI3 negatively regulates JAZ1 expression by occupying its upstream regulatory sequence and enriching repressive histone modification mark H3K27 trimethylation, thereby occluding RNAPII occupancy. Previous studies have shown that JAZ1 interacts with ABI1, the protein phosphatase 2C, that works during ABA signalling. Our results indicate that in the absence of ABI3, when JAZ1 expression levels are high, the ABI1 protein shows increased stability, compared to when JAZ1 is absent, or ABI3 is overexpressed. Consequently, in the abi3‐6 mutant, due to the higher stability of ABI1, reduced phosphorylation of plasma membrane H+‐ATPase (AHA2) occurs. HPTS staining further indicated that abi3‐6 root cell apoplasts show reduced protonation, compared to wild‐type and ABI3 overexpressing seedlings. Such impeded proton extrusion negatively affects cell length in the primary root elongation zone. ABI3 therefore controls cell elongation in the primary root by affecting the ABI1‐dependent protonation of root cell apoplasts. In summary, ABI3 controls the expression of JAZ1 and in turn modulates the function of ABI1 to regulate cell length in the elongation zone during primary root growth.
ACVECC‐Veterinary Committee on Trauma registry report 2020–2021
Authors: Talbot Charles T. , Raffe Marc R. , Boller Manuel , Edwards Melissa L. , Hall Kelly E.
Published: November 2024

Objective

To report summative data from the American College of Veterinary Emergency and Critical Care (ACVECC)‐Veterinary Committee on Trauma (VetCOT) registry, with further individual evaluation of university and private practices and level I and II Veterinary Trauma Centers (VTCs).

Design

Multi‐institutional registry data report, January 1, 2020, to December 31, 2021.

Setting

VTCs identified and verified by ACVECC‐VetCOT.

Animals

Dogs and cats with evidence of trauma.

Interventions

Data were input to a web‐based data capture system (REDCap) by data entry personnel trained in registry software use and operational definitions of data variables. Patient data on demographics, trauma type, preadmission care, trauma severity assessment at presentation (modified Glasgow Coma Score and Animal Trauma Triage score), key laboratory parameters, interventions, and outcome were collected. Summary descriptive data for each species are reported.

Measurements and Main Results

Twenty‐two VTCs contributed data to the VetCOT registry during a 24‐month period, culminating in a total of 9758 complete trauma case records for dogs and 11734 for cats. Head trauma in dogs and cats was seen at a higher percentage in both university‐only VTCs (encompassing both level I and II) (20.1% and 24.1%, respectively) and level I‐only VTCs (24.3% and 24.1%, respectively), in comparison to private‐only VTCs (encompassing both level I and II) (13.5% and 16.2%, respectively) and individual level II VTCs (14.1% and 18.9%, respectively). Canine and feline surgical procedures were performed at a higher percentage at university VTCs (50% and 40.5%, respectively) compared to private VTCs (39.2% and 28.6%, respectively). Overall survival to discharge for dogs and cats remains high at 93.1% and 83.6%, respectively.

Conclusions

The VetCOT registry has continued to show powerful potential in collating a large, multifaceted, international dataset in trauma for both dogs and cats. As published in previous VetCOT registry reports, survival to discharge has remained static across both university and private practice veterinary hospitals; however, further breakdown has identified university and level I VTCs admitting and managing a higher number of head traumas, as well as university VTCs performing a higher proportion of surgical procedures. Data from this registry will continue to aid in the design of clinical trials, prospective observational studies, and translational research, which will improve the understanding and outcome of trauma patients.
Exploring third spaces during pre‐service teacher online intercultural conversations
Authors: Mesker Peter , de Jager Sarina
Published: November 2024

We examined intercultural conversations in English between South African and Dutch pre‐service teachers during a Collaborative Online International Learning (COIL) project. Unlike traditional COIL research, which emphasizes good practices and professional development, our approach explored the significance of everyday conversations in finding common ground. Through video analysis, we explored instances when common ground fostered a third space—a hybrid, in‐between space—with the potential to promote equity and inclusivity. Results highlight how intercultural, professional, and personal conversations created temporary moments of third space. The role of “connection” in a COIL project shows how specific snapshots of intercultural communication and personal and normative conversations give alternative insights into pre‐service teacher professional development. These dynamics suggest the importance of a more humanistic approach through descriptions of small, everyday conversational snapshots. Results in this study confirm that a North‐South COIL project using English as a lingua franca is an effective way to promote inclusion and mutual understanding.
Haagerup and Størmer's conjecture on pointwise inner automorphisms
Authors: Isono Yusuke
Published: November 2024

In 1988, Haagerup and Størmer conjectured that every pointwise inner automorphism of a type ${\rm III_1}$ factor is a composition of an inner and a modular automorphism. We study this conjecture and prove that every type ${\rm III_1}$ factor with trivial bicentralizer indeed satisfies this condition. In particular, this shows that Haagerup and Størmer's conjecture holds in full generality if Connes’ bicentralizer problem has an affirmative answer. Our proof is based on Popa's intertwining theory and Marrakchi's recent work on relative bicentralizers.
Robust Design Optimization of a Compressor Rotor Using Recursive Cokriging Based Multi-Fidelity Uncertainty Quantification and Multi-Fidelity Optimization
Authors: Wiegand Marcus , Prots Andriy , Meyer Marcus , Schmidt Robin , Voigt Matthias , Mailach Ronald
Published: November 2024

This work focuses on the application of multi-fidelity methods for the robust design optimization of engine components. The robust design optimization approach yields geometric designs that have high efficiencies and are less sensitive to uncertainties from manufacturing and wear. However, the uncertainty quantification techniques required to evaluate the robustness are computationally expensive, which limits their use in robust optimization. Multi-fidelity methods offer a promising solution to reduce the computational cost while maintaining accuracy in both uncertainty quantification and optimization. A Kriging and a multi-fidelity recursive Cokriging framework are developed, implemented, and applied to a test function. In addition, a multi-fidelity super efficient global optimization algorithm is developed. The optimizer is surrogate model-based and can handle constraints. The developed methods are then applied to a compressor test case of a high pressure compressor blade row with 9 uncertainty and 24 design parameters of the geometry. The 2.5% quantile of the stage efficiency is used as a robustness measure and it is therefore optimized. Design bounds and performance constraints are applied. In addition, various uncertainty quantification techniques are analyzed. A multi-fidelity uncertainty quantification approach is developed that combines simplified coarse-grid low-fidelity results with high-fidelity results to reduce the computational cost while maintaining high accuracy. Uncertainty quantification techniques of three fidelity levels are then developed and used for the multi-fidelity approach in the design space. The robust design optimization of the compressor is performed and the optimal designs obtained from the multi-fidelity approach show superior performance compared to existing robust design optima in the literature.
Effectiveness of ultrasound-guided ilioinguinal and iliohypogastric nerve block in pediatric inguinal hernia surgery: a systematic review and meta-analysis of randomized controlled trials
Authors: Zhang Ling , Liu Zhina , Guo Jifeng , Jin Hongquan , Zhang Zhimin
Published: November 2024

Aim: To evaluate the efficacy of ultrasound-guided ilioinguinal and iliohypogastric nerve block (IIHB) in children undergoing surgery for inguinal hernias.Material and methods: PubMed, Embase, Cochrane Library, and Web of Science databases were searched to January 4, 2024. For continuous data, the effect sizes were presented as weighted mean differences (WMDs), and for categorical data, they were reported as relative ratios (RR), each accompanied by 95% confidence intervals (CIs).Results: IIHB demonstrated a longer duration before the need for the first analgesic compared to transverse abdominis plane (TAP), caudal epidural block (CEB), and pre-incisional wound infiltration (PWI), but a shorter duration than quadratus lumborum block (QLB). The IIHB group had a higher probability of requiring rescue analgesics compared to other blocks or PWI (RR: 1.69, 95% CI: 1.25 to 2.28, p=0.001). Higher FLACC scores were noted at 12 hours for the IIHB group (WMD:0.50, 95% CI: 0.13 to 0.86, p=0.008). IIHB required more intraoperative fentanyl compared to controls (RR: 2.14, 95% CI:1.17 to 3.92, p=0.014).Conclusion: While IIHB may have some benefits, it does not appear to be more effective overall in managing postoperative pain in pediatric inguinal hernia surgery patients compared to other blocks or PWI.
A Potential Mechanism Involved in the Regularity of Center-of-Pressure Displacements During Achieving Unipedal Equilibrium on Stable and Unstable Surfaces
Authors: Promsri Arunee
Published: November 2024

Sample entropy (SampEn) is a widely used measure for estimating the regularity of center-of-pressure (COP) trajectories, with high COP regularity (low SampEn) commonly interpreted as ineffective postural control. The current study aimed to investigate one possible source of COP regularity—agonist–antagonist coactivation—resulting in joint stiffness or action stability. A cross-correlation analysis was conducted to determine the similarity (coactivation) level of 5 pairs of lower limb agonist–antagonist electromyographic signals. SampEn was applied to anteroposterior (ap) and mediolateral (ml) COP displacements. Electromyographic and COP signals were simultaneously derived from 25 active young adults (25.6 ± 4.0 years) during unipedal balancing on stable and multiaxial-unstable surfaces. Then, the correlation between individual agonist–antagonist cross-correlation coefficients and SampEn-COP was explored. The results show that only the tibialis anterior–peroneus longus (TA–PL) coactivations are negatively correlated with SampEn-COPap/ml (P ≤ .030) in both surface conditions, with greater TA–PL coactivation appearing with lower SampEn-COPap/ml. In addition, sex effects as one factor that might influence postural control were also tested. Women exhibited greater TA–PL coactivation (P = .017) and lower SampEn-COPap (P = .005) than men. Together, TA–PL coactivation could be one possible origin of COP regularity, but its effects might be detrimental to unipedal postural control, especially for women.
Genome sequences of nine
Clostridium scindens
strains isolated from human feces
Authors: Fernandez-Materan Francelys V. , Olivos-Caicedo Kelly Yovani , Daniel Steven L. , Walden Kimberly K. O. , Fields Christopher J. , Hernandez Alvaro G. , Alves Joao M. P. , Ridlon Jason M.
Published: November 2024

Clostridium scindens
is an important member of the gut microbiome. Strains of
C. scindens
are model organisms for bile acid and steroid metabolism studies. The genome sequences for nine
C. scindens
strains isolated from human feces are reported. Genomes ranged from 3,403,497 to 4,318,168 bp, 46.5% to 48% G+C content, and 3,386 to 4,137 protein-coding total genes.
New PALM-compatible integration vectors for use in the Gram-positive model bacterium
Bacillus subtilis
Authors: Altinoglu Ipek , Carballido-Lopez Rut
Published: November 2024

Improvements in super-resolution and single-molecule techniques, along with the development of new fluorescent proteins and labeling methods, have allowed super-resolution imaging of bacterial cells. Cloning vectors are important tools for engineering fluorescent fusions and perform efficient labeling. Here, we report the construction of four photoactivated localization microscopy (PALM)-compatible integration plasmids for the Gram-positive model organism
Bacillus subtilis
. These plasmids carry genes encoding either the photoswitchable green fluorescent protein dronPA or the photoactivatable red fluorescent protein PAmCherry1, codon-optimized or not for expression in
B. subtilis
. For fast and flexible cloning, multiple cloning sites were added at both the C-terminal and the N-terminal ends of the fluorescent protein genes. The plasmids replicate in
Escherichia coli
and allow integration at the ectopic
amyE
or
thrC
loci of
B. subtilis
via double homologous recombination, for stable chromosomal insertions of single copy number
dronPA
and
PAmCherry1
fusions, respectively. Two-color imaging is accessible with the simultaneous use of both vectors. Insertion of the LacI repressor gene under control of a constitutive promoter in each plasmid yielded four derivative vectors that, combined with an array of
lacO
operator sites, allow fluorescent repressor-operator system localization studies. We demonstrated the effective photoactivation of the LacI-dronPA and LacI-PAmCherry1 fusions, and used them to report with nanoscale precision bacteriophage SPP1 DNA within infected
B. subtilis
cells, both live and fixed, as proof of concept. Our integration vectors provide a convenient and versatile workflow for qualitative and quantitative, single- and dual-color PALM studies in
B. subtilis
.

IMPORTANCE

Super-resolution microscopy techniques allow localization of proteins and cellular components in prokaryotic and eukaryotic cells with unprecedented spatial resolution. Plasmids remain a powerful approach to clone fluorescent protein fusions in bacterial cells. In the current work, we expanded the toolbox of vectors available to engineer the Gram-positive model organism
Bacillus subtilis
for PALM studies. Four integrative vectors in total, two carrying the gene encoding the photoswitchable green fluorescent protein dronPA and two carrying the gene encoding the photoactivatable red fluorescent protein PAmCherry1, were constructed and tested by generating translational fusions to the LacI repressor. The LacI fluorescent fusions successfully reported the subcellular localization of viral DNA in infected
B. subtilis
cells, either live or upon fixation, by PALM. Our dronPA and PAmCherry1 integration vectors expand the genetic toolbox for single-molecule localization microscopy studies in
B. subtilis
.
Interspecies interactions alter the antibiotic sensitivity of
Pseudomonas aeruginosa
Authors: Koumans C. I. M. , Tandar S. T. , Liakopoulos A. , van Hasselt J. G. C.
Published: November 2024

Polymicrobial infections are infections that are caused by multiple pathogens and are common in patients with cystic fibrosis (CF). Although polymicrobial infections are associated with poor treatment responses in CF, the effects of the ecological interactions between co-infecting pathogens on antibiotic sensitivity and treatment outcome are poorly characterized. To this end, we systematically quantified the impact of these effects on the antibiotic sensitivity of
Pseudomonas aeruginosa
for nine antibiotics in medium conditioned by 13 secondary cystic fibrosis-associated bacterial and fungal pathogens through time-kill assays. We fitted pharmacodynamic models to these kill curves for each antibiotic-species combination and found that interspecies interactions changing the antibiotic sensitivity of
P. aeruginosa
are abundant. Interactions that lower antibiotic sensitivity are more common than those that increase it, with generally more substantial reductions than increases in sensitivity. For a selection of co-infecting species, we performed pharmacokinetic–pharmacodynamic modeling of
P. aeruginosa
treatment. We predicted that interspecies interactions can either improve or reduce treatment response to the extent that treatment is rendered ineffective from a previously effective antibiotic dosing schedule and
vice versa
. In summary, we show that quantifying the ecological interaction effects as pharmacodynamic parameters is necessary to determine the abundance and the extent to which these interactions affect antibiotic sensitivity in polymicrobial infections.

IMPORTANCE

In cystic fibrosis (CF) patients, chronic respiratory tract infections are often polymicrobial, involving multiple pathogens simultaneously. Polymicrobial infections are difficult to treat as they often respond unexpectedly to antibiotic treatment, which might possibly be explained because co-infecting pathogens can influence each other’s antibiotic sensitivity, but it is unknown to what extent such effects occur. To investigate this, we systematically quantified the impact of co-infecting species on antibiotic sensitivity, focusing on
P. aeruginosa
, a common CF pathogen. We studied for a large set co-infecting species and antibiotics whether changes in antibiotic response occur. Based on these experiments, we used mathematical modeling to simulate
P. aeruginosa
’s response to colistin and tobramycin treatment in the presence of multiple pathogens. This study offers comprehensive data on altered antibiotic sensitivity of
P. aeruginosa
in polymicrobial infections, serves as a foundation for optimizing treatment of such infections, and consolidates the importance of considering co-infecting pathogens.
Nitrogen (N) and its isotopes in serpentinized forearc wedges and implications for N cycling across subduction zones
Authors: Bustos-Moreno Juan Felipe , Bebout Gray E. , Savov Ivan P.
Published: November 2024

We investigated nitrogen (N) sources and incorporation in the shallow forearc of an active subduction zone by studying samples from two serpentinite seamounts (South Chamorro and Conical; Ocean Drilling Program Legs 195 and 125) along the Mariana convergent margin. We report N concentrations and δ15N values for serpentinized peridotites, serpentinite muds, and metabasaltic clasts. All are enriched in N relative to likely ultramafic and mafic protoliths. A modest positive correlation between N and δ15N for the serpentinized peridotites could reflect extents of N infiltration by N-bearing fluids. Mixing calculations identify the source of the fluids as dehydrating metasediments and/or altered oceanic crust from the subducting Pacific slab. Such addition is consistent with that of other fluid mobile elements (B, Li, As, and Cs), but their concentrations show little correlation with N. The general lack of correlation in concentrations of N and major and trace elements complicates the identification of mineral hosts and N residency (e.g., loose adsorption on serpentine minerals). The enrichment of N in these samples indicates that serpentinized mantle wedges could be a globally significant N reservoir. If subducted, this reservoir could provide significant amounts of isotopically heavy N to sub-arc depths and beyond.
Variation in organisational factors across high- and low-performing hospitals with regard to spontaneous vaginal birth for Black women in four states: a cross-sectional descriptive study
Authors: Clark Rebecca RS , Boland Mary Regina
Published: November 2024

Objective

To describe variation in hospital organisational factors across high- and low-performing hospitals with regard to spontaneous vaginal birth (SVB) for Black women.

Design

Cross-sectional descriptive.

Setting

We conducted a cross-sectional study using three datasets in four states from 2016, including the American Hospital Association Annual Survey, administrative discharge abstracts and a survey in which nurses served as informants about the organisational factors in their hospitals. Hospitals were categorised based on whether they achieved (1) the SVB rate target for Black women at low risk for caesarean birth, (2) the SVB rate target for Black women at low risk for caesarean birth and equivalent SVB rates between Black and White women at low risk for caesarean birth, or (3) neither of these metrics. The first two categories above were considered ‘high performing’ and the third ‘low performing’. Analysis of variances were used to compare organisational factors between hospital categories.

Participants

There were 257 hospitals in the sample.

Primary and secondary outcome measures

Outcomes were meeting the SVB rate targets for Black women at low risk for caesarean birth and SVB rate equivalence between Blacks and White patients.

Results

High-performing hospitals had better nurse work environments (2.84 vs 2.695, p =0.04), including better nurse-physician relationships (2.77 vs 2.695, p =0.02). There were statistically significantly more advanced practice nurses (APNs) on average in maternity units in high-performing hospitals compared with low performing (3.51 to 2.76; p=0.003).

Conclusions

Better rated nurse work environments and the presence of APNs were distinguishing characteristics of high-performing hospitals. These organisational factors may be system-level targets for hospital-level interventions to improve SVB rates and equity therein.
Effect of preoperative inspiratory muscle training combined with preoperative education on postoperative pulmonary complications in high-risk patients with lung cancer: protocol for a randomised controlled trial
Authors: Lu Ting , Wang Xichen , Shi Zhixuan , Lv Lan , Huang Shuna , Ma Ke , Ni Jun
Published: November 2024

Introduction

Preoperative inspiratory muscle training (IMT) is recognised as an important component of the preoperative management of lung cancer, although there is limited evidence for the delivery of a home-based IMT programme combined with preoperative education. We developed a programme combining short-term home-based IMT and preoperative physiotherapy education (‘the programme’). This study aims to evaluate the effectiveness of this programme in reducing postoperative pulmonary complications (PPCs) after lung cancer resection compared with standard care.

Methods and analysis

In this randomised controlled trial, 114 participants scheduled for lung cancer surgery at the First Affiliated Hospital of Fujian Medical University will be randomly assigned (1:1) to either receive usual care (information booklet) or usual care combined with the programme, which consist of short-term home-based IMT and preoperative physiotherapy education. The primary outcome measure will be PPCs using the Melbourne Group Score. Secondary outcomes will include health-related quality of life, maximal inspiratory pressure, 6 min walk distance, length of hospital stay, anxiety and depression levels, and hospital costs.

Ethics and dissemination

The study has received ethics approval from the ethics committee of the first affiliated hospital of Fujian Medical University (approval no: MRCTA, ECFAH of MFU [2021]569). Participants will be required to provide written informed consent. The results of the study will be submitted for publication in peer-reviewed journals.

Trial registration number

ChiCTR2300067464.
Efficacy and safety of non-pharmacological interventions for cancer-related insomnia: a study protocol for a systematic review and network meta-analysis
Authors: Chen Qiang , Kan Mengfan , Jiang Xiaoyu , Bi Hongyan , Zhang Linlin
Published: November 2024

Introduction

Cancer-related insomnia (CRI), a significant concurrent symptom of cancer, profoundly impacts patients. Non-pharmacological interventions include cognitive behavioural therapy, mindfulness-based stress reduction programmes, bright light, acupuncture, exercise and music therapies and tai chi. These approaches, unlike pharmacological treatments, exhibit minimal adverse effects, without drug–drug interactions. They are a promising treatment strategy for CRI patients. However, a comprehensive comparative study evaluating the efficacy and safety of all non-pharmacological interventions for CRI is lacking. Accordingly, we aim to conduct a relatively comprehensive systematic review and network meta-analysis.

Methods and analysis

We will conduct an extensive search across various databases, including Pubmed, Web of Science, Cochrane Library, Embase, Google Scholar, China National Knowledge Infrastructure (CNKI), China Biomedical Literature Database (CBM), Wanfang and Vip databases (VIP). The search will focus on non-pharmacological therapeutic interventions related to CRI in randomised controlled trials published from the inception of these databases until 15 May 2024. The primary outcomes of this study will encompass the Pittsburgh Sleep Quality Index (PSQI) and the Insomnia Severity Index (ISI), while the secondary outcomes will evaluate sleep parameters, fatigue levels, anxiety-depressive mood, quality of life and any potential adverse effects. Paired meta-analyses and network meta-analyses will be conducted utilising ADDIS V.1.16.8, Stata V.14.2 and V.R4.1.2. Bias risk will be independently assessed using the Cochrane Risk of Bias tool (ROB V.2.0), and the evidence quality will be evaluated according to Grading of Recommendations Assessment, Development, and Evaluation (GRADE) standards.

Ethics and dissemination

There are no ethical issues as this study did not conduct any experiments, surveys, or human trials. We will ensure that the findings are shared through pertinent channels.

PROSPERO registration number

CRD42023427752.
Multicenter validation of an RNA-based assay to predict anti-PD-1 disease control in patients with recurrent or metastatic head and neck squamous cell carcinoma: the PREDAPT study
Authors: Flanagan Kevin C , Earls Jon , Hiken Jeffrey , Wellinghoff Rachel L , Ponder Michelle M , McLeod Howard L , Westra William H , Vavinskaya Vera , Sutton Leisa , Deichaite Ida , Macdonald Orlan K , Welaya Karim , Wade James , Azzi Georges , Pippas Andrew W , Slim Jennifer , Bank Bruce , Sui Xingwei , Kossman Steven E , Shenkenberg Todd D , Alexander Warren L , Price Katharine A , Ley Jessica , Messina David N , Glasscock Jarret I , Colevas A Dimitrios , Cohen Ezra E W , Adkins Douglas , Duncavage Eric J
Published: November 2024

Background

Despite advances in cancer care and detection, >65% of patients with squamous cell cancer of the head and neck (HNSCC) will develop recurrent and/or metastatic disease. The prognosis for these patients is poor with a 5-year overall survival of 39%. Recent treatment advances in immunotherapy, including immune checkpoint inhibitors like pembrolizumab and nivolumab, have resulted in clinical benefit in a subset of patients. There is a critical clinical need to identify patients who benefit from these antiprogrammed cell death protein 1 (anti-PD-1) immune checkpoint inhibitors.

Methods

Here, we report findings from a multicenter observational study, PREDicting immunotherapy efficacy from Analysis of Pre-treatment Tumor biopsies (PREDAPT), conducted across 17 US healthcare systems. PREDAPT aimed to validate OncoPrism-HNSCC, a clinical biomarker assay predictive of disease control in patients with recurrent or metastatic HNSCC treated with anti-PD-1 immune checkpoint inhibitors as a single agent (monotherapy) and in combination with chemotherapy (chemo-immunotherapy). The test used RNA-sequencing data and machine learning models to score each patient and place them into groups of low, medium, or high.

Results

The OncoPrism-HNSCC prediction significantly correlated with disease control in both the monotherapy cohort (n=62, p=0.004) and the chemo-immunotherapy cohort (n=50, p=0.01). OncoPrism-HNSCC also significantly predicted progression-free survival in both cohorts (p=0.015 and p=0.037, respectively). OncoPrism-HNSCC had more than threefold higher specificity than programmed death-ligand 1 combined positive score and nearly fourfold higher sensitivity than tumor mutational burden for predicting disease control.

Conclusions

Here, we demonstrate the clinical validity of the OncoPrism-HNSCC assay in identifying patients with disease control in response to anti-PD-1 immune checkpoint inhibitors.

Trial registration number

NCT04510129.
Dual symmetries of dense isotopically and chirally asymmetric QCD
Authors: Klimenko K. G. , Zhokhov R. N.
Published: November 2024

In the present paper, the dual symmetries of dense quark matter phase diagram found in some massless three- and two-color NJL models in the mean field approximation have been shown to exist at a more fundamental level as dual transformations of fields and chemical potentials leaving the Lagrangian invariant. As a result, the corresponding dual symmetries of the full phase diagram can be shown without any approximation. And it has been shown not only in the NJL models, but also in framework of two- and three-color massless QCD itself. This is quite interesting, since one might say that it is not very common to show something completely non-perturbatively in QCD.
Confidential Computing or Cryptographic Computing?
Authors: Popa Raluca Ada
Published: November 2024

Trade-offs between secure computation via cryptography and hardware enclaves.
MXene/NiCu-MOF//AC Nanocomposite Electrode: A Dual-Functional Platform for Energy Storage and Real-Time Monitoring of Monosodium Glutamate Based Sensors
Authors: Safdar Samia , Anjam Nimra , Muzaffar Nimra , Imran Muhammad , Afzal Amir Muhammad , Iqbal Muhammad Waqas , Mumtaz Sohail , Almutairi Tahani Mazyad , Shahbaz Muhammad Ali Hamza , Imran Hamid , Razzaq Arfan
Published: November 2024

Monosodium glutamate (MSG), also known as sodium glutamate, is a widely used food additive in commercial foods, and controlling its level is essential for ensuring food safety and quality. For the detection of MSG, the hydrothermal approach is used to synthesize both MXene and NiCu-MOF. Scanning electron microscopy, X-ray diffraction, and X-ray photoelectron spectroscopy were manipulated to examine the composite morphology, structure, and composition. The MXene/NiCu-MOF electrode displayed an exceptional specific capacity of 277 Cg−1 at a scanning speed of 1.3 mVs−1. The MXene/NiCu-MOF//AC electrode exhibited an exceptional (Cs) of 271.64 Cg−1 at 2 Ag−1 when employed in a supercapattery. The device demonstrated excellent performance, attaining a (Pd) of 1946.21 W kg−1 and (Ed) of 37.17 Wh kg−1. Furthermore, MXene/NiCu-MOF//AC demonstrated exceptional capacity retention of 81% after 5,000 cycles in the reliability test. The MSG was utilized as a glassy carbon electrode which was enhanced with gold nanoparticles. The current detection technique implemented NiCu- MOF/MXene as a conductive matrix, with the use of an anti-glutamate antibody. The correlation remained stable from 0.05 to 200 μM detection range. The multipurpose MXene/NiCu-MOF nanocomposite electrode material opens up possibilities for developing novel hybrid devices in energy harvesting.
Synergistic Effects of Bismuth Oxide on the Radiation Attenuation Characteristics of Borosilicate Glasses
Authors: Al Huwayz Maryam , Almuqrin Aljawhara H. , Alharbi F. F. , Sayyed M. I. , Albarzan B.
Published: November 2024

This work explores Bi2O3-doped borosilicate glasses’ synthesis and radiation shielding characterization, and their applicability as radiation shields. The glasses are prepared via melt quenching in the composition series of 60B2O3-(22-x) SiO2−10CaO-(8+x)Bi2O3 (where x = 4,8,12 and 16 mol%). The produced glasses’ radiation shielding properties, such as the mass attenuation coefficient (MAC), the transmission factor (TF), and the effective atomic number (Zeff), were examined, and the effect of Bi2O3 on the samples’ radiation shielding performance was explored. The glass sample with 24 mol% Bi2O3 exhibited notable efficiency in shielding against gamma radiation. This is evidenced by the favourable change in the MAC, TF, and Zeff with increasing Bi2O3 content. We examined the relation between the glass thickness and the TF, with the results revealing that the 0.6 cm thickness glass possesses the highest TF compared to a thickness of 1.2 cm, indicating that at the thickness of 1.2 cm, the glass material attenuates better compared to 0.6 cm. The relation between the glasses’ density and their half value layer was also examined.
Black Mulberry (Morus nigra L.): A Review of Attributes as an Anticancer Agent to Encourage Pharmaceutical Development
Authors: Ferraz Ana Paula Costa Rodrigues , Figueiredo Patrícia de Oliveira , Yoshida Nídia Cristiane
Published: November 2024

Recent considerations of natural sources as potential anticancer agents have arisen due to the origins of numerous drugs commonly used in chemotherapy. Plant‐based drugs, in particular, have attracted attention for offering the advantage of low adverse effects. Among these, the black mulberry plant (Morus nigra L.) stands out as a natural source of polyphenols, widely used to treat metabolic dysfunctions and confer benefits on human health. This study explores the potential of this plant as an anticancer agent, examining its effectiveness based on the type of application of the plant extracts or isolated substances, extraction methods, and its potential biological effects on cancer cells. Consequently, this study contributes to a better understanding of the distribution of phytochemicals in M. nigra and their applications in the context of cancer field. Among the compounds found in black mulberry are flavonoids, chlorogenic acid, cryptochlorogenic acid, and protocatechuic acid, along with cyanidin‐3‐O‐glucoside as the main anthocyanin on the fruit. The phytochemicals derived from M. nigra exhibit antinociceptive and antimicrobial activities, while also showing protective effects, such as antioxidant properties that underline their potential as anticancer agents. The black mulberry’s roots, stem bark, pulp, and leaves are particularly rich sources of anti‐inflammatory compounds. Ethanol and methanol extraction methods appear to be the most effective in cancer management, offering compounds that facilitate the integration of apoptosis induction, cell growth inhibition, and cytotoxicity modulation. These results collectively represent the salient biological attributes that positioned black mulberry as a promising anticancer agent. Therefore, these findings highlight the multifaceted potential of M. nigra as an anticancer agent, making a compelling case for further research to advance prospects in the medical field.
Analysis and Assessment of BDS‐3 Five Single‐Frequency Civilian Signals Single Point Positioning Considering Time Group Delay and Intersignal Correction
Authors: Sun Xingli
Published: November 2024

The BeiDou Global Navigation Satellite System (BDS‐3) has been providing global positioning, navigation, and timing (PNT) services for over 3 years. Single‐frequency single point positioning (SPP) receivers have significant advantages such as low hardware cost and easy implementation, making them widely used in engineering practice. The time group delay (TGD) and intersignal correction (ISC) are the main parameters for single‐frequency SPP and must be corrected. On‐orbit 30 BDS‐3 satellites have upgraded and maintained operation in 2022, while more multi‐GNSS experiment (MGEX) stations can simultaneously receive all five frequency civilian signals of BDS‐3, namely, B1I, B1C, B2a, B2b, and B3I. So now, it is worth assessing the SPP of BDS‐3 five single‐frequency civilian signals considering TGD and ISC corrections, respectively. Then, with 7 days of 73 MGEX stations simultaneously receiving all BDS‐3 five frequencies, GPS L1 and Galileo E1 civilian signals were selected, and the root mean square (RMS) error was used to assess the SPP performance. The BDS‐3 single‐frequency SPP static and kinematic results show that the order of accuracy from high to low is B1C, B1I, B3I, B2b, and B2a. More thorough static results reveal that B1C’s RMS errors in the north, east, and up (NEU) three directions are 1.12, 0.41, and 1.78 m, respectively, and B1C outperforms B2a by 0.85, 0.28, and 1.23 m. More detailed kinematic results reveal that B1C’s NEU RMS errors are 1.47, 0.77, and 2.72 m, respectively, and that B1C outperforms B2a by 1.04, 0.47, and 1.78 m. The single‐frequency SPP has a higher positioning accuracy at mid to high latitudes in the northern hemisphere than at mid to low latitudes in the southern. The single‐frequency SPP of BDS‐3 B1I is competitive with GPS L1 and Galileo E1. BDS‐3’s five single‐frequency signals, GPS L1, and Galileo E1 all perform well in the east direction, while the up direction performs badly in static and kinematic modes.
Supplemental Table 3 from Targeting YES1 Disrupts Mitotic Fidelity and Potentiates the Response to Taxanes in Triple-Negative Breast Cancer
Authors: Piemonte Katrina M. , Ingles Natasha N. , Weber-Bonk Kristen L. , Valentine Mitchell J. , Majmudar Parth R. , Singh Salendra , Keri Ruth A.
Published: November 2024

Overlapping DEGs sgYES1
Supplemental Table 2 from Targeting YES1 Disrupts Mitotic Fidelity and Potentiates the Response to Taxanes in Triple-Negative Breast Cancer
Authors: Piemonte Katrina M. , Ingles Natasha N. , Weber-Bonk Kristen L. , Valentine Mitchell J. , Majmudar Parth R. , Singh Salendra , Keri Ruth A.
Published: November 2024

Significant GOs for Dot Plots
Table S4 from Molecular Characterization and Classification of HER2-Positive Breast Cancer Inform Tailored Therapeutic Strategies
Authors: Li Yu-Wei , Dai Lei-Jie , Wu Xiang-Rong , Zhao Shen , Xu Yu-Zheng , Jin Xi , Xiao Yi , Wang Ying , Lin Cai-Jin , Zhou Yi-Fan , Fu Tong , Yang Wen-Tao , Li Ming , Lv Hong , Chen Siyuan , Grigoriadis Anita , Jiang Yi-Zhou , Ma Ding , Shao Zhi-Ming
Published: November 2024

Table S4
Supplementary Table 6 from CRISPR Screening of Transcribed Super-Enhancers Identifies Drivers of Triple-Negative Breast Cancer Progression
Authors: Lewis Michael W. , King Caitlin M. , Wisniewska Kamila , Regner Matthew J. , Coffey Alisha , Kelly Michael R. , Mendez-Giraldez Raul , Davis Eric S. , Phanstiel Douglas H. , Franco Hector L.
Published: November 2024

List of direct and indirect target genes for each super-enhancer based on Activity-by-Contact scores calculated from HiC data
Supplementary Data Figure S6 from Neuroendocrine Differentiation in Prostate Cancer Requires ASCL1
Authors: Rodarte Kathia E. , Nir Heyman Shaked , Guo Lei , Flores Lydia , Savage Trisha K. , Villarreal Juan , Deng Su , Xu Lin , Shah Rajal B. , Oliver Trudy G. , Johnson Jane E.
Published: November 2024

Differential expression of genes and gene signatures in RPM and RPMA allografts.
Data from Targeting YES1 Disrupts Mitotic Fidelity and Potentiates the Response to Taxanes in Triple-Negative Breast Cancer
Authors: Piemonte Katrina M. , Ingles Natasha N. , Weber-Bonk Kristen L. , Valentine Mitchell J. , Majmudar Parth R. , Singh Salendra , Keri Ruth A.
Published: November 2024

Abstract
Clinical trials examining broad-spectrum Src family kinase (SFK) inhibitors revealed significant dose-limiting toxicities, preventing advancement for solid tumors. SFKs are functionally heterogeneous, thus targeting individual members is a potential strategy to elicit antitumor efficacy while avoiding toxicity. Here, we identified that YES1 is the most highly overexpressed SFK in triple-negative breast cancer (TNBC) and is associated with poor patient outcomes. Disrupting YES1, genetically or pharmacologically, induced aberrant mitosis, centrosome amplification, multipolar spindles, and chromosomal instability. Mechanistically, YES1 sustained FOXM1 protein levels and elevated expression of FOXM1 target genes that control centrosome function and are essential for effective and accurate mitotic progression. In both in vitro and in vivo TNBC models, YES1 suppression potentiated the efficacy of taxanes, cornerstone drugs for TNBC that require elevated chromosomal instability for efficacy. Clinically, elevated expression of YES1 was associated with worse overall survival of patients with TNBC treated with taxane and anthracycline combination regimens. Together, this study demonstrates that YES1 is an essential regulator of genome stability in TNBC that can be leveraged to improve taxane efficacy.

 Significance: YES1 is a sentinel regulator of genomic maintenance that controls centrosome homeostasis and chromosome stability through FOXM1, revealing this pathway as a therapeutic vulnerability for enhancing taxane efficacy in triple-negative breast cancer.
Supplementary Figure S3 from Durvalumab ± Tremelimumab + Platinum-Etoposide in Extensive-Stage Small Cell Lung Cancer (CASPIAN): Outcomes by PD-L1 Expression and Tissue Tumor Mutational Burden
Authors: Paz-Ares Luis , Garassino Marina Chiara , Chen Yuanbin , Reinmuth Niels , Hotta Katsuyuki , Poltoratskiy Artem , Trukhin Dmytro , Hochmair Maximilian J. , Özgüroğlu Mustafa , Ji Jun Ho , Statsenko Galina , Conev Nikolay , Bondarenko Igor , Havel Libor , Losonczy György , Xie Mingchao , Lai Zhongwu , Godin-Heymann Nadia , Mann Helen , Jiang Haiyi , Shrestha Yashaswi , Goldman Jonathan W.
Published: November 2024

Subgroup analysis of PFS by PD-L1 TC and IC expression for (A) durvalumab plus tremelimumab plus EP versus EP and (B) durvalumab plus EP versus EP. In each panel, the shaded band shows the confidence interval for the ITT population; circle sizes are proportional to the number of events.
Supplementary Table 1 from GEN-1 in Combination with Neoadjuvant Chemotherapy for Patients with Advanced Epithelial Ovarian Cancer: A Phase I Dose-escalation Study
Authors: Thaker Premal H. , Bradley William H. , Leath Charles A. , Gunderson Jackson Camille , Borys Nicholas , Anwer Khursheed , Musso Lauren , Matsuzaki Junko , Bshara Wiam , Odunsi Kunle , Alvarez Ronald D.
Published: November 2024

Adverse Events by Body System and Grade
Supplementary Table 1 from Circulating Tumor DNA Analysis Detects FGFR2 Amplification and Concurrent Genomic Alterations Associated with FGFR Inhibitor Efficacy in Advanced Gastric Cancer
Authors: Jogo Tomoko , Nakamura Yoshiaki , Shitara Kohei , Bando Hideaki , Yasui Hisateru , Esaki Taito , Terazawa Tetsuji , Satoh Taroh , Shinozaki Eiji , Nishina Tomohiro , Sunakawa Yu , Komatsu Yoshito , Hara Hiroki , Oki Eiji , Matsuhashi Nobuhisa , Ohta Takashi , Kato Takeshi , Ohtsubo Koushiro , Kawakami Takeshi , Okano Naohiro , Yamamoto Yoshiyuki , Yamada Takanobu , Tsuji Akihito , Odegaard Justin I. , Taniguchi Hiroya , Doi Toshihiko , Fujii Satoshi , Yoshino Takayuki
Published: November 2024

BAC clones used for FISH analysis