bluuebunny/crossref_metadata_2025 huggingface dataset:
Predicting accurate batch queue wait times on production supercomputers by combining machine learning techniques
Authors: Brown Nick , Gibb Gordon , Belikov Evgenij , Nash Rupert
Published: April 2024

The ability to accurately predict when a job on a supercomputer will leave the queue and start to run is not only beneficial for providing insights to users, but can also help enable non‐traditional HPC workloads that are not necessarily suited to the batch queue style‐approach that is ubiquitous on production HPC machines. However there are numerous challenges in achieving such a prediction with high accuracy, not least because the queue's state can change rapidly and depend upon many factors. In this work, we explore a novel machine learning approach for predicting queue wait times, hypothesising that such a model can capture the complex behavior resulting from the queue policy and other interactions to generate accurate job start times. For ARCHER2 (HPE Cray EX), Cirrus (HPE 8600), and 4‐cabinet (HPE Cray EX) we explore how different machine learning approaches and techniques improve the accuracy of our predictions, comparing against the estimation generated by Slurm. By combining categorization and regression models, we demonstrate that our approach delivers the most accurate predictions across our machines of interest, with the result of this work being the ability to predict job start times within 1 min of the actual start time for around 65% of jobs on ARCHER2 and 4‐cabinet, and 76% of jobs on Cirrus. When compared against what Slurm can deliver, via the backfill plugin, this represents around 3.8 times better accuracy on ARCHER2 and 18 times better for Cirrus. Furthermore our approach can accurately predicting the start time for three quarters of all job within 10 min of the actual start time on ARCHER2 and 4‐cabinet, and for 90% of jobs on Cirrus. Whilst the initial driver of this work was to better facilitate non‐traditional, interactive and urgent, workloads on HPC machines, the insights gained can also be used to provide wider benefits to users, enrich existing batch queue systems, and inform supercomputing center policy also.
Sustaining professionalism: Teachers as co‐enquirers in curriculum design
Authors: Swift Diane , Clowes Gemma , Gilbert Sarah , Lambert Alex
Published: April 2024

In England, the development of teachers' curriculum design capabilities has been identified as a ‘challenge remaining’ (Department for Education [DfE]. (2022). Opportunity for all: Strong schools with great teachers for your child. https://www.gov.uk/government/publications/opportunity‐for‐all‐strong‐schools‐with‐great‐teachers‐for‐your‐child). A recent White Paper (Department for Education [DfE]. (2022). Opportunity for all: Strong schools with great teachers for your child. https://www.gov.uk/government/publications/opportunity‐for‐all‐strong‐schools‐with‐great‐teachers‐for‐your‐child) offered access to a publicly funded online platform as a solution. Drawing on Stenhouse's concepts of teachers as researchers and curriculum as an inquiry process, this article argues that such a policy initiative restricts both curriculum and professional development. An alternative approach to curriculum design, one based on Stenhouse's conception of the iterative development of teachers' professional and curriculum knowledge is profiled. In this article, we, as four teacher‐researchers, analyse a project which featured the Curriculum Design Coherence (CDC) model. We share insights gained from our involvement, both in relation to our professional learning and the impact of our curriculum design work on our pupils. We argue that the ‘othering’ of teachers in research contributes towards the under valuing of practice‐informed evidence in policy making. We draw on the work of Lawrence Stenhouse to inform a different means of generating educational research evidence, one that sustains teacher‐researchers through engagement with principles and concepts so as to inform policy and curriculum development.
Bat–flower trait matching: Extreme phenotypic specialization affects diet preferences but not diet breadth
Authors: Muchhala Nathan , Maguiña‐Conde Rossana , Caiza Angelica , Proaño Daniela
Published: April 2024

Nectarivorous bats have evolved various adaptations to feeding from flowers, such as long, extensible tongues and the ability to hover. The champion of tongue length, Anoura fistulata, can extend its tongue to 150% of its body length, yet little is known about its interactions with flowers in the wild. Here we analyzed the diet of A. fistulata and co‐occurring nectar bats in eight sites across Ecuador. Results demonstrate that, despite its phenotypic specialization, A. fistulata is no more ecologically specialized in its dietary breadth than co‐occurring nectar bats. However, it prefers deeper flowers, and is the sole visitor to two species (Centropogon nigricans and Marcgravia williamsii) whose extremely deep flowers make their nectar inaccessible to other bats. Furthermore, A. fistulata only occurred in sites with at least one flower deeper than the tongue length of other nectar bats, suggesting it needs such a guaranteed nectar source to maintain a population. Finally, we found strong covariation across sites between the local tongue length of A. fistulata and the depth of the deepest flowers it visits. This suggests that the coevolutionary race that selected for the exceptional tongue length of this bat over time is also playing out in a geographic mosaic across space.
Prescribed fire placement matters more than increasing frequency and extent in a simulated Pacific Northwest landscape
Authors: Deak Alison L. , Lucash Melissa S. , Coughlan Michael R. , Weiss Shelby , Silva Lucas C. R.
Published: April 2024

Prescribed fire has been increasingly promoted to reduce wildfire risk and restore fire‐adapted ecosystems. Yet, the complexities of forest ecosystem dynamics in response to disturbances, climate change, and drought stress, combined with myriad social and policy barriers, have inhibited widespread implementation. Using the forest succession model LANDIS‐II, we investigated the likely impacts of increasing prescribed fire frequency and extent on wildfire severity and forest carbon storage at local and landscape scales. Specifically, we ask how much prescribed fire is required to maintain carbon storage and reduce the severity and extent of wildfires under divergent climate change scenarios? We simulated four prescribed fire scenarios (no prescribed fire, business‐as‐usual, moderate increase, and large increase) in the Siskiyou Mountains of northwest California and southwest Oregon. At the local site scale, prescribed fires lowered the severity of projected wildfires and maintained approximately the same level of ecosystem carbon storage when reapplied at a ~15‐year return interval for 50‐year simulations. Increased frequency and extent of prescribed fire decreased the likelihood of aboveground carbon combustion during wildfire events. However, at the landscape scale, prescribed fire did not decrease the projected severity and extent of wildfire, even when large increases (up to 10× the current levels) of prescribed fire were simulated. Prescribed fire was most effective at reducing wildfire severity under a climate change scenario with increased temperature and precipitation and on sites with north‐facing aspects and slopes greater than 30°. Our findings suggest that placement matters more than frequency and extent to estimate the effects of prescribed fire, and that prescribed fire alone would not be sufficient to reduce the risk of wildfire and promote carbon sequestration at regional scales in the Siskiyou Mountains. To improve feasibility, we propose targeting areas of high concern or value to decrease the risk of high‐severity fire and contribute to meeting climate mitigation and adaptation goals. Our results support strategic and targeted landscape prioritization of fire treatments to reduce wildfire severity and increase the pace and scale of forest restoration in areas of social and ecological importance, highlighting the challenges of using prescribed fire to lower wildfire risk.
Baroreflex activation therapy in patients with heart failure and a reduced ejection fraction: Long‐term outcomes
Authors: Zile Michael R. , Lindenfeld JoAnn , Weaver Fred A. , Zannad Faiez , Galle Elizabeth , Rogers Tyson , Abraham William T.
Published: April 2024

Aims

Carotid baroreflex activation therapy (BAT) restores baroreflex sensitivity and modulates the imbalance in cardiac autonomic function in patients with heart failure with reduced ejection fraction (HFrEF). We tested the hypothesis that treatment with BAT significantly reduces cardiovascular mortality and heart failure morbidity and provides long‐term safety and sustainable symptomatic improvement.

Methods and results

BeAT‐HF was a prospective, multicentre, randomized, two‐arm, parallel‐group, open‐label, non‐implanted control trial. New York Heart Association (NYHA) class III subjects, ejection fraction ≤35%, previous heart failure hospitalization or N‐terminal pro‐B‐type natriuretic peptide (NT‐proBNP) >400 pg/ml, no class I indication for cardiac resynchronization therapy and NT‐proBNP <1600 pg/ml were randomized to BAT plus optimal medical management (BAT group) or optimal medical management alone (control). The primary endpoint was cardiovascular mortality and HF morbidity; additional pre‐specified endpoints included durability of safety, quality of life (QOL), exercise capacity (6‐min hall walk distance [6MHWD]), functional status (NYHA class), hierarchical composite win ratio, freedom from all‐cause death, left ventricular assists device (LVAD) implantation, heart transplant. Overall, 323 patients had 332 primary events, median follow‐up was 3.6 years/patient. Both primary endpoint (rate ratio 0.94, 95% confidence interval [CI] 0.57–1.57; p = 0.82) and components of the primary endpoints were not significantly different between BAT and control. The system‐ and procedure‐related major adverse neurological and cardiovascular event‐free rate remained 97% throughout the trial. Symptom improvement (QOL, 6MHWD, NYHA class, all nominal p < 0.001) in the BAT group was durable in time, sustainable in extent. Win ratio (1.26, 95% CI 1.02–1.58) and freedom from all‐cause death, LVAD implantation, heart transplant (hazard ratio 0.66, 95% CI 0.43–1.01) favoured the BAT group but did not reach statistical significance.

Conclusion

The BeAT‐HF primary endpoint was neutral; however, BAT provided safe, effective, and sustainable improvements in HFrEF patient's functional status, 6MHWD and QOL.
Photo‐Induced Cross‐Dehydrogenative Coupling of Quinoxalin‐2(1H)‐ones with Aldehydes under Metal Free Conditions without an External Photocatalyst
Authors: Wang Chunmiao , Jiang Jiangtao , Wang Min , Zhu Weichang , Li Pinhua
Published: April 2024

A simple strategy to 3‐acylated quinoxalin‐2(1H)‐ones via a photo‐induced cross‐dehydrogenative coupling of quinoxalin‐2(1H)‐ones with commercially available aldehyde under metal free conditions without an external photocatalyst was developed. In this transformation, various 3‐acylated quinoxalin‐2(1H)‐ones were generated in high yields with good functional‐group tolerance.
Optimization of formulation and processing conditions for the production of functional noodles containing orange‐fleshed sweet potatoes and biofortified beans
Authors: Natocho Janet , Mugabi Robert , Muyonga John H.
Published: April 2024

The global demand for noodles continues to increase due to their convenience, wide appeal, and affordability. Instant noodles, in particular, are popular for their easy preparation. With annual consumption reaching 106 billion servings in 2019, there is a growing awareness of the importance of healthy food options. However, most noodle types currently available commercially are of low nutritional value. This study sought to develop a protocol for the production of functional noodles consisting of orange‐fleshed sweet potatoes (OFSP) puree and biofortified bean powder (BBP). Response surface methodology (RSM) was used to optimize product formulation and processing parameters. Reduced quartic models were found to adequately represent the relationship between dependent variables (hardness, moisture, protein, dietary fiber, iron, and zinc content) and independent variables (dough thickness, drying temperature, and drying time). R2 values were 0.86–0.99, with a nonsignificant lack‐of‐fit (p < .05). Using numerical optimization, the optimal protocol for the production of functional noodles was determined to include formulation consisting of wheat 73%, OFSP 21.5%, and BBP 5.5%; dough thickness of 2.0 mm; drying temperature and time of 80.0°C and 143.4 min, respectively. These conditions yielded noodles with 5.9% moisture, 11.0 N hardness, 34.5% protein, 11.9% dietary fiber, 86.9 ppm (parts per million) iron, and 50.53 ppm zinc, with a desirability value of 0.82. Experimental validation demonstrated no significant difference from predicted values. Sensory evaluation rated the noodles as acceptable to consumers, with an overall acceptability of 7.8 on a 9‐point hedonic scale. These results show the potential of OFSP and BBP as ingredients for acceptable and nutrient‐rich noodles.
Effect of delay time of working face pressure change on airflow direction in gob: A simulation study
Authors: Wang Kai , Sun Chuanwen
Published: April 2024

For shallow buried mines, the cracks generated due to the mining activities will connect the surface ground and the working face through the gob, which may result in the gas exchange between the surface and underground. In this study, we proposed the gob gas flow model and verified its applicability based on the measured data on site in our previous research and discussed the effect of delay time of pressure variation between working face and surface ground on the airflow direction according to the simulation. The results suggest that the delay time of pressure variation is the main factor affecting the pressure difference between surface and working face and airflow direction. Due to the characteristics of the surface pressure changes, the effect of delay time on airflow in gob is small in a short time, but this effect gradually increases with time. According to the airflow law in a cycle of pressure variation, the airflow direction in the gob is predictable when the delay time reaches a certain value, which can be interpreted clearly on the surface pressure variation diagram. This research may provide references for the measures taken against mine disasters caused by different airflow directions. © 2024 Society of Chemical Industry and John Wiley & Sons, Ltd.
Developmental human resource and exploitative leadership interact to influence Employees' creative idea championing and application
Authors: Huang Jie , Li Yali , Tang Chunyong
Published: April 2024

Based on the human resource development (HRD) literature, this study considers HR system and leadership together, focusing on how to promote employees to champion and apply creative ideas. Based on multi‐wave and multilevel field survey data of 252 Chinese employees nested in 42 groups, Study 1 found that developmental HR and exploitative leadership interact to influence creative idea championing and application via reciprocated obligation. The positive effects of developmental HR on creative idea championing and application were stronger and significant when exploitative leadership was lower (vs. higher), and reciprocated obligation mediated these effects. Study 2 replicated these findings with a scenario experimental design utilizing a sample of 186 MBA students from different companies. Our findings remind supervisors that they should not use exploitative leadership as it will reduce the positive effects of developmental HR, providing unique insights into HRD theory and practice.
Perceived overqualification and employee outcomes: The dual pathways and the moderating effects of dual‐focused transformational leadership
Authors: Liu Zhiqiang , Huang Yuqi , Kim Tae‐Yeol , Yang Jing
Published: April 2024

Research findings concerning the effects of perceived overqualification on task performance are mixed. To reconcile the disparate findings, drawing on person‐environment theory, we propose cynicism toward the job and constructive deviance as contrasting dual pathways that explain the negative and positive effects of perceived overqualification on task performance and employee creativity. We also examine the moderating effects of dual‐focused transformational leadership (TFL) on the relationships between perceived overqualification and the two mediating mechanisms. We test this model using data collected from 469 employees and their 135 supervisors via two‐wave surveys. The results support the negative and positive mediating mechanisms. In addition, based on one field study and two online experiments, we find that individual‐focused TFL mitigates the relationship between perceived overqualification and cynicism toward the job, but that team‐focused TFL enhances the relationship between perceived overqualification and constructive deviance.
STAT activation in regulatory CD4+ T cells of patients with primary sclerosing cholangitis
Authors: Dold Leona , Kalthoff Sandra , Frank Leonie , Zhou Taotao , Esser Pia , Lutz Philipp , Strassburg Christian P. , Spengler Ulrich , Langhans Bettina
Published: April 2024

Introduction

Regulatory CD4+ T cells (Tregs) are pivotal for inhibition of autoimmunity. Primary sclerosing cholangitis (PSC) is an autoimmune cholestatic liver disease of unknown etiology where contribution of Tregs is still unclear. Activation of the JAK‐STAT pathway critically modifies functions of Tregs. In PSC, we studied activation of STAT proteins and Treg functions in response to cytokines.

Methods

In 51 patients with PSC, 10 disease controls (chronic replicative hepatitis C), and 36 healthy controls we analyzed frequencies of Foxp3+CD25+CD127lowCD4+ Tregs, their expression of ectonucleotidase CD39, and cytokine‐induced phosphorylation of STAT1, 3, 5, and 6 using phospho‐flow cytometry. In parallel, we measured cytokines IFN‐gamma, interleukin (IL)‐6, IL‐2, and IL‐4 in serum via bead‐based immunoassays.

Results

In patients with PSC, ex vivo frequencies of peripheral Tregs and their expression of CD39 were significantly reduced (p < .05 each). Furthermore, serum levels of IFN‐gamma, IL‐6, IL‐2, and IL‐4 were markedly higher in PSC (p < .05 each). Unlike activation of STAT1, STAT5, and STAT6, IL‐6 induced increased phosphorylation of STAT3 in Tregs of PSC‐patients (p = .0434). Finally, STAT3 activation in Tregs correlated with leukocyte counts.

Conclusions

In PSC, we observed enhanced STAT3 responsiveness of CD4+ Tregs together with reduced CD39 expression probably reflecting inflammatory activity of the disease.
Factors affecting the long‐term prognosis of patients in the AYA generation with epithelial ovarian cancer: A multicenter propensity score matching analysis
Authors: Miyamoto Emiri , Yoshihara Masato , Iyoshi Shohei , Mogi Kazumasa , Uno Kaname , Fujimoto Hiroki , Kitami Kazuhisa , Yoshikawa Nobuhisa , Kajiyama Hiroaki
Published: April 2024

Objective

Ovarian carcinoma (OvCa) is more common in the elderly, but also affects the adolescent and young adult (AYA) generation, which refers to those aged 15–39 years. Although the characteristics of OvCa may differ between AYAs and non‐AYAs, limited information is currently available on differences in prognostic factors. Therefore, we herein investigated prognostic factors for and the prognosis of OvCa in AYAs. We also examined the prognostic impact of fertility‐sparing surgery in a subgroup analysis.

Methods

We retrospectively collected data on 4897 patients with OvCa from the databases of multiple institutions and ultimately included 1161 patients with epithelial ovarian cancer (EOC). We performed a survival analysis to compare AYAs and non‐AYAs with backgrounds that conformed to those of AYAs using the propensity score (PS) matching method. A Cox regression analysis was also conducted to evaluate each predictor of recurrence‐free survival (RFS) and overall survival (OS) in the original population. As a subgroup analysis, a multivariate analysis stratified by the AYA and non‐AYA generations was performed.

Results

In total, 119 AYA patients were included in this study. After PS adjustments, no significant differences were observed in RFS or OS between AYAs and non‐AYAs. Prognostic factors differed between AYAs and non‐AYAs, particularly in histology and cytology. A multivariate analysis stratified by the AYA and non‐AYA generations described that uterine‐preserving surgery (UPS) did not have a significant impact on the prognosis of AYAs or non‐AYAs. In cases with recurrence, no significant differences were observed in RFS and recurrent sites in the two groups.

Conclusion

Characteristic prognostic factors for EOC in AYAs were identified. The present results indicate the limited prognostic impact of UPS for EOC in AYAs.
Awareness of von Willebrand disease among gynecologists: Investigating the referral of women with heavy menstrual bleeding to hematologists
Authors: Schmiedl Jolana , Castaman Giancarlo
Published: April 2024

Synopsis

Awareness of bleeding disorders, including von Willebrand disease, as a cause of heavy menstrual bleeding is low among gynecologists/obstetricians, potentially delaying diagnosis and appropriate treatment.
Visualizing set relationships: EVenn's comprehensive approach to Venn diagrams
Authors: Yang Mei , Chen Tong , Liu Yong‐Xin , Huang Luqi
Published: April 2024

Venn diagrams serve as invaluable tools for visualizing set relationships due to their ease of interpretation. Widely applied across diverse disciplines such as metabolomics, genomics, transcriptomics, and proteomics, their utility is undeniable. However, the operational complexity has been compounded by the absence of standardized data formats and the need to switch between various platforms for generating different Venn diagrams. To address these challenges, we introduce the EVenn platform, a versatile tool offering a unified interface for efficient data exploration and visualization of diverse Venn diagrams. EVenn (http://www.ehbio.com/test/venn) streamlines the data upload process with a standardized format, enhancing the capabilities for multimodule analysis. This comprehensive protocol outlines various applications of EVenn, featuring representative results of multiple Venn diagrams, data uploads in the centralized data center, and step‐by‐step case demonstrations. Through these functionalities, EVenn emerges as a valuable and user‐friendly tool for the in‐depth exploration of multiomics data.
New paradigms in the study of the cholinergic system and metabolic diseases: Acetyl‐and‐butyrylcholinesterase
Authors: Villeda‐González Juan David , Gómez‐Olivares José Luis , Baiza‐Gutman Luis Arturo
Published: April 2024

Acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) are enzymes that belong to the neuromuscular cholinergic system, their main function is to hydrolyze the neurotransmitter acetylcholine (ACh), through their hydrolysis these enzymes regulate the neuronal and neuromuscular cholinergic system. They have recently attracted considerable attention due to the discovery of new enzymatic and nonenzymatic functions. These discoveries have aroused the interest of numerous scientists, consolidating the relevance of this group of enzymes. Recent investigations have revealed a positive correlation between several risk factors for metabolic syndrome (MetS) and the expression of cholinesterases (ChE's), which underscore the impact of high ChE's activity on the pro‐inflammatory state associated with MetS. In addition, the excessive hydrolysis of ACh and other choline esters (succinylcholine, propionylcholine, butyrylcholine, etc.) by both ChE's results in the overproduction of fatty acid precursor metabolites, which facilitate the synthesis of very low‐density lipoproteins and triacylglycerols. Participation in these processes may represent the link between ChE's and metabolic disorders. However, further scientific research is required to fully elucidate the involvement of ChE's in metabolic diseases. This review aims to collect recent research studies that contribute to understanding the association between the cholinergic system and metabolic diseases.
Diagnostic accuracy of a novel ultrasound imaging index for knee osteoarthritis: Evaluation of sensitivity, specificity, and predictive values
Authors: Kiso Takeharu , Okada Yukinori , Kawata Satoru , Shichiji Kouta , Okumura Eiichiro , Hatsumi Noritaka , Matsuura Ryohei , Kaminaga Masaki , Kuwano Hikaru , Okumura Erika
Published: April 2024

Purpose

We aimed to develop and validate a new ultrasonography (US) index for the diagnosis of primary medial‐type knee osteoarthritis (OA).

Methods

In total, 156 patients (203 limbs) underwent standing knee radiography and the US for suspected knee OA. Total osteophyte height (TOH) and distance between bones (DBB) aided diagnosis. Logistic regression identified optimal cutoff values. Thresholds from logistic regression informed recipient operating characteristic curve (ROC) analysis, balancing sensitivity and specificity. These thresholds were then applied in the differential thermal analysis (DTA) to construct a 2 × 2 table.

Results

The TOH‐DBB index showed that a DBB of 5.6 mm or less was required to diagnose primary medial‐type knee arthropathy. The results in the 2 × 2 table were 41 true‐positive (TP), 10 false negative (FN), 22 true‐negative (TN), and 7 false positive (FP). A DBB of 5.6 mm or less and TOH of 4.7 mm or more were necessary to diagnose severe deformity. The results in the 2 × 2 table were 10 TP, 4 FN, 23 TN, and 4 FP.

Conclusion

The TOH‐DBB index was confirmed to capture changes in primary medial‐type knee OA across various stages.
From the grapevine to the glass: A wine metabolomics tale by FT‐ICR‐MS
Authors: Sousa Silva Marta , Soeiro Mónica , Cordeiro Carlos
Published: April 2024

Wine is one of the most consumed beverages around the world. Its unique characteristics arise from numerous processes, from the selection of grapevine varieties and grapes, the effect of the terroir and geographical origin, through the biochemical process of fermentation by microorganisms, until its aging. All molecules found in wine define its chemical fingerprint and can be used to tell the story of its origin, production, authenticity and quality. Wine's chemical composition can be characterized using an untargeted metabolomics approach based on extreme resolution mass spectrometry. Fourier transform ion cyclotron resonance mass spectrometry (FT‐ICR‐MS) is currently the most powerful analytical technique to analyse such complex sample, providing the most comprehensive analysis of the chemical fingerprint of wine.
Investigating direct current potentials that affect native protein conformation during trapped ion mobility spectrometry–mass spectrometry
Authors: Voeten Robert L. C. , Majeed Hany A. , Bos Tijmen S. , Somsen Govert W. , Haselberg Rob
Published: April 2024

Trapped ion mobility spectrometry–time‐of‐flight mass spectrometry (TIMS‐TOFMS) has emerged as a tool to study protein conformational states. In TIMS, gas‐phase ions are guided across the IM stages by applying direct current (DC) potentials (D1–6), which, however, might induce changes in protein structures through collisional activation. To define conditions for native protein analysis, we evaluated the influence of these DC potentials using the metalloenzyme bovine carbonic anhydrase (BCA) as primary test compound. The variation of DC potentials did not change BCA‐ion charge and heme content but affected (relative) charge‐state intensities and adduct retention. Constructed extracted‐ion mobilograms and corresponding collisional cross‐section (CCS) profiles gave useful insights in (alterations of) protein conformational state. For BCA, the D3 and D6 potential (which are applied between the deflection transfer and funnel 1 [F1] and the accumulation exit and the start of the ramp, respectively) had most profound effects, showing multimodal CCS distributions at higher potentials indicating gradual unfolding. The other DC potentials only marginally altered the CCS profiles of BCA. To allow for more general conclusions, five additional proteins of diverse molecular weight and conformational stability were analyzed, and for the main protein charge states, CCS profiles were constructed. Principal component analysis (PCA) of the obtained data showed that D1 and D3 exhibit the highest degree of correlation with the ratio of folded and unfolded protein (F/U) as extracted from the mobilograms obtained per set D potential. The correlation of D6 with F/U and protein charge were similar, and D2, D4, and D5 showed an inverse correlation with F/U but were correlated with protein charge. Although DC boundary values for induced conformational changes appeared protein dependent, a set of DC values could be determined, which assured native analysis of most proteins.
Removal of isobaric interference using pseudo‐multiple reaction monitoring and energy‐resolved mass spectrometry for the isotope dilution quantification of a tryptic peptide
Authors: Maroto Alicia , dit Fouque Dany Jeanne , Lartia Rémy , Memboeuf Antony
Published: April 2024

Energy‐resolved mass spectrometry (ERMS) and an isotopically labelled internal standard were successfully combined to accurately quantify a tryptic peptide despite the presence of an isobaric interference. For this purpose, electrospray ionisation tandem mass spectrometry (ESI‐MS/MS) experiments were conducted into an ion trap instrument using an unconventional 8 m/z broadband isolation window, which encompassed both the tryptic peptide and its internal standard. Interference removal was assessed by determining an excitation voltage that was high enough to maintain a constant value for the analyte/internal standard peaks intensity ratio, thus ensuring accurate quantification even in the presence of isobaric contamination. Pseudo‐multiple reaction monitoring (MRM) was employed above this excitation voltage to quantify the trypic peptide. The internal standard calibration model showed no lack of fit and exhibited a linear dynamic range from 0.5 μM up to 2.5 μM. The detection limit was 0.08 μM. The accuracy of the method was evaluated by quantifying the tryptic peptide of three reference samples intentionally contaminated with the isobaric interference. All the reference samples were accurately quantified with ∼1% deviation despite the isobaric contamination. Furthermore, we have demonstrated that this methodology can also be applied to quantify the isobaric peptide by standard additions down to 0.2 μM. Finally, liquid chromatography ERMS (LC ERMS) experiments yielded similar results, suggesting the potential of the proposed methodology for analysing complex samples.
Impact of a carrageenan gel on viral load of genital human papillomavirus infections in sexually active women: Findings from the Carrageenan‐gel Against Transmission of Cervical Human papillomavirus (CATCH) trial
Authors: Laurie Cassandra , El‐Zein Mariam , Tota Joseph E. , Tellier Pierre‐Paul , Coutlée François , Burchell Ann N. , Franco Eduardo L.
Published: April 2024

Previous research has shown that women's use of a carrageenan gel reduces the risk of acquiring genital human papillomavirus (HPV) infections but does not help to clear existing ones. Although gel use may not result in complete clearance, it may decrease the viral load of HPV infections. We tested this hypothesis in the Carrageenan‐gel Against Transmission of Cervical Human papillomavirus (CATCH) randomized controlled trial. Participants of the CATCH study were selected for viral load testing if they had completed the first four study visits and tested positive for HPV42 or HPV51 in at least one of these visits. HPV42 and HPV51 were chosen as they were among the most abundant low‐ and high‐risk types, respectively, in the study sample. We measured viral load with a type‐specific real‐time polymerase chain reaction. Results were displayed using summary statistics. Of 461 enrolled participants, 39 were included in the HPV42 analysis set and 56 in the HPV51 analysis set. The median time between visits 1 and 4 was 3.7 months. The viral load (copies/cell) of HPV42 ranged from <0.001 to 13 434.1, and that of HPV51 from <0.001 to 967.1. The net median change in HPV42 viral load over all four visits was −1.04 copies/cell in the carrageenan and −147 copies/cell in the placebo arm (Wilcoxon rank sum test, p = 0.26). There was no net median change in HPV51 viral load over all four visits in either arm (p = 0.45). The use of a carrageenan‐based gel is unlikely to reduce the viral load of HPVs 42 or 51.
Patient awareness of the association between periodontal and systemic diseases in an academic setting
Authors: Carter William , Tiwari Tamanna , Elangovan Satheesh , Johnson Lonnie , Parsegian Karo , Chandrasekaran Sangeetha
Published: April 2024

Background

Periodontal diseases (PD) have been increasingly associated with several systemic conditions such as cardiovascular disease (CVD), diabetes mellitus (DM), rheumatoid arthritis (RA), and Alzheimer's disease (AD). This study aimed to gain insight into patients’ awareness of the association between PD and systemic diseases.

Methods

A survey was developed to analyze patient awareness of the association between PD and systemic diseases. Descriptive and categorical variables were summarized with counts and percentages. Chi‐squared tests were used to evaluate differences between variables. A linear logistical regression model was used to assess the simultaneous, independent association between each variable.

Results

Data from 161 completed surveys were analyzed. The majority of the participants (61.49%) reported awareness of symptoms of PD, but only 36.36% identified all its major symptoms. Individuals reporting awareness of the association between PD and systemic diseases was 48.4%, 31.7%, 14.9%, and 9.9% for CVD, DM, RA, and AD, respectively. Patients aged ≥51 years and males were more aware of the association between PD and CVD. Increased awareness of an association between PD and DM was observed among patients who had a higher frequency of dental visits and those with a self‐reported history of DM.

Conclusions

This study provides insight that, even with the vast amount of scientific knowledge on the inter‐relationships that exist between PD and systemic diseases, most patients are still unaware of these associations. This research identified that improvement of health literacy surrounding PD, their symptoms, and their association with systemic diseases may be warranted.
Contemporary conditional cancer‐specific survival rates in surgically treated nonmetastatic primary urethral carcinoma
Authors: Morra Simone , Scheipner Lukas , Baudo Andrea , Jannello Letizia M. I. , de Angelis Mario , Siech Carolin , Goyal Jordan A. , Touma Nawar , Tian Zhe , Saad Fred , Shariat Shahrokh F. , Creta Massimiliano , Califano Gianluigi , Celentano Giuseppe , Colla' Ruvolo Claudia , Ahyai Sascha , Carmignani Luca , de Cobelli Ottavio , Musi Gennaro , Briganti Alberto , Chun Felix K. H. , Longo Nicola , Karakiewicz Pierre I.
Published: April 2024

Background

We examined the effect of disease‐free interval (DFI) duration on cancer‐specific mortality (CSM)‐free survival, otherwise known as the effect of conditional survival, in radical urethrectomy nonmetastatic primary urethral carcinoma (PUC) patients.

Methods

Using the Surveillance, Epidemiology, and End Results (SEER) database 2000–2020, patient (age, sex, race/ethnicity, and marital status) and tumor (stage and histology) characteristics, as well as systemic therapy exposure status of nonmetastatic PUC patients were tabulated. Conditional survival estimates at 5‐year were assessed based on DFI duration and according to stage at presentation (T1 –2N0 vs. T3–4N0–2).

Results

Of all 512 radical urethrectomy PUC patients, 278 (54%) harbored T1–2N0 stage versus 234 (46%) harbored T3–4N0–2 stage. In 512 PUC patients, 5‐year CSM‐free survival at initial diagnosis was 61.8%. Provided a DFI duration of 36 months, 5‐year CSM‐free survival was 85.6%. In 278 T1–2N0 PUC patients, 5‐year CSM‐free survival at initial diagnosis was 68.4%. Provided a DFI duration of 36 months, 5‐year CSM‐free survival was 86.9%. In 234 T3–4N0–2 PUC patients, 5‐year CSM‐free survival at initial diagnosis was 53.8%. Provided a DFI duration of 36 months, 5‐year CSM‐free survival was 83.6%.

Conclusions

Although intuitively, clinicians and patients are well aware of the concept that increasing DFI duration improves survival probability, only a few clinicians can accurately estimate the magnitude of survival improvement, as was done within the current study. Such information is crucial to survivors, especially in those diagnosed with rare malignancies, where the survival estimation according to DFI duration is even more challenging.
Direct 3D Imaging through Spatial Coherence of Light
Authors: Massaro Gianlorenzo , Barile Barbara , Scarcelli Giuliano , Pepe Francesco V. , Nicchia Grazia Paola , D'Angelo Milena
Published: April 2024

Wide‐field imaging is widely adopted due to its fast acquisition, cost‐effectiveness, and ease of use. Its extension to direct volumetric applications, however, is burdened by the trade‐off between resolution and depth of field (DOF), dictated by the numerical aperture of the system. It is demonstrated that such trade‐off is not intrinsic to wide‐field imaging, but stems from the spatial incoherence of light: images obtained through spatially coherent illumination are shown to have resolution and DOF independent of the numerical aperture. This fundamental discovery enables to demonstrate an optimal combination of coherent resolution‐DOF enhancement and incoherent tomographic sectioning for scanning‐free, wide‐field 3D microscopy on a multicolor histological section.
Influence of vitamins and food on the fluorescence spectrum of human urine
Authors: Chalissery Praveen , Homann Christian , Stepp Herbert , Eisel Maximilian , Aumiller Maximilian , Rühm Adrian , Buchner Alexander , Sroka Ronald
Published: April 2024

Objectives

Fluorescence spectroscopy of human urine is a method with the potential to gain importance as a diagnostic tool in the medical field, e.g., for measuring Coproporphyrin III (CPIII) as an indicator of cancer and acute types of porphyria. Food can change human urine's color, which could influence the urine fluorescence spectrum and the detection of CPIII in urine. To determine if there is a noticeable influence on the urine fluorescence spectrum or on the detection of CPIII in urine, 16 vitamin supplements, and three food items were tested. Such investigation may also prevent false interpretation of measured data.

Methods

Urine samples were collected before and after (overnight, ca. 8 h) intake of each test substance. Samples were investigated by fluorescence spectrum analysis. At excitation wavelengths from 300 to 500 nm and emission wavelengths from 400 to 700 nm excitation‐emission‐matrices were measured. Data obtained from urine before intake were compared to the data from overnight urine. Furthermore, the investigation of any interference with the CPIII concentration was performed at an excitation wavelength of 407 ± 3 nm and emission wavelengths of 490−800 nm.

Results

Only vitamin B2, but none of the other tested substances, showed noticeable influence on the urine fluorescence spectrum. None of the tested substances showed noticeable interference with the recovery rate of CPIII.

Conclusions

The correct interpretation of measured data by fluorescence spectroscopy is possible with the exception if vitamin B2 supplementation was performed; thus, the consumption of vitamin B2 supplements before fluorescence testing of the patient's urine should be avoided and/or must be requested. CPIII concentrations could reliably be measured in all cases.
NITES, a nocturnal bladder score to aid diagnosis during the transition to older age care
Authors: Bower Wendy F. , Da Silva Alisha , Gibson William , Wagg Adrian , Whishaw D Michael
Published: April 2024

Background

As adults transition to older age, bothersome nocturnal lower urinary tract symptoms (LUTS) become common. There is need for a reliable assessment metric to detect and measure specific symptoms.

Objective

To subject the nocturnal LUTS score for older individuals, Nocturia, Incontinence, Toileting and Enuresis Symptom Score (NITES), to psychometric analysis.

Material and Methods

Factor analysis of the metric was conducted with completed questionnaires from 151 older individuals who were either admitted to a tertiary hospital or attending an outpatient continence clinic. Test re‐test reliability involved 18 older community dwelling individuals attending a Geriatrician clinic completing the metric at two timepoints separated by at least 1 week. Intra‐class correlation coefficients were determined for reliability of each factor and item.

Results

The NITES metric was completed by 98 hospitalized older individuals and 53 attending a continence clinic (mean age 83.2 years [SD 7.0]). Factor analysis demonstrated that one item had a floor effect and two items had poor endorsement. After test re‐test reliability analysis, a further three items were removed: one due to poor correlation between timepoints and two demonstrating inadequate internal consistency. The final NITES metric is comprised of three factors: Sleep 4‐items, Incontinence 4‐items, and Personal Bother 2‐items. A 4‐item short form for symptom screening was extracted from the longer measure.

Conclusion

The final NITES metric is a 10‐item questionnaire with an embedded 4‐item short symptom screen. It has utility utilized to detect nocturnal bladder symptoms in both community dwelling and hospitalized older adults.
A bibliometric analysis of HIV nursing research between 1999 and 2022
Authors: Hao Jiaqi , Zhang Qian , Du Xiaoyu , Wang Fan , Liu Jing , Chen Jia
Published: April 2024

Aim

Human immunodeficiency virus (HIV) nursing has become more prominent with the increase in chronic HIV infections. This study examined articles related to HIV nursing to determine how the profession has developed and its future direction.

Design

A bibliometric analysis was conducted.

Methods

HIV nursing‐related articles published in the Web of Science core collection between 1999 and 2022 were searched. VOSviewer was used to identify the contributions of countries, institutions and authors in HIV‐related care. Collaborative maps, hot topics and keywords trends were analysed using VOSviewer and CiteSpace.

Results

A total of 1513 publications were extracted. An increase in articles published between 1999 and 2012 was observed. After 2012, the increase in the number of publications was relatively stable. Since 2016, a downward trend in the number of publications has occurred. The USA, South Africa and the UK were the leading contributors to publications related to HIV nursing. The focus of the HIV nursing research has gradually shifted from “HIV infection”, “risk factors”, and “transmission routes” to “social support”, “depression”, and “public health”. The result shows that increased collaboration among countries/regions can improve the development of HIV nursing and effectively reduce the global HIV infection rate. The mental health of patients has become a research centre in the field of HIV nursing. This study provides direction in clinical practice and future research areas in this field.
A Comprehensive Flow Cytometry Panel for Analysis of Idiopathic Subglottic Stenosis
Authors: So Raymond J. , Collins Samuel L. , Chan‐Li Yee , Lina Ioan , Gelbard Alexander , Motz Kevin M. , Hillel Alexander T.
Published: April 2024

Abstract

Objective

To present a comprehensive flow cytometry panel for idiopathic subglottic stenosis (iSGS).

Study Design

Controlled ex vivo cohort study.

Setting

Tertiary care academic hospital in a metropolitan area.

Methods

Flow cytometry and single‐cell RNA sequencing were performed on 9 paired normal and scar tissue samples from iSGS patients. Flow cytometry was used to assess the presence of myeloid (CD11b, CD14, CD15, Siglec8), lymphoid (CD3, CD4, CD8, gamma delta [γδ], FOXP3), endothelial (CD31), fibroblast (CD90, SMA), and epithelial (CD326, CK5) markers.

Results

On flow cytometry, iSGS scar is characterized by an increased presence of myeloid, lymphoid, endothelial, and fibroblast cell types, but a decreased presence of epithelial cells. In the myeloid lineage, iSGS scar samples demonstrated increased CD11b+ monocytes (P < .001), Siglec8+ eosinophils (P = .03), and CD14+ monocytes (P = .02). In the lymphoid lineage, iSGS scar demonstrated increased CD3+ T‐cells (P < .001), CD4+ helper T‐cells (P < .001), γδ+ T‐cells (P < .001), and FOXP3+ regulatory T‐cells (P = .002). iSGS scar exhibited specific increases in CD90+ (P = .04) and SMA+ (P < .001) fibroblasts but decreased CD326+ (E‐cadherin) epithelial cells (P = .01) relative to normal samples.

Conclusion

We present a comprehensive flow cytometry panel for iSGS. This flow panel may serve as a common platform among airway scientists to elucidate the cellular mechanisms underpinning iSGS and other upper airway pathologies. Scar iSGS samples demonstrate a distinct cellular profile relative to normal iSGS specimens, exhibiting increased fibroblast, endothelial, and inflammatory cell types but decreased epithelium.
Product Distribution of Steady–State and Pulsed Electrochemical Regeneration of 1,4‐NADH and Integration with Enzymatic Reaction
Authors: Al‐Shaibani Mohammed Ali Saif , Sakoleva Thaleia , Živković Luka A. , Austin Harry P. , Dörr Mark , Hilfert Liane , Haak Edgar , Bornscheuer Uwe T. , Vidaković‐Koch Tanja
Published: April 2024

The direct electrochemical reduction of nicotinamide adenine dinucleotide (NAD+) results in various products, complicating the regeneration of the crucial 1,4‐NADH cofactor for enzymatic reactions. Previous research primarily focused on steady–state polarization to examine potential impacts on product selectivity. However, this study explores the influence of dynamic conditions on the selectivity of NAD+ reduction products by comparing two dynamic profiles with steady‐state conditions. Our findings reveal that the main products, including 1,4‐NADH, several dimers, and ADP‐ribose, remained consistent across all conditions. A minor by–product, 1,6‐NADH, was also identified. The product distribution varied depending on the experimental conditions (steady state vs. dynamic) and the concentration of NAD+, with higher concentrations and overpotentials promoting dimerization. The optimal yield of 1,4‐NADH was achieved under steady–state conditions with low overpotential and NAD+ concentrations. While dynamic conditions enhanced the 1,4‐NADH yield at shorter reaction times, they also resulted in a significant amount of unidentified products. Furthermore, this study assessed the potential of using pulsed electrochemical regeneration of 1,4‐NADH with enoate reductase (XenB) for cyclohexenone reduction.