bluuebunny/crossref_metadata_2025 huggingface dataset:
Enhancing photoluminescence performance and pH photostability of nitrogen-doped graphene quantum dots via surface-passivated by polyethylene glycol
Authors: Pham Tri Bao Ngoc , Vo Thuy Ngoc Thi
Published: November 2023

The photoluminescence (PL) properties of nitrogen-doped graphene quantum dots (NGQDs) are highly dependent on reaction parameters. In this study, we developed new and fast protocols to surface passivate NGQDs with polyethylene glycol (PEG) using microwave irradiation. The resulting NGQDs-PEG exhibited highly stable PL with an emission peak at 424 nm when excited at 325 nm. The PL intensity of NGQDs with PEG increased with the volume of capping agents due to the enhancing luminescence effect of the surface functional group of polyethylene glycol. The optimal PEG amount of 2 wt% was found to improve the PL effect of NGQDs. Interestingly, the surface passivation of NGQDs with PEG enabled the NGQDs to exhibit strong PL performance across varying pH environments (from acidic to alkaline), addressing the issue of quenching of quantum dots in biological environments. Our research also focused on the ultrafast synthesis of NGQDs, where process parameters such as power value, catalyst volume, and reaction time were identified as important factors affecting NGQD luminescence. Our results showed that the optimal microwave power was 640 W, lower than that used in previous synthesis methods. Increasing the volume of catalyst promoted faster NGQD formation. The optimal reaction time was found to be 5 min, catalyst volume of 5 ml resulted in the highest PL intensity of NGQDs.
Symmetric monoidal equivalences of topological quantum field theories in dimension two and Frobenius algebras
Authors: Ocal Pablo
Published: November 2023

We show that the canonical equivalences of categories between 2-dimensional (unoriented) topological quantum field theories valued in a symmetric monoidal category and (extended) commutative Frobenius algebras in that symmetric monoidal category are symmetric monoidal equivalences. As an application, we recover that the invariant of 2-dimensional manifolds given by the product of (extended) commutative Frobenius algebras in a symmetric tensor category is the multiplication of the invariants given by each of the algebras.
Sleep Disturbances in Early Gestation and the Risks of Hypertensive Disorders of Pregnancy: A Prospective Cohort Study
Authors: Zhu Jing , Zheng Tao , Jin Hong , Wei Mengdan , Yu Jun , Ni Jiaying , Sun Kun , Zhang Jun ,   for the Early Life Plan Project
Published: November 2023

Maternal poor sleep quality may increase blood pressure during pregnancy, but sound evidence is still limited and inconsistent. To evaluate whether sleep disturbances in early gestation are risk factors for the development of hypertensive disorders of pregnancy, we conducted the Early Life Plan Project from June 2016 to December 2019. Maternal sleep patterns were assessed at 12–16 weeks of gestation by using the Pittsburgh Sleep Quality Index questionnaire. For gestational hypertension and preeclampsia, we estimated adjusted odds ratios (ORs) and 95% confidence intervals (CIs) using multinomial logistic regression models adjusting for potential confounders. Among 5,532 eligible women, we observed that maternal blood pressure in early gestation was significantly higher in women with low sleep efficiency (≤85%), long sleep duration (≥9 hours/night), and snoring. Compared with nonsnorers, snoring in early gestation was independently associated with preeclampsia (OR = 1.72 (95% CI: 1.09, 2.73) for snoring once or twice per week; OR = 2.06 (95% CI: 1.01, 4.31) for snoring 3 or more times per week), particularly for term preeclampsia (OR = 1.79 (95% CI: 1.08, 2.95) and 2.26 (95% CI: 1.03, 4.95), respectively). Results suggest that snoring in early gestation may be a significant risk factor for preeclampsia, with a dose-response pattern.
Towards the Cli-Fi Historical Novel; Or, Climate Futures Past in Recent Fiction
Authors: Forter Greg
Published: November 2023

In The Antinomies of Realism, Fredric Jameson argues that the historical novel of the future will have to be science-fictional. My essay contends that it will have to be climate-fictional. Like Jameson, I focus on the connections between late capital’s reification of the present and the forms of time-consciousness that such reifications foreclose. But, I place Jameson into dialogue with Jonathan Crary and Andreas Malm to show that the foreclosed modes of time are intimately linked to a natural world that contemporary capital purports to have vanquished.

This essay discusses two examples of cli-fi historical fiction—Matt Bell’s Appleseed (2021) and Amitav Ghosh’s Gun Island (2019)—in this context. Despite important differences, these works are both concerned with thinking the climate crisis historically. Both explore how the natural world persists in our “postnatural” present in the form of an uncanniness that denaturalizes the social. This uncanniness liberates traces of the past and future from a present that declares itself bereft of such ghosts. Each novel develops a fantastical form to grasp this temporal heterogeneity, and each retrieves the kernels of utopian futurity from the material history of our present—even and especially, from the climate-devastated and inexorably destructive tendencies of that present.When the deep time of the natural-historical negates yet preserves the historical time of intensified reprisal . . . then and only then will a new universality of the planetary be born.
Purpose and Strategic Engagement in Informal English Digital Activities and Aspects of Vocabulary Knowledge
Authors: Lai Chun , Liu Yang , Lin Yun
Published: November 2023

Research has established positive associations between informal digital activities and vocabulary knowledge. However, understanding how different types of digital activities relate to various aspects of vocabulary knowledge is limited. This study examined how the purpose of informal digital activities and strategic engagement during and/or after technological activities relate to receptive (meaning recognition) and productive (form recall) knowledge of form-meaning links as well as knowledge of word association. Structural Equation Modelling analysis of the questionnaire and vocabulary test data from 339 university EFL learners revealed that two purpose factors (informal digital activities for instructional and socialization purposes) and two strategic engagement factors (dual focus on meaning and form; depth of lexical processing) were key determinants of form-meaning mapping. The interplay of purpose and strategic engagement manifested differently for receptive and productive knowledge of form-meaning links. In contrast, depth of lexical processing was the only predictor of knowledge of word association. The findings underscore activity purpose and strategic engagement as crucial factors in researching and bolstering the relationship between informal digital activities and different aspects of vocabulary knowledge.
Higher Responder Rates Observed With Live Participant Assessment Versus Photographic Assessment After VYC-20L Hyaluronic Acid Treatment for Chin Augmentation
Authors: Dayan Steven , Green Jeremy B , Schlesinger Todd , Dimitrijevic Elena , Chawla Smita , Sangha Sara
Published: November 2023

Background

In an evaluator-blinded, randomized controlled trial, the hyaluronic acid soft-tissue filler VYC-20L injectable gel was safe and effective for correcting volume deficits and retrusion in the chin.

Objectives

The objective of this subanalysis was to compare responder rates obtained with photographic vs live assessments.

Methods

Participants were randomized 3:1 to VYC-20L treatment or a 6-month, no-treatment control period followed by optional treatment. Responder rates (≥1-point improvement from baseline on the validated Allergan Chin Retrusion Scale [ACRS]) obtained with photographic assessments and live assessments at Month 6 were compared. Prespecified subgroup analyses compared responder rates by baseline ACRS severity, filler volume, cannula usage, and investigation site.

Results

VYC-20L was effective for chin augmentation as evaluated with both live and photographic assessments. The ACRS responder rates at Month 6 were 91.8% with live assessments and 56.3% with photographic assessments. Consistently higher response rates were observed by live vs photographic assessment regardless of baseline ACRS severity, filler volume, cannula usage, and investigation site.

Conclusions

Live assessment of ACRS response after VYC-20L treatment resulted in higher responder rates than photographic assessment, supporting the use of live assessment for this indication to approximate real-world clinical practice.

Level of Evidence: 1
In vivo dynamic volumetric imaging of mouse testis and epididymis with optical coherence tomography
Authors: Umezu Kohei , Musina Guzel R , Larina Irina V
Published: November 2023

The implementation of live imaging in reproductive research is crucial for studying the physiological dynamics. Sperm transport is a highly dynamic process regulated by tubular contractions and luminal flows within the male reproductive tract. However, due to the lack of imaging techniques to capture these dynamics in vivo, there is little information on the physiological and biomechanical regulation of sperm transport through the male reproductive tract. Here, we present a functional in vivo imaging approach using optical coherence tomography, enabling live, label-free, depth-resolved, three-dimensional, high-resolution visualization of the mouse testis and epididymis. With this approach, we spatiotemporally captured tubular contractility in mouse testis and epididymis, as well as microstructures of these reproductive organs. Our findings demonstrated that the contraction frequency varies significantly depending on the epididymal regions, suggesting the spatial regulation of epididymal contractility. Furthermore, we implemented quantitative measurements of the contraction wave and luminal transport through the epididymal duct, revealing the physiological dynamics within the male reproductive tract. The results show that the contraction wave propagates along the epididymal duct and the wave propagation velocity was estimated in vivo. In conclusion, this is the first study to develop in vivo dynamic volumetric imaging of the male reproductive tract, which allows for quantitative analysis of the dynamics associated with sperm transport. This study sets a platform for various studies investigating normal and abnormal male reproductive physiology as well as the pharmacological and environmental effects on reproductive functions in mouse models, ultimately contributing to a comprehensive understanding of male reproductive disorders.
Projective independence tests in high dimensions: the curses and the cures
Authors: Zhang Yaowu , Zhu Liping
Published: November 2023

Testing independence between high-dimensional random vectors is fundamentally different from testing independence between univariate random variables. Taking the projection correlation as an example, it suffers from at least three problems. First, it has a high computational complexity of O{n3(p+q)}, where n, p and q are the sample size and dimensions of the random vectors; this limits its usefulness substantially when n is extremely large. Second, the asymptotic null distribution of the projection correlation test is rarely tractable; therefore, random permutations are often suggested as a means of approximating the asymptotic null distribution, which further increases the complexity of implementing independence tests. Third, the power performance of the projection correlation test deteriorates in high dimensions. To address these issues, the projection correlation is improved by using a modified weight function, which reduces the complexity to O{n2(p+q)}. We estimate the improved projection correlation with U-statistic theory. Importantly, its asymptotic null distribution is standard normal, thanks to the high dimesnionality of the random vectors. This expedites the implementation of independence tests substantially. To enhance the power performance in high dimensions, we propose incorporating a cross-validation procedure with feature screening into the projection correlation test. The implementation efficacy and power enhancement are confirmed through extensive numerical studies.
CGRP signalling in migraine: time to look downstream?
Authors: Levy Dan
Published: November 2023

This scientific commentary refers to ‘Second messenger signalling bypasses CGRP receptor blockade to provoke migraine attacks in humans’ by Do et al. (https://doi.org/10.1093/brain/awad261).
Splicing factor ESRP1 derived circ_0068162 promotes the progression of oral squamous cell carcinoma via the miR-186/JAG axis
Authors: Chen Shuai , Zong Yingrui , Hou Zhenzhen , Deng Zhifen , Xia Zongping
Published: November 2023

Objectives

Oral squamous cell carcinoma (OSCC) is a common malignancy in the oral and maxillofacial regions with an increasing incidence rate. Circular RNA (circRNA) is a recently discovered long-chain non-coding RNA family member. The objective of this study was to analyze the role of circ_0068162 in OSCC development.

Methods

We downloaded sample data GSE145608 from the Gene Expression Omnibus database. Online databases Starbase, TargetScan and miRDB were used to predict the target microRNAs (miRNAs) and genes. Cell viability and proliferation were assessed using the CCK-8 and EdU assays, respectively. Cell migration and invasion abilities were detected using transwell assay. The double luciferase reporter and RNA immunoprecipitation (RIP) assays were performed to verify the interaction relationship between the identified target molecules. RNase R and actinomycin D treatment were performed to analyze the stability of circ_0068162.

Results

We found that circ_0068162 was overexpressed in the cytoplasm of OSCC cells and clinical OSCC tissues. Knockdown of circ_0068162 inhibited the growth, migration and invasion of OSCC cells. We also identified miR-186 as the target miRNA of circ_0068162, and JAG1 and JAG2 as the target genes of miR-186. The miR-186 inhibitor rescued the effects of sh-circ_0068162 and JAG1/JAG2 overexpression rescued the effects of miR-186 mimic in OSCC cells. Furthermore, ESRP1 promoted the biosynthesis of circ_0068162.

Conclusions

The circ_0068162/miR-186/JAGs/ESRP1 feedback loop is closely related to OSCC development.
Serve Somebody: Musings of a Pastoral Care Practitioner on the Covenant of Care
Authors: Morse Hal
Published: November 2023

In this article, I explore what it means to “serve somebody,” drawing from my own experience as a full-time chaplain. Chaplains must serve many different parties, but are ultimately called to care for their patients via a covenental relationship of care.
The Triple Beholdenness of Polish Hospital Chaplains: How to Avoid Confusion?
Authors: Mikuczewski Jarosław L
Published: November 2023

Polish hospital chaplaincy, because of the unique political and sociological context in which it finds itself, presents a sort of triple beholdenness. It carries particular loyalties to the state, to Catholic doctrine, and above all, it is called to be faithful to the unique suffering person. In this article, I argue that the biggest challenge for Polish chaplaincy resides within the domain of loyalty to the patient, where the profound and immediate need for robust formation of individual Christian conscience through catechesis is needed. Although hospital chaplaincy’s involvement in catechesis and instructing the faithful might not be clearly evident for the reader, nevertheless I prove my point by bringing a story from my practice as a chaplain in one of Poland’s hospitals.
Optimization of guideline-directed medical therapies in patients with diabetes and chronic kidney disease
Authors: Neumiller Joshua J , Alicic Radica Z , Tuttle Katherine R
Published: November 2023

Diabetes is the leading cause of chronic kidney disease (CKD) and kidney failure worldwide. CKD frequently coexists with heart failure and atherosclerotic cardiovascular disease in the broader context of cardio-kidney-metabolic syndrome. Diabetes and CKD are associated with increased risk of all-cause and cardiovascular death as well as decreased quality of life. The role of metabolic and hemodynamic abnormalities has long been recognized as an important contributor to the pathogenesis and progression of CKD in diabetes, while a more recent and growing body of evidence supports activation of both systemic and local inflammation as important contributors. Current guidelines recommend therapies targeting pathomechanisms of CKD in addition to management of traditional risk factors such as hyperglycemia and hypertension. Sodium-glucose cotransporter-2 inhibitors are recommended for treatment of patients with CKD and type 2 diabetes (T2D) if eGFR is ≥20 ml/min/173 m2 on a background of renin-angiotensin system inhibition. For patients with T2D, CKD, and atherosclerotic cardiovascular disease, a glucagon-like peptide-1 receptor agonist is recommended as additional risk-based therapy. A non-steroidal mineralocorticoid receptor antagonist is also recommended as additional risk-based therapy for persistent albuminuria in patients with T2D already treated with renin-angiotensin system inhibition. Implementation of guideline-directed medical therapies is challenging in the face of rapidly accumulating knowledge, high cost of medications, and lack of infrastructure for optimal healthcare delivery. Furthermore, studies of new therapies have focused on T2D and CKD. Clinical trials are now planned to inform the role of these therapies in people with type 1 diabetes (T1D) and CKD.
Hybridization Protection Reaction for Sensitive and Robust Gene Expression Profiling of Clinical Formalin-Fixed Paraffin-Embedded Samples
Authors: Hsu Feng-Ming , Chang Yih-Leong , Chen Chung-Yung , Lin Shu-Rung , Cheng Jason Chia-Hsien
Published: November 2023

Background

RNA profiling of formalin-fixed paraffin-embedded (FFPE) tumor tissues for the molecular diagnostics of disease prognosis or treatment response is often irreproducible and limited to a handful of biomarkers. This has led to an unmet need for robust multiplexed assays that can profile several RNA biomarkers of interest using a limited amount of specimen. Here, we describe hybridization protection reaction (HPR), which is a novel RNA profiling approach with high reproducibility.

Methods

HPR assays were designed for multiple genes, including 10 radiosensitivity-associated genes, and compared with TaqMan assays. Performance was tested with synthetic RNA fragments, and the ability to analyze RNA was investigated in FPPE samples from 20 normal lung tissues, 40 lung cancer, and 30 esophageal cancer biopsies.

Results

Experiments performed on 3 synthetic RNA fragments demonstrated a linear dynamic range of over 1000-fold with a replicate correlation coefficient of 0.99 and high analytical sensitivity between 3.2 to 10 000 pM. Comparison of HPR with standard quantitative reverse transcription polymerase chain reaction on FFPE specimens shows nonsignificant differences with > 99% confidence interval between 2 assays in transcript profiling of 91.7% of test transcripts. In addition, HPR was effectively applied to quantify transcript levels of 10 radiosensitivity-associated genes.

Conclusions

Overall, HPR is an alternative approach for RNA profiling with high sensitivity, reproducibility, robustness, and capability for molecular diagnostics in FFPE tumor biopsy specimens of lung and esophageal cancer.
Focal atrial tachycardia mimicking catecholaminergic polymorphic ventricular tachycardia: a case report
Authors: Seewald Maria Sabine , Huttelmaier Moritz Till , Kriebel Thomas , Fischer Thomas H
Published: November 2023

Background

In childhood and adolescence, cardiac arrhythmias are often benign in the absence of congenital heart defects. Nevertheless, life-threatening inherited arrhythmogenic syndromes can become clinically manifest in early childhood. As early symptoms may be similar in both conditions, thorough workup is fundamental to avoid delayed diagnosis and misdiagnosis.

Case summary

We present the case of a 26-year-old Caucasian female patient who presented with recurrent non-sustained polymorphic wide complex tachycardia. Structural heart disease was excluded by echocardiography as well as cardiac magnetic resonance imaging. Due to wide complex extrasystoles and couplets with alternating QRS axis occurring at low levels of physical exertion, catecholaminergic polymorphic ventricular tachycardia (CPVT) was suspected and further investigated. Epinephrine testing in combination with an electrophysiological (EP) study with placement of a coronary sinus catheter and subsequent programmed stimulation ruled out CPVT and unmasked wide complex tachycardia as varying aberrant conduction of focal atrial tachycardia (FAT). 3D-navigated mapping of FAT revealed a direct parahisian origin. Due to significantly increased risk of atrio-ventricular (AV) block during ablation, the patient refused ablation and preferred medical antiarrhythmic therapy.

Discussion

Given the consequences of both, delayed diagnosis and misdiagnosis of CPVT, thorough workup is fundamental. In case of doubt regarding potential aberrant AV conduction in the context of wide complex tachycardia, an invasive EP study may easily and safely prove or rule out aberrancy.
Prelude to Re-education: US Internationalists, Students and the German Problem, 1919–1949
Authors: Piller Elisabeth
Published: November 2023

Much has been written about US efforts to solve the ‘German problem’ after the Second World War. Scholars have carefully studied US attempts to de-Nazify, pacify and democratise post-war Germany and have identified the creation of large-scale student exchange programmes as an integral part of that agenda. As this article shows, 1945 was not the first time in the twentieth century that US policy-makers and educators had pondered the German problem and sought to address Germany’s apparently deficient democratisation and excessive militarism, as well as the alarmingly narrow horizons of its youth. Based on long-neglected or inaccessible archival materials in Europe and the United States, this article charts the development of US student exchanges with inter-war Germany and demonstrates that a fuller understanding of US re-education policies in West Germany requires paying attention to the 1920s and 1930s. The article traces the discovery of the German student as an object of US democratisation efforts in the inter-war period and shows that US re-education policy after 1945 was deeply informed by the experiences made, connections forged and convictions won (sometimes without reliable evidence) by US internationalists in the inter-war years. Facing the German problem after the First World War, the article argues, helped establish a modus operandi—and a modus cogitandi—with regard to the German student that would inform US cultural diplomacy well into the Cold War.
Populist partner: the influence of partner characteristics on populist radical right voting
Authors: Sipma Take , Lubbers Marcel , Spierings Niels
Published: November 2023

In this study, the role of the partner’s self-assessed socio-economic status and political attitudes on populist radical right voting is studied. We made use of a survey among the adult Dutch population (the LISS panel), with information on the self-assessed occupational class, education and political preferences of both partners in cohabiting heterosexual couples. Our results show that, next to the more often found effect of one’s own socio-economic status, the lower the self-assessed occupational class and educational level of the partner, the more likely one is to vote for the PVV, a Dutch populist radical right party. Whereas previous literature has shown that partner’s socio-economic status affects voting behaviour through economic policy preferences, we show the partner’s self-assessed position, for both men and women, is also relevant in explaining behaviour via other political attitudes, such as anti-immigration views. Regardless of one’s own political attitudes, the attitudes of the partner affect one’s likelihood to vote for the populist radical right. With this study, we thus show that including partner characteristics provides further insight into the role of occupation, education, gender, and political attitudes in populist radical right voting, providing evidence of the importance of people’s strong ties in voting behaviour outcomes.
The cardiovascular effects of novel weight loss therapies
Authors: Usman Muhammad Shariq , Davies Melanie , Hall Michael E , Verma Subodh , Anker Stefan D , Rosenstock Julio , Butler Javed
Published: November 2023

The prevalence of overweight and obesity has reached pandemic proportions. Obesity is known to increase the risk for Type 2 diabetes and hypertension, as well as the risk for overt cardiovascular (CV) disease, including myocardial infarction, heart failure, and stroke. The rising prevalence of obesity may counteract the recent advances in primary and secondary prevention of CV disease. Overweight and obesity are common in patients with CV disease; however, cardiologists face several challenges in managing body weight in this population. Many may not consider obesity as a therapeutic target probably because there were no previous highly effective and safe pharmacologic interventions to consider. In addition, they may not have the expertise or resources to implement lifestyle interventions and may have limited familiarity with obesity pharmacotherapy. Moreover, the long-term CV effects of obesity pharmacotherapy remain uncertain due to limited CV outcome data with weight loss as the primary intervention. Although current CV guidelines recognize the importance of weight loss, they primarily focus on lifestyle modifications, with fewer details on strategies to utilize obesity pharmacotherapy and surgery. However, the recent 2022 American Diabetes Association/European Association for the Study of Diabetes consensus on the management of Type 2 diabetes has moved up weight management to the front of the treatment algorithm, by prioritizing the use of pharmacologic interventions such as glucagon-like peptide-1 receptor agonists and dual glucose-dependent insulinotropic polypeptide/glucagon-like peptide-1 receptor agonists, which have potent weight-lowering effects, in addition to glucose-lowering effects. This review appraises the current evidence regarding the CV effects of weight-loss interventions. Considering this evidence, practical guidance is provided to assist cardiologists in developing and implementing treatment plans, which may allow optimal weight management while maximizing CV benefits and minimizing side effects to improve the overall well-being of people with CV disease.
Limited host availability disrupts the genetic correlation between virulence and transmission
Authors: Godinho Diogo P , Rodrigues Leonor R , Lefèvre Sophie , Delteil Laurane , Mira André F , Fragata Inês R , Magalhães Sara , Duncan Alison B
Published: November 2023

Virulence is expected to be linked to parasite fitness via transmission. However, it is not clear whether this relationship is genetically determined, nor if it differs when transmission occurs continuously during, or only at the end of, the infection period. Here, we used inbred lines of the macroparasitic spider mite Tetranychus urticae to disentangle genetic vs. nongenetic correlations among traits, while varying parasite density and opportunities for transmission. A positive genetic correlation between virulence and the number of transmitting stages produced was found under continuous transmission. However, if transmission occurred only at the end of the infection period, this genetic correlation disappeared. Instead, we observed a negative relationship between virulence and the number of transmitting stages, driven by density dependence. Thus, within-host density dependence caused by reduced opportunities for transmission may hamper selection for higher virulence, providing a novel explanation as to why limited host availability leads to lower virulence.
Placental evolution from a three-dimensional and multiscale structural perspective
Authors: Laundon Davis , Gostling Neil J , Sengers Bram G , Chavatte-Palmer Pascale , Lewis Rohan M
Published: November 2023

The placenta mediates physiological exchange between the mother and the fetus. In placental mammals, all placentas are descended from a single common ancestor and functions are conserved across species; however, the placenta exhibits radical structural diversity. The selective pressures behind this structural diversity are poorly understood. Traditionally, placental structures have largely been investigated by grouping them into qualitative categories. Assessing the placenta on this basis could be problematic when inferring the relative “efficiency” of a placental configuration to transfer nutrients from mother to fetus. We argue that only by considering placentas as three-dimensional (3D) biological structures, integrated across scales, can the evolutionary questions behind their enormous structural diversity be quantitatively determined. We review the current state of placental evolution from a structural perspective, detail where 3D imaging and computational modeling have been used to gain insight into placental function, and outline an experimental roadmap to answer evolutionary questions from a multiscale 3D structural perspective. Our approach aims to shed light on placental evolution, and can be transferred to evolutionary investigations in any organ system.
Eating patterns contribute to shaping the gut microbiota in the mucosal simulator of the human intestinal microbial ecosystem
Authors: Minnebo Yorick , De Paepe Kim , Raes Jeroen , Van de Wiele Tom
Published: November 2023

Eating patterns, i.e. meal frequency and circadian timing of meals, are often modified in weight loss and metabolic healing strategies. However, in-depth research into the effects on the gut microbiome remains scarce, particularly across various colon regions and niches. We identified eating patterns to contribute in shaping the in vitro gut biomass production, metabolism, and microbial community compositions by subjecting four faecal microbiomes to a pattern that is standardized for a dynamic gut model (feeding at 09, 17, and 01 h), a typical Western (breakfast, lunch, and dinner at 09, 13, and 19 h, respectively), and a time-restricted pattern (single meal at 09 h). While eating patterns moderately affected the microbiome (2.4% and 1.8% significant variation in proportional and quantitative microbial compositions, respectively), significant changes were noted in the time-restricted pattern, including increased Bacteroides, Butyricicoccus, Dialister, and Faecalibacterium abundances. Sampling every 4 h revealed no significant circadian fluctuations in biomass production, microbial community compositions, or functionality. Longer fasting times favoured the growth of slower-growing species, such as Akkermansia, Dialister, and Parasutterella over faster-growers, such as Pseudomonas and Stenotrophomonas. Our findings illustrate the importance of recording and considering eating patterns as a gut microbiome determinant in in vivo and in vitro dietary intervention studies.
Mutations in yeast Pcf11, a conserved protein essential for mRNA 3′ end processing and transcription termination, elicit the Environmental Stress Response
Authors: Graber Joel H , Hoskinson Derick , Liu Huiyun , Kaczmarek Michaels Katarzyna , Benson Peter S , Maki Nathaniel J , Wilson Christian L , McGrath Caleb , Puleo Franco , Pearson Erika , Kuehner Jason N , Moore Claire
Published: November 2023

The Pcf11 protein is an essential subunit of the large complex that cleaves and polyadenylates eukaryotic mRNA precursor. It has also been functionally linked to gene-looping, termination of RNA Polymerase II (Pol II) transcripts, and mRNA export. We have examined a poorly characterized but conserved domain (amino acids 142–225) of the Saccharomyces cerevisiae  Pcf11 and found that while it is not needed for mRNA 3′ end processing or termination downstream of the poly(A) sites of protein-coding genes, its presence improves the interaction with Pol II and the use of transcription terminators near gene promoters. Analysis of genome-wide Pol II occupancy in cells with Pcf11 missing this region, as well as Pcf11 mutated in the Pol II CTD Interacting Domain, indicates that systematic changes in mRNA expression are mediated primarily at the level of transcription. Global expression analysis also shows that a general stress response, involving both activation and suppression of specific gene sets known to be regulated in response to a wide variety of stresses, is induced in the two pcf11 mutants, even though cells are grown in optimal conditions. The mutants also cause an unbalanced expression of cell wall-related genes that does not activate the Cell Wall Integrity pathway but is associated with strong caffeine sensitivity. Based on these findings, we propose that Pcf11 can modulate the expression level of specific functional groups of genes in ways that do not involve its well-characterized role in mRNA 3′ end processing.
Euler characteristic curves and profiles: a stable shape invariant for big data problems
Authors: Dłotko Paweł , Gurnari Davide
Published: November 2023

Tools of topological data analysis provide stable summaries encapsulating the shape of the considered data. Persistent homology, the most standard and well-studied data summary, suffers a number of limitations; its computations are hard to distribute, and it is hard to generalize to multifiltrations and is computationally prohibitive for big datasets. In this article, we study the concept of Euler characteristics curves for 1-parameter filtrations and Euler characteristic profiles for multiparameter filtrations. While being a weaker invariant in one dimension, we show that Euler characteristic–based approaches do not possess some handicaps of persistent homology; we show efficient algorithms to compute them in a distributed way, their generalization to multifiltrations, and practical applicability for big data problems. In addition, we show that the Euler curves and profiles enjoy a certain type of stability, which makes them robust tools for data analysis. Lastly, to show their practical applicability, multiple use cases are considered.
‘It doesn’t happen any other way’: relationship-building and reflexivity for equity-focused intersectoral practice (EquIP)
Authors: Phipps Erica , Bumstead Lynda , Butt Tanya , Crighton Eric J , Desjardins Nadine , Hart Robert , Oickle Dianne , Sánchez-Pimienta Carlos E , Schlonies Renee , Schonauer Misty , Umbach Jill , Masuda Jeffrey R
Published: November 2023

Intersectoral processes that bring together public institutions, civil society organizations and affected community members are essential to tackling complex health equity challenges. While conventional wisdom points to the importance of human relationships in fostering collaboration, there is a lack of practical guidance on how to do intersectoral work in ways that support authentic relationship-building and mitigate power differentials among people with diverse experiences and roles. This article presents the results of RentSafe EquIP, a community-based participatory research initiative conducted in Owen Sound, Canada, in the midst of a housing crisis. The research explored the potential utility of equity-focused intersectoral practice (EquIP), a novel approach that invests in human relationships and knowledge co-creation among professionals and affected members of the community. The three-phase EquIP methodology centred the grounded expertise of community members with lived/living experience of housing inadequacy to catalyze reflexive thinking by people in professional roles about the institutional gaps and barriers that prevent effective intersectoral response to housing-related inequities. The research demonstrated that EquIP can support agency professionals and community members to (i) engage in (re)problematization to redefine the problem statement to better include upstream drivers of inequity, (ii) support reflexivity among those in professional roles to identify institutional practices, policies and norms that perpetuate stigma and impede effective intersectoral response and (iii) spark individual and collective agency and commitment towards a more equity-focused intersectoral system. We conclude that the EquIP methodology is a promising approach for communities seeking to address persistent health equity and social justice challenges.
High-quality assembly and methylome of a Tibetan wild tree peony genome (Paeonia ludlowii) reveal the evolution of giant genome architecture
Authors: Xiao Pei-Xuan , Li Yuanrong , Lu Jin , Zuo Hao , Pingcuo Gesang , Ying Hong , Zhao Fan , Xu Qiang , Zeng Xiuli , Jiao Wen-Biao
Published: November 2023

Tree peony belongs to one of the Saxifragales families, Paeoniaceae. It is one of the most famous ornamental plants, and is also a promising woody oil plant. Although two Paeoniaceae genomes have been released, their assembly qualities are still to be improved. Additionally, more genomes from wild peonies are needed to accelerate genomic-assisted breeding. Here we assemble a high-quality and chromosome-scale 10.3-Gb genome of a wild Tibetan tree peony, Paeonia ludlowii, which features substantial sequence divergence, including around 75% specific sequences and gene-level differentials compared with other peony genomes. Our phylogenetic analyses suggest that Saxifragales and Vitales are sister taxa and, together with rosids, they are the sister taxon to asterids. The P. ludlowii genome is characterized by frequent chromosome reductions, centromere rearrangements, broadly distributed heterochromatin, and recent continuous bursts of transposable element (TE) movement in peony, although it lacks recent whole-genome duplication. These recent TE bursts appeared during the uplift and glacial period of the Qinghai–Tibet Plateau, perhaps contributing to adaptation to rapid climate changes. Further integrated analyses with methylome data revealed that genome expansion in peony might be dynamically affected by complex interactions among TE proliferation, TE removal, and DNA methylation silencing. Such interactions also impact numerous recently duplicated genes, particularly those related to oil biosynthesis and flower traits. This genome resource will not only provide the genomic basis for tree peony breeding but also shed light on the study of the evolution of huge genome structures as well as their protein-coding genes.
Incidental Dysplasia During Total Proctocolectomy With Ileoanal Pouch: Is It Associated With Worse Outcomes?
Authors: Maspero Marianna , Otero Ana , Lavryk Olga , Holubar Stefan D , Lipman Jeremy , Gorgun Emre , Liska David , Kessler Hermann , Valente Michael , Steele Scott R , Hull Tracy
Published: November 2023

Background

Patients with inflammatory bowel disease (IBD) are at increased risk of colorectal cancer. In cases of invisible or nonendoscopically resectable dysplasia found at colonoscopy, total proctocolectomy with ileal pouch anal anastomosis can be offered with good long-term outcomes; however, little is known regarding cancer-related outcomes when dysplasia is found incidentally after surgery on final pathology.

Methods

Using our prospectively collected pouch registry, we identified patients who had preoperative colonic dysplasia or dysplasia found only after colectomy. Patients with cancer preoperatively or after colectomy were excluded. Included patients were divided into 3 groups: PRE (+preoperative biopsy, negative final pathology), BOTH (+preoperative biopsy and final pathology), and POST (negative preoperative biopsy, +final pathology). Long-term outcomes in the 3 groups were assessed.

Results

In total, 517 patients were included: PRE = 125, BOTH = 254, POST = 137. After a median follow-up of 12 years (IQR 3-21), there were no differences in overall, disease-free, or pouch survival between groups. Cancer/dysplasia developed in 11 patients: 3 (2%) in the PRE, 5 (2%) in the BOTH, and 3 (2%) in the POST group. Only 1 cancer-related death occurred in the entire cohort (PRE group). Disease-free survival at 10 years was 98% for all groups (P = .97). Pouch survival at 10 years was 96% for PRE, 99% for BOTH, and 97% for POST (P = .24).

Conclusions

The incidental finding of dysplasia on final pathology after proctocolectomy was not associated with worsened outcomes compared with preoperatively diagnosed dysplasia.
Machine-learning-based prediction of survival and mitral regurgitation recurrence in patients undergoing mitral valve repair
Authors: Kang Yoonjin , Sohn Suk Ho , Choi Jae Woong , Hwang Ho Young , Kim Kyung Hwan
Published: November 2023

OBJECTIVES

This study was conducted to assess long-term clinical outcomes after mitral valve repair using machine-learning techniques.

METHODS

We retrospectively evaluated 436 consecutive patients (mean age: 54.7 ± 15.4; 235 males) who underwent mitral valve repair between January 2000 and December 2017. Actuarial survival and freedom from significant (≥ moderate) mitral regurgitation (MR) were clinical end points. To evaluate the independent risk factors, random survival forest (RSF), extreme gradient boost (XGBoost), support vector machine, Cox proportional hazards model and general linear models with elastic net regularization were used. Concordance indices (C-indices) of each model were estimated.

RESULTS

The operative mortality was 0.9% (N = 4). Reoperation was required in 15 patients (3.5%). In terms of C-index, the overall performance of the XGBoost (C-index 0.806) and RSF models (C-index 0.814) was better than that of the Cox model (C-index 0.733) in overall survival. For the recurrent MR, the C-index for XGBoost was 0.718, which was the highest among the 5 models. Compared to the Cox model (C-index 0.545), the C-indices of the XGBoost (C-index 0.718) and RSF models (C-index 0.692) were higher.

CONCLUSIONS

Machine-learning techniques can be a useful tool for both prediction and interpretation in the survival and recurrent MR. From the machine-learning techniques examined here, the long-term clinical outcomes of mitral valve repair were excellent. The complexity of MV increased the risk of late mitral valve-related reoperation.
Brill–Noether Theory of Hilbert Schemes of Points on Surfaces
Authors: Bayer Arend , Chen Huachen , Jiang Qingyuan
Published: November 2023

We show that Brill–Noether loci in Hilbert scheme of points on a smooth connected surface $S$ are non-empty whenever their expected dimension is positive and that they are irreducible and have expected dimensions. More precisely, we consider the loci of pairs $(I, s)$, where $I$ is an ideal that locally at the point $s$ of $S$ needs a given number of generators. We give two proofs. The first uses Iarrobino’s description [9] of the Hilbert–Samuel stratification of local punctual Hilbert schemes, and the second is based on induction via birational relationships between different Brill–Noether loci given by nested Hilbert schemes.
The Costly Vicious Cycle of Infections and Malnutrition
Authors: Sinha Pranay , Guerrant Richard L
Published: November 2023

Malnutrition, which continues to affect hundreds of millions of people worldwide, is both a cause and consequence of a range of infectious diseases. In this perspective piece, we provide an overview of the bidirectional relationship between malnutrition and infectious diseases. In addition to enteric infections, we use tuberculosis as a case study of this relationship between malnutrition and infectious diseases, and to demonstrate the potential of nutritional interventions to mitigate mortality and morbidity from infectious diseases. We conclude with suggestions on advancing our understanding of the vicious cycle of microbes and malnutrition and finding ways to break it.
WGS of a cluster of MDR Shigella sonnei utilizing Oxford Nanopore R10.4.1 long-read sequencing
Authors: Ritchie Gordon , Chorlton Samuel D , Matic Nancy , Bilawka Jennifer , Gowland Leah , Leung Victor , Stefanovic Aleksandra , Romney Marc G , Lowe Christopher F
Published: November 2023

Objectives

To utilize long-read nanopore sequencing (R10.4.1 flowcells) for WGS of a cluster of MDR Shigella sonnei, specifically characterizing genetic predictors of antimicrobial resistance (AMR).

Methods

WGS was performed on S. sonnei isolates identified from stool and blood between September 2021 and October 2022. Bacterial DNA from clinical isolates was extracted on the MagNA Pure 24 and sequenced on the GridION utilizing R10.4.1 flowcells. Phenotypic antimicrobial susceptibility testing was interpreted based on CLSI breakpoints. Sequencing data were processed with BugSeq, and AMR was assessed with BugSplit and ResFinder.

Results

Fifty-six isolates were sequenced, including 53 related to the cluster of cases. All cluster isolates were identified as S. sonnei by sequencing, with global genotype 3.6.1.1.2 (CipR.MSM5), MLST 152 and PopPUNK cluster 3. Core genome MLST (cgMLST, examining 2513 loci) and reference-based MLST (refMLST, examining 4091 loci) both confirmed the clonality of the isolates. Cluster isolates were resistant to ampicillin (blaTEM-1), trimethoprim/sulfamethoxazole (dfA1, dfrA17; sul1, sul2), azithromycin (ermB, mphA) and ciprofloxacin (gyrA S83L, gyrA D87G, parC S80I). No genomic predictors of resistance to carbapenems were identified.

Conclusions

WGS with R10.4.1 enabled rapid sequencing and identification of an MDR S. sonnei community cluster. Genetic predictors of AMR were concordant with phenotypic antimicrobial susceptibility testing.
Embedding deep neural network in enhanced Schapery theory for progressive failure analysis of fiber reinforced laminates
Authors: Lin Shiyao , Post Alex , Waas Anthony M
Published: November 2023

Computational progressive failure analysis of carbon fiber reinforced polymer composite is of vital importance in the verification and validation process of the structural integrity and damage tolerance of modern lightweight aeronautical structures. Enhanced Schapery theory (EST) has been developed and applied to predict the damage pattern and load-bearing capacity of various composite structures. In this paper, EST is enhanced by a deep neural network (DNN) model, which enables fast and accurate predictions of matrix cracking angles under arbitrary stress states of any composite laminate. The DNN model is trained by TensorFlow based on data generated by a damage initiation criterion, which originates from the Mohr–Coulomb failure theory. The EST-DNN model is applied to open-hole tension/compression problems. The results from the EST-DNN model are obtained with no loss in accuracy. The results presented combine the efficient and accurate predicting capabilities brought by machine learning tools and the robustness and user-friendliness of the EST finite element model.