bluuebunny/crossref_metadata_2025 huggingface dataset:
Integrated home dialysis model: facilitating home-to-home transition
Authors: Desbiens Louis-Charles , Bargman Joanne M , Chan Christopher T , Nadeau-Fredette Annie-Claire
Published: June 2024

Peritoneal dialysis (PD) and home hemodialysis (HHD) are the two home dialysis modalities offered to patients. They promote patient autonomy, enhance independence, and are generally associated with better quality of life compared to facility hemodialysis. PD offers some advantages (enhanced flexibility, ability to travel, preservation of residual kidney function, and vascular access sites) but few patients remain on PD indefinitely due to peritonitis and other complications. By contrast, HHD incurs longer and more intensive training combined with increased upfront health costs compared to PD, but is easier to sustain in the long term. As a result, the integrated home dialysis model was proposed to combine the advantages of both home-based dialysis modalities. In this paradigm, patients are encouraged to initiate dialysis on PD and transfer to HHD after PD termination. Available evidence demonstrates the feasibility and safety of this approach and some observational studies have shown that patients who undergo the PD-to-HHD transition have clinical outcomes comparable to patients who initiate dialysis directly on HHD. Nevertheless, the prevalence of PD-to-HHD transfers remains low, reflecting the multiple barriers that prevent the full uptake of home-to-home transitions, notably a lack of awareness about the model, home-care “burnout,” clinical inertia after a transfer to facility HD, suboptimal integration of PD and HHD centers, and insufficient funding for home dialysis programs. In this review, we will examine the conceptual advantages and disadvantages of integrated home dialysis, present the evidence that underlies it, identify challenges that prevent its success and finally, propose solutions to increase its adoption.
Towards a better uptake of home dialysis in Europe: understanding the present and looking to the future
Authors: Brown Edwina A , Brivio Giulia Boni , Van Biesen Wim
Published: June 2024

Use of peritoneal dialysis and home haemodialysis remains low in Europe, with the highest use in Scandinavian countries and the lowest in Eastern and Central Europe despite the advantages for people on dialysis and economic advantages for healthcare systems. This is partly due to the impact of the haemodialysis industry resulting in proliferation of haemodialysis units and nephrologist reimbursement related to use of haemodialysis. Equally important is the bias against home dialysis at both clinician and healthcare system levels. The underlying causes of this bias are discussed in relation to a mechanistic view of the human body, lack of compassion, failure to adjust dialysis provision for older age and frailty, proliferation of small dialysis centres, and complexity of decision-making and clinical care. For home dialysis to flourish, we need to foster a change in attitude to and vision of the aims of healthcare so that enabling meaningful activities of people requiring dialysis, as explored in the Standardized Outcomes in Nephrology initiative, rather than achieving biological numbers become the focus of care delivery.
Monitoring the stress physiology of free-ranging mugger crocodiles (Crocodylus palustris) across diverse habitats within Central Gujarat, India
Authors: Desai Brinky , Bhowmik Tathagata , Srinivasan Rohith , Whitaker Nikhil , Ghosal Ratna
Published: June 2024

Animals face several challenges in their natural environment, and to cope with such conditions, they may exhibit contrasting physiological responses that directly affect their overall well-being and survival. In this study, we assessed physiological responses via faecal glucocorticoid metabolite (fGCM) measurements in free-ranging mugger crocodiles inhabiting diverse habitats in Gujarat, India. We sampled muggers within Charotar, a rural area (Zone A) with local people having high tolerance towards the presence of muggers, and Vadodara, a region having both urban (Zone B) and rural (Zone C) areas with high levels of human–mugger conflict (HMC). Further, muggers in Vadodara live in water bodies that are mostly polluted due to sewage disposal from adjoining chemical industries. To measure fGCM (mean ± SEM, ng/g dry faeces) levels in muggers, scats were collected during both breeding (N = 107 scats) and non-breeding (N = 22 scats) seasons from all three zones. We used captive muggers (a focal enclosure) to biologically validate (via capture and restraint) the selected fGCM assay (11-oxoetiocholanolone assay). We showed a significant (P < 0.05) 11-fold increase in fGCM levels between pre-capture (540.9 ± 149.2, N = 11) and post-capture (6259.7 ± 1150.5, N = 11) samples. The validated assay was applied to free-ranging muggers during the breeding season, and Zone A showed significantly (P < 0.05) lower fGCM levels (542.03 ± 71.3) compared to muggers of Zone B (1699.9 ± 180.8) and Zone C (1806.4 ± 243.2), both zones having high levels of HMC with polluted water bodies. A similar contrast in fGCM levels was also observed during the non-breeding season. Overall, the study demonstrated that fGCM levels in muggers varied across habitats, and such variation could be due to a multitude of ecological factors that the species experience in their immediate local environment. Moreover, high fGCM levels in muggers of Vadodara during both breeding and non-breeding seasons may indicate a condition of chronic stress, which could be maladaptive for the species.
Transient stabilization of human cardiovascular progenitor cells from human pluripotent stem cells in vitro reflects stage-specific heart development in vivo
Authors: Bolesani Emiliano , Bornhorst Dorothee , Iyer Lavanya M , Zawada Dorota , Friese Nina , Morgan Michael , Lange Lucas , Gonzalez David M , Schrode Nadine , Leffler Andreas , Wunder Julian , Franke Annika , Drakhlis Lika , Sebra Robert , Schambach Axel , Goedel Alexander , Dubois Nicole C , Dobreva Gergana , Moretti Alessandra , Zelaráyan Laura C , Abdelilah-Seyfried Salim , Zweigerdt Robert
Published: June 2024

Aims

Understanding the molecular identity of human pluripotent stem cell (hPSC)-derived cardiac progenitors and mechanisms controlling their proliferation and differentiation is valuable for developmental biology and regenerative medicine.

Methods and results

Here, we show that chemical modulation of histone acetyl transferases (by IQ-1) and WNT (by CHIR99021) synergistically enables the transient and reversible block of directed cardiac differentiation progression on hPSCs. The resulting stabilized cardiovascular progenitors (SCPs) are characterized by ISL1pos/KI-67pos/NKX2-5neg expression. In the presence of the chemical inhibitors, SCPs maintain a proliferation quiescent state. Upon small molecules, removal SCPs resume proliferation and concomitant NKX2-5 up-regulation triggers cell-autonomous differentiation into cardiomyocytes. Directed differentiation of SCPs into the endothelial and smooth muscle lineages confirms their full developmental potential typical of bona fide cardiovascular progenitors. Single-cell RNA-sequencing-based transcriptional profiling of our in vitro generated human SCPs notably reflects the dynamic cellular composition of E8.25-E9.25 posterior second heart field of mouse hearts, hallmarked by nuclear receptor sub-family 2 group F member 2 expression. Investigating molecular mechanisms of SCP stabilization, we found that the cell-autonomously regulated retinoic acid and BMP signalling is governing SCP transition from quiescence towards proliferation and cell-autonomous differentiation, reminiscent of a niche-like behaviour.

Conclusion

The chemically defined and reversible nature of our stabilization approach provides an unprecedented opportunity to dissect mechanisms of cardiovascular progenitors’ specification and reveal their cellular and molecular properties.
Killip scale reclassification according to lung ultrasound: Killip pLUS
Authors: Carreras-Mora José , Vidal-Burdeus María , Rodríguez-González Clara , Simón-Ramón Clara , Rodríguez-Sotelo Laura , Sionis Alessandro , Giralt-Borrell Teresa , Martínez-Membrive María José , Izquierdo-Marquisá Andrea , Cainzos-Achirica Miguel , Vaquerizo-Montilla Beatriz , Rivas-Lasarte Mercedes , Ribas-Barquet Núria
Published: June 2024

Aims

The Killip scale remains a fundamental tool for prognostic assessment in ST-segment elevation myocardial infarction (STEMI) due to its simplicity and predictive value. Lung ultrasound (LUS) has emerged as a valuable adjunct for diagnosing and predicting outcomes in heart failure (HF) and STEMI patients, even those with subclinical congestion. We created a new classification (Killip pLUS), which reclassifies Killip I and II patients into an intermediate category (Killip I pLUS) based on LUS results. This category included Killip I patients and ≥1 positive zone (≥3 B-lines) and Killip II with 0 positive zones. We aimed to evaluate this new classification by comparing it with the Killip scale and a previous LUS-based reclassification scale (LUCK scale).

Methods and results

Lung ultrasound was performed within 24 h of admission in a multicentre cohort of 373 patients admitted for STEMI. In-hospital mortality and major adverse cardiovascular events within one year after admission, comprising mortality or readmission for HF, acute coronary syndrome, or stroke, were analysed. When predicting in-hospital mortality, the global comparison of these three classifications was statistically significant: Killip pLUS area under the curve (AUC) 0.90 (95% CI 0.85–0.95) vs. Killip AUC 0.85 (95% CI 0.73–0.96) vs. LUCK 0.83 (95% CI 0.70–0.95), P = 0.024. To predict events during follow-up, the comparison between scales was also significant: Killip pLUS 0.77 (95% CI 0.71–0.85) vs. Killip 0.72 (95% CI 0.65–0.79) vs. LUCK 0.73 (95% CI 0.66–0.81), P = 0.033.

Conclusion

The Killip pLUS scale provides enhanced risk stratification compared to the Killip and LUCK scales while preserving simplicity.
Severe multifocal coronary artery spasms after cessation of vasodilators in a patient with a spontaneous coronary artery dissection: a case report
Authors: Steffek Zdenek , Kurz David J , Bernheim Alain M , Meyer Matthias R
Published: June 2024

Background

Vasospastic angina (VSA) and spontaneous coronary artery dissection (SCAD) are challenging causes of non-atherosclerotic acute coronary syndromes (ACS). Here, we report a unique ACS case with coexisting VSA and SCAD, highlighting specific strategies in diagnosis and management of these poorly studied conditions.

Case summary

A woman in her mid-60s with a history of suspected microvascular angina and no atherosclerosis in a previously performed coronary computed tomography angiography presented with worsening chest pain. Invasive coronary angiography revealed a focal SCAD with a resulting high-degree stenosis of the right coronary artery. Shortly after successful percutaneous coronary intervention with stent implantation and stopping her previous vasodilator therapy with nitroglycerine and molsidomine, the patient developed recurrent anterior non-ST-segment elevation myocardial infarction. Surprisingly, repeat coronary angiography revealed severe multifocal coronary artery spasms that were successfully treated with intracoronary nitroglycerine. Vasospastic angina was subsequently managed with diltiazem, molsidomine, and nitrates.

Discussion

Our report underscores the challenges in diagnosing and managing SCAD and VSA in ACS. The possible interplay between SCAD and VSA highlights the need for careful vasodilator therapy management, as seen in our patient, where therapy discontinuation led to severe multifocal VSA. This emphasizes the need for a comprehensive approach for optimal outcomes in complex ACS cases.
Impact of epicardial adipose tissue on diastolic dysfunction in patients with chronic coronary syndrome and preserved left ventricular ejection fraction
Authors: Ishikawa Hirotoshi , Sugiyama Takatoshi , Otsuka Kenichiro , Yamaura Hiroki , Hojo Kana , Kono Yasushi , Ito Asahiro , Yamazaki Takanori , Shimada Kenei , Kasayuki Noriaki , Fukuda Daiju
Published: June 2024

Aims

This study aims to investigate the association between left ventricular diastolic dysfunction (LVDD) and epicardial adipose tissue (EAT) accumulation in patients with chronic coronary syndrome (CCS) and preserved left ventricular ejection fraction (LVEF).

Methods and results

The study included 314 patients with preserved LVEF who underwent coronary computed tomographic angiography (CCTA) and thoracic tissue Doppler echocardiography (TTDE). The EAT volume was measured using CCTA. LVDD was categorized into three groups: absent LVDD, undetermined LVDD, and LVDD. Multivariate logistic regression analysis was performed to assess the association between the clinical parameters, TTDE and CCTA findings, and LVDD. Patients (mean age: 66 ± 13 years; 52% men) were divided into LVDD present (30 patients, 9.6%), LVDD absent (219 patients, 69.7%), and LVDD undetermined (65 patients, 20.7%) groups. CCTA showed that patients with LVDD had a significantly higher coronary artery calcium (CAC) score and % plaque volume (%PV) than those without LVDD, whereas the prevalence of obstructive coronary artery disease was comparable between the groups. The EAT volume index correlated with each LVDD diagnostic component, except for tricuspid regurgitation velocity. A multivariate model showed that age [odds ratio (OR), 1.13; P < 0.001] and EAT volume index (OR, 1.02; P = 0.038) were independently associated with LVDD, even after adjusting for left ventricular mass index (OR, 1.05; P = 0.005). There was no significant association between the CAC score and %PV or LVDD.

Conclusion

This study demonstrated that EAT volume index and left ventricular mass index were robust predictors of LVDD; however, there was no independent association between coronary atherosclerotic disease burden and LVDD.
Eligibility for lipid-lowering therapy when applying systemic coronary risk estimation 2 according to guidelines on apparently healthy middle-aged individuals
Authors: Yari Ali , Ueda Peter , Lundman Pia , Alfredsson Joakim , Ravn-Fischer Annica , Söderberg Stefan , Yndigegn Troels , Hagström Emil , Jernberg Tomas
Published: June 2024

Aims

To estimate the proportion eligible for lipid-lowering therapy (LLT) when using the systemic coronary risk estimation 2 (SCORE2) on apparently healthy individuals.

Methods and results

Individuals aged 50–64 years were randomly invited to The Swedish Cardiopulmonary Bioimage Study (n = 30 154). Participants with previous atherosclerotic cardiovascular disease (CVD), diabetes mellitus, or chronic kidney disease were excluded. The 10-year risk of CVD was estimated using the SCORE2 equation and the multicell chart. Eligibility for LLT was estimated according to the 2021 European Society of Cardiology CVD prevention guidelines. Presence of coronary atherosclerosis was determined using coronary computed tomography angiography (CCTA). Among 26 570 apparently healthy individuals, 32% had high and 4% had very high 10-year CVD risk, according to the SCORE2 equation. Among high- and very-high-risk individuals, 99% had low-density lipoprotein cholesterol levels above guideline goals making 35% of the total population eligible for LLT. Of those eligible, undergoing imaging, 38% had no signs of coronary atherosclerosis according to CCTA. Using the SCORE2 chart, 52% of the population were eligible for LLT, of which 44% had no signs of coronary atherosclerosis. In those with high or very high risk, ongoing LLT was reported in 7% and another 11% received LLT within 6 months after study participation.

Conclusion

Nearly all apparently healthy individuals with high and very high CVD risk, or 35% of the total population, were eligible for LLT according to guidelines, and a large proportion had no signs of atherosclerosis. Compared with the SCORE2 equation, the SCORE2 chart resulted in more individuals being eligible for LLT.
Multiple variants of the type VII secretion system in Gram-positive bacteria
Authors: Garrett Stephen R , Higginson Andrew B , Palmer Tracy
Published: June 2024

Type VII secretion systems (T7SS) are found in bacteria across the Bacillota and Actinomycetota phyla and have been well described in Staphylococcus aureus, Bacillus subtilis, and pathogenic mycobacteria. The T7SS from Actinomycetota and Bacillota share two common components, a membrane-bound EccC/EssC ATPase and EsxA, a small helical hairpin protein of the WXG100 family. However, they also have additional phylum-specific components, and as a result they are termed the T7SSa (Actinomycetota) and T7SSb (Bacillota), respectively. Here, we identify additional organizations of the T7SS across these two phyla and describe eight additional T7SS subtypes, which we have named T7SSc–T7SSj. T7SSd is found exclusively in Actinomycetota including the Olselnella and Bifodobacterium genus, whereas the other seven are found only in Bacillota. All of the novel subtypes contain the canonical ATPase (TsxC) and the WXG100-family protein (TsxA). Most of them also contain a small ubiquitin-related protein, TsxB, related to the T7SSb EsaB/YukD component. Protein kinases, phosphatases, and forkhead-associated (FHA) proteins are often encoded in the novel T7SS gene clusters. Candidate substrates of these novel T7SS subtypes include LXG-domain and RHS proteins. Predicted substrates are frequently encoded alongside genes for additional small WXG100-related proteins that we speculate serve as cosecretion partners. Collectively our findings reveal unexpected diversity in the T7SS in Gram-positive bacteria.
The micromammals
Authors: Forsburg Susan L
Published: June 2024

In this editorial, Senior Editor Susan Forsburg examines the reasons to keep studying eukaryotic microbes like S. pombe and S. cerevisiae—and other yeasts, algae, amoeba, and fungi—even as genetic and genomic technologies now allow manipulation and study of practically any organism. She explores the challenges and opportunities of working in these tiny organisms, pointing to the substantial biology their study has uncovered.
Comprehensive analysis of CXXX sequence space reveals that Saccharomyces cerevisiae GGTase-I mainly relies on a2X substrate determinants
Authors: Sarkar Anushka , Hildebrandt Emily R , Patel Khushi V , Mai Emily T , Shah Sumil A , Kim June H , Schmidt Walter K
Published: June 2024

Many proteins undergo a post-translational lipid attachment, which increases their hydrophobicity, thus strengthening their membrane association properties or aiding in protein interactions. Geranylgeranyltransferase-I (GGTase-I) is an enzyme involved in a 3-step post-translational modification (PTM) pathway that attaches a 20-carbon lipid group called geranylgeranyl at the carboxy-terminal cysteine of proteins ending in a canonical CaaL motif (C—cysteine, a—aliphatic, L—often leucine, but can be phenylalanine, isoleucine, methionine, or valine). Genetic approaches involving 2 distinct reporters were employed in this study to assess Saccharomyces cerevisiae GGTase-I specificity, for which limited data exist, toward all 8,000 CXXX combinations. Orthogonal biochemical analyses and structure-based alignments were also performed to better understand the features required for optimal target interaction. These approaches indicate that yeast GGTase-I best modifies the Cxa[L/F/I/M/V] sequence that resembles but is not an exact match for the canonical CaaL motif. We also observed that minor modification of noncanonical sequences is possible. A consistent feature associated with well-modified sequences was the presence of a nonpolar a2 residue and a hydrophobic terminal residue, which are features recognized by mammalian GGTase-I. These results thus support that mammalian and yeast GGTase-I exhibit considerable shared specificity.
Differential Responses to Aging Among the Transcriptome and Proteome of Mesenchymal Progenitor Populations
Authors: Feehan Jack , Tripodi Nicholas , Kondrikov Dmitry , Wijeratne Tissa , Gimble Jeffrey , Hill William , Apostolopoulos Vasso , Duque Gustavo
Published: June 2024

The biological aging of stem cells (exhaustion) is proposed to contribute to the development of a variety of age-related conditions. Despite this, little is understood about the specific mechanisms which drive this process. In this study, we assess the transcriptomic and proteomic changes in 3 different populations of mesenchymal progenitor cells from older (50–70 years) and younger (20–40 years) individuals to uncover potential mechanisms driving stem cell exhaustion in mesenchymal tissues. To do this, we harvested primary bone marrow mesenchymal stem and progenitor cells (MPCs), circulating osteoprogenitors (COP), and adipose-derived stem cells (ADSCs) from younger and older donors, with an equal number of samples from men and women. These samples underwent RNA sequencing and label-free proteomic analysis, comparing the younger samples to the older ones. There was a distinct transcriptomic phenotype in the analysis of pooled older stem cells, suggestive of suppressed proliferation and differentiation; however, these changes were not reflected in the proteome of the cells. Analyzed independently, older MPCs had a distinct phenotype in both the transcriptome and proteome consistent with altered differentiation and proliferation with a proinflammatory immune shift in older adults. COP cells showed a transcriptomic shift to proinflammatory signaling but no consistent proteomic phenotype. Similarly, ADSCs displayed transcriptomic shifts in physiologies associated with cell migration, adherence, and immune activation but no proteomic change with age. These results show that there are underlying transcriptomic changes with stem cell aging that may contribute to a decline in tissue regeneration. However, the proteome of the cells was inconsistently regulated.
Life Chances, Subjective Perceptions, and Healthy Lifestyles in Older Adults: Longitudinal Evidence From China
Authors: Wang Bin , Lu Jiehua
Published: June 2024

Objectives

Previous studies and theories show that healthy lifestyles are affected by life chances and subjective perceptions. However, it remains unclear how older adults change between different lifestyle profiles as they age. We proposed the healthy lifestyle duality framework and tested it among older Chinese adults using a longitudinal design.

Methods

Data were obtained from 4 Chinese Longitudinal Healthy Longevity Surveys conducted between 2008 and 2018 (N = 31,445). Latent transition analysis and hierarchical multinomial growth curve models were performed to investigate healthy lifestyle profiles and their associations with life chances and subjective perceptions over time.

Results

Four distinct healthy lifestyle profiles were identified: healthy, risky, low-standard, and mixed groups, and their changes show path dependency. Across 10 years, the proportion of the healthy group ranged from 11.16% to 16.97%. Both life chances and subjective perceptions were longitudinally associated with healthy lifestyles, with age and cohort effects observed.

Discussion

Our findings support the healthy lifestyle duality framework and reveal that life chances and subjective perceptions influence lifestyle changes over time. Public health policies and health intervention programs should adapt to the specific needs of different age groups and generations.
Physiological Profiling of Agitation in Dementia: Insights From Wearable Sensor Data
Authors: Davidoff Hannah , Van Kraaij Alex , Van den Bulcke Laura , Lutin Erika , Vandenbulcke Mathieu , Van Helleputte Nick , De Vos Maarten , Van Hoof Chris , Van Den Bossche Maarten
Published: June 2024

Background and Objectives

The number of people with dementia is expected to triple to 152 million in 2050, with 90% having accompanying behavioral and psychological symptoms (BPSD). Agitation is among the most critical BPSD and can lead to decreased quality of life for people with dementia and their caregivers. This study aims to explore objective quantification of agitation in people with dementia by analyzing the relationships between physiological and movement data from wearables and observational measures of agitation.

Research Design and Methods

The data presented here is from 30 people with dementia, each included for 1 week, collected following our previously published multimodal data collection protocol. This observational protocol has a cross-sectional repeated measures design, encompassing data from both wearable and fixed sensors. Generalized linear mixed models were used to quantify the relationship between data from different wearable sensor modalities and agitation, as well as motor and verbal agitation specifically.

Results

Several features from wearable data are significantly associated with agitation, at least the p < .05 level (absolute β: 0.224-0.753). Additionally, different features are informative depending on the agitation type or the patient the data were collected from. Adding context with key confounding variables (time of day, movement, and temperature) allows for a clearer interpretation of feature differences when a person with dementia is agitated.

Discussion and Implications

The features shown to be significantly different, across the study population, suggest possible autonomic nervous system activation when agitated. Differences when splitting the data by agitation type point toward a need for future detection models to tailor to the primary type of agitation expressed. Finally, patient-specific differences in features indicate a need for patient- or group-level model personalization. The findings reported in this study both reinforce and add to the fundamental understanding of and can be used to drive the objective quantification of agitation.
Hecatomb: an integrated software platform for viral metagenomics
Authors: Roach Michael J , Beecroft Sarah J , Mihindukulasuriya Kathie A , Wang Leran , Paredes Anne , Cárdenas Luis Alberto Chica , Henry-Cocks Kara , Lima Lais Farias Oliveira , Dinsdale Elizabeth A , Edwards Robert A , Handley Scott A
Published: June 2024

Background

Modern sequencing technologies offer extraordinary opportunities for virus discovery and virome analysis. Annotation of viral sequences from metagenomic data requires a complex series of steps to ensure accurate annotation of individual reads and assembled contigs. In addition, varying study designs will require project-specific statistical analyses.

Findings

Here we introduce Hecatomb, a bioinformatic platform coordinating commonly used tasks required for virome analysis. Hecatomb means “a great sacrifice.” In this setting, Hecatomb is “sacrificing” false-positive viral annotations using extensive quality control and tiered-database searches. Hecatomb processes metagenomic data obtained from both short- and long-read sequencing technologies, providing annotations to individual sequences and assembled contigs. Results are provided in commonly used data formats useful for downstream analysis. Here we demonstrate the functionality of Hecatomb through the reanalysis of a primate enteric and a novel coral reef virome.

Conclusion

Hecatomb provides an integrated platform to manage many commonly used steps for virome characterization, including rigorous quality control, host removal, and both read- and contig-based analysis. Each step is managed using the Snakemake workflow manager with dependency management using Conda. Hecatomb outputs several tables properly formatted for immediate use within popular data analysis and visualization tools, enabling effective data interpretation for a variety of study designs. Hecatomb is hosted on GitHub (github.com/shandley/hecatomb) and is available for installation from Bioconda and PyPI.
ntsm: an alignment-free, ultra-low-coverage, sequencing technology agnostic, intraspecies sample comparison tool for sample swap detection
Authors: Chu Justin , Rong Jiazhen , Feng Xiaowen , Li Heng
Published: June 2024

Background

Due to human error, sample swapping in large cohort studies with heterogeneous data types (e.g., mix of Oxford Nanopore Technologies, Pacific Bioscience, Illumina data, etc.) remains a common issue plaguing large-scale studies. At present, all sample swapping detection methods require costly and unnecessary (e.g., if data are only used for genome assembly) alignment, positional sorting, and indexing of the data in order to compare similarly. As studies include more samples and new sequencing data types, robust quality control tools will become increasingly important.

Findings

The similarity between samples can be determined using indexed k-mer sequence variants. To increase statistical power, we use coverage information on variant sites, calculating similarity using a likelihood ratio–based test. Per sample error rate, and coverage bias (i.e., missing sites) can also be estimated with this information, which can be used to determine if a spatially indexed principal component analysis (PCA)–based prescreening method can be used, which can greatly speed up analysis by preventing exhaustive all-to-all comparisons.

Conclusions

Because this tool processes raw data, is faster than alignment, and can be used on very low-coverage data, it can save an immense degree of computational resources in standard quality control (QC) pipelines. It is robust enough to be used on different sequencing data types, important in studies that leverage the strengths of different sequencing technologies. In addition to its primary use case of sample swap detection, this method also provides information useful in QC, such as error rate and coverage bias, as well as population-level PCA ancestry analysis visualization.
The telomere-to-telomere (T2T) genome of Peucedanum praeruptorum Dunn provides insights into the genome evolution and coumarin biosynthesis
Authors: Bai Mingzhou , Jiang Sanjie , Chu Shanshan , Yu Yangyang , Shan Dai , Liu Chun , Zong Liang , Liu Qun , Liu Nana , Xu Weisong , Mei Zhanlong , Jian Jianbo , Zhang Chi , Zhao Shancen , Chiu Tsan-Yu , Simonsen Henrik Toft
Published: June 2024

Background

Traditional Chinese medicine has used Peucedanum praeruptorum Dunn (Apiaceae) for a long time. Various coumarins, including the significant constituents praeruptorin (A–E), are the active constituents in the dried roots of P. praeruptorum. Previous transcriptomic and metabolomic studies have attempted to elucidate the distribution and biosynthetic network of these medicinal-valuable compounds. However, the lack of a high-quality reference genome impedes an in-depth understanding of genetic traits and thus the development of better breeding strategies.

Results

A telomere-to-telomere (T2T) genome was assembled for P. praeruptorum by combining PacBio HiFi, ONT ultra-long, and Hi-C data. The final genome assembly was approximately 1.798 Gb, assigned to 11 chromosomes with genome completeness >98%. Comparative genomic analysis suggested that P. praeruptorum experienced 2 whole-genome duplication events. By the transcriptomic and metabolomic analysis of the coumarin metabolic pathway, we presented coumarins’ spatial and temporal distribution and the expression patterns of critical genes for its biosynthesis. Notably, the COSY and cytochrome P450 genes showed tandem duplications on several chromosomes, which may be responsible for the high accumulation of coumarins.

Conclusions

A T2T genome for P. praeruptorum was obtained, providing molecular insights into the chromosomal distribution of the coumarin biosynthetic genes. This high-quality genome is an essential resource for designing engineering strategies for improving the production of these valuable compounds.
Deep-Sea Benthic Response to the Deepwater Horizon Oil Spill: Harpacticoid Families as Sentinels of Impact Through Space and Time
Authors: Baldrighi Elisa , Bang Hyun Woo , Fast Justus , Baguley Jeffrey G
Published: June 2024

Synopsis

The Deepwater Horizon (DWH) oil spill in the northern Gulf of Mexico, occurred in 2010 at 1525 meters depth, releasing approximately 507 M liters of oil. Research cruises in 2010 and 2011 were conducted to assess the initial and subsequent effects of the oil spill on deep-sea infauna. The spatial-temporal response of the deep-sea meiofaunal harpacticoid community composition to the DWH oil spill was investigated at 34 stations ranging from < 1 km to nearly 200 km from the wellhead in 2010 and 2011. The pattern of reduced harpacticoid diversity in impacted zones compared to non-impacted zones in 2010 persisted in 2011. However, an increase in Hill’s diversity index (N1) and the family richness across the two years in some of the impacted stations could suggest a first signal of a tentative recovery and an improvement of environmental conditions. The multivariate analysis of harpacticoid family composition revealed the persistence of an impact in 2011 with moderately high values of turnover diversity in the harpacticoid communities through time (37%) and space (38–39%). The consistent presence in all years and stations of long-term tolerant families (e.g., Ameiridae), the sharp decrease of fast-responding opportunistic families (e.g., Tisbidae), and the increase of more sensitive ones (e.g., Ectinosomatidae, Canthocamptidae, Cletopsyllidae, and Laophontidae) lead to the preliminary conclusion that some initial signals of recovery are evident. However, as impacts were still evident in 2011, and because recruitment and succession rates can be extremely slow in the deep sea, full community recovery had not yet occurred one year after the DWH disaster. This study confirmed that harpacticoid copepod family diversity can offer an accurate assessment of oil-spill impacts on deep-sea benthic communities over space and time as well as a better understanding of the recovery mode of the system after an oil spill event.
Proof-of-principle of a lung sealant based on functionalized polyoxazolines: experiments in an ovine acute aerostasis model
Authors: Hermans Bob P , Ten Broek Richard P G , Li Wilson W L , Roozen Edwin A , Vos Shoko , Van Der Heijden Erik H F M , Van Goor Harry , Verhagen Ad F T M
Published: June 2024

OBJECTIVES

More effective lung sealants are needed to prevent prolonged pulmonary air leakage (AL). Polyoxazoline-impregnated gelatin patch (N-hydroxysuccinimide ester functionalized poly(2-oxazoline)s; NHS-POx) was promising for lung sealing ex vivo. The aim of this study is to confirm sealing effectiveness in an in vivo model of lung injury.

METHODS

An acute aerostasis model was used in healthy adult female sheep, involving bilateral thoracotomy, amputation lesions (bronchioles Ø > 1.5 mm), sealant application, digital chest tube for monitoring AL, spontaneous ventilation, obduction and bursting pressure measurement. Two experiments were performed: (i) 3 sheep with 2 lesions per lung (N = 4 NHS-POx double-layer, N = 4 NHS-POx single-layer, N = 4 untreated) and (ii) 3 with 1 lesion per lung (N = 3 NHS-POx single-layer, N = 3 untreated). In pooled linear regression, AL was analysed per lung (N = 7 NHS-POx, N = 5 untreated) and bursting pressure per lesion (N = 11 NHS-POx, N = 7 untreated).

RESULTS

Baseline AL was similar between groups (mean 1.38–1.47 l/min, P = 0.90). NHS-POx achieved sealing in 1 attempt in 8/11 (72.7%) and in 10/11 (90.9%) in >1 attempt. Application failures were only observed on triangular lesions requiring 3 folds around the lung. No influences of methodological variation between experiments was detected in linear regression (P > 0.9). AL over initial 3 h of drainage was significantly reduced for NHS-POx [median: 7 ml/min, length of interquartile range: 333 ml/min] versus untreated lesions (367 ml/min, length of interquartile range: 680 ml/min, P = 0.036). Bursting pressure was higher for NHS-POx (mean: 33, SD: 16 cmH2O) versus untreated lesions (mean: 19, SD: 15 cmH2O, P = 0.081).

CONCLUSIONS

NHS-POx was effective for reducing early AL, and a trend was seen for improvement of bursting strength of the covered defect. Results were affected by application characteristics and lesion geometry.
Geometric optimization of the space around the buildings based on the improvement of thermal comfort efficiency of the building
Authors: Cui Guolian
Published: June 2024

This stud introduces a pioneering investigation into the geometric optimization of building surroundings to elevate thermal comfort efficiency and foster sustainable development within the construction industry. Employing the ENVI-met simulation tool and a novel crow search optimization algorithm, the research rigorously quantifies occupants' dissatisfaction utilizing the predicted percentage dissatisfied model, meticulously considering various environmental parameters. The simulations are based on the weather data of Nanjing, China, and the numerical results were validated against the observed data. The results reveal a remarkable 7% reduction in energy consumption and a corresponding 7.2% decrease in CO2 emissions compared to baseline configurations, underscoring the substantial impact of the proposed crow search algorithm. Notably, the study identifies an optimal configuration, characterized by a 30% vegetation cover, west–east orientation, and a three-story building, highlighting the algorithm's effectiveness in identifying configurations that concurrently enhance thermal comfort and mitigate energy consumption. These findings highlight the critical influence of geometric factors on thermal performance and underscore the significance of integrating innovative methodologies to address contemporary challenges in sustainable building design. By offering novel insights and practical solutions, this research contributes to advancing sustainable practices in architecture and urban planning, ultimately promoting occupant well-being and fostering energy-efficient construction practices.
Global existence and steady states of the density-suppressed motility model with strong Allee effect
Authors: Song Cui , Wang Zhi-Cheng , Feng Zhaosheng
Published: June 2024

This paper considers a density-suppressed motility model with a strong Allee effect under the homogeneous Neumman boundary condition. We first establish the global existence of bounded classical solutions to a parabolic–parabolic system over an $N $-dimensional $\mathbf{(N\le 3)}$ bounded domain $\varOmega $, as well as the global existence of bounded classical solutions to a parabolic–elliptic system over the multidimensional bounded domain $\varOmega $ with smooth boundary. We then investigate the linear stability at the positive equilibria for the full parabolic case and parabolic–elliptic case, respectively, and find the influence of Allee effect on the local stability of the equilibria. By treating the Allee effect as a bifurcation parameter, we focus on the one-dimensional stationary problem and obtain the existence of non-constant positive steady states, which corresponds to small perturbations from the constant equilibrium $(1,1)$. Furthermore, we present some properties through theoretical analysis on pitchfork type and turning direction of the local bifurcations. The stability results provide a stable wave mode selection mechanism for the model considered in this paper. Finally, numerical simulations are performed to demonstrate our theoretical results.
Nilpotent Aspherical Sasakian Manifolds
Authors: De Nicola Antonio , Yudin Ivan
Published: June 2024

We show that every compact aspherical Sasakian manifold with nilpotent fundamental group is diffeomorphic to a Heisenberg nilmanifold.
Recurrent Group B Streptococcus Neonatal Invasive Infections, France, 2007–2021
Authors: Sbaa Ghalia , Delettre Nicolas , Guyonnet Cécile , Le Huu Nghia Sébastien , Joubrel-Guyot Caroline , Plainvert Céline , Poyart Claire , Tazi Asmaa
Published: June 2024

Recurrence is a rare complication of group B Streptococcus (GBS) neonatal infections. We conducted a retrospective observational study on GBS neonatal invasive infections in France from 2007 to 2021. A total of 1527 cases were reported, of which 36 (2.36%) were recurrent. Recurrence mainly concerned preterm (68%) and low-birth-weight (72%) infants and was associated with the hypervirulent GBS clonal complex 17 (83%; odds ratio, 2.86 [95% confidence interval, 1.18–6.92]). No β-lactam–tolerant strains were identified, and bacterial whole-genome sequencing could not reveal any specific feature associated with recurrence. Large-cohort studies should be undertaken to address the optimal management of these uncommon diseases.
Advanced Age Worsens Respiratory Function and Pulmonary Inflammation After Burn Injury and This Correlates With Changes in the Fecal Microbiome in Mice
Authors: McMahan Rachel H , Boe Devin , Giesy Lauren E , Najarro Kevin M , Khair Shanawaj , Walrath Travis , Frank Daniel N , Kovacs Elizabeth J
Published: June 2024

Cutaneous burn injury in the elderly is associated with poor clinical outcomes and increased pulmonary-related complications. We and others have shown that burn injury triggers a cascade of inflammatory mediators which increase gut permeability and dysbiosis of the fecal microbiota and this is more dramatic in the aged. Since crosstalk between intestinal microbes and the lung, termed the “gut-lung axis,” impacts immunity and homeostasis in the airway, we hypothesized that the increased intestinal dysbiosis in age and burn injury may contribute to excessive pulmonary inflammation and poor prognosis after injury. To explore this hypothesis, we used a clinically relevant murine model of burn injury in which young and aged mice are subjected to a 12% TBSA dorsal scald burn or sham injury. About 24 h after injury, lung function was assessed and lungs and feces were collected for analysis of inflammatory mediators and fecal microbial species. The results show that, when compared to younger mice, burn injury in aged mice triggers a decline in respiratory function and exacerbates pulmonary inflammation. In addition to heightened levels of the neutrophil recruiting chemokine CXCL1, aged mice displayed a profound increase in the pro-inflammatory protein, calprotectin, in the lung after burn injury. Comparison of the fecal microbiome and inflammatory markers in the lung revealed unique, age-dependent, correlation patterns between individual taxa and pulmonary inflammation. Taken together, these findings suggest that the postburn dysbiosis of the gut flora in aged mice may contribute to the changes in pulmonary inflammatory profiles.
Yield analysis and corn earworm feeding in Bt and non-Bt corn hybrids across diverse locations
Authors: Reisig Dominic , Heiniger Ryan
Published: June 2024

Corn, Zea mays L. (Poales: Poaceae), growers in the US Cotton Belt are required to plant 20% of total corn acres to non-Bt hybrids for resistance management (non-Bt refuge). Most growers do not meet this requirement, in part, because they perceive non-Bt hybrids to yield less than Bt hybrids. We planted multiple non-Bt and Bt hybrids from a single company in small-plot replicated trials at a single location from 2019 to 2023, as well as in small-plot replicated trials at multiple locations during 2022 and 2023. In the single location, we measured kernel injury from corn earworm, Helicoverpa zea Boddie (Lepidoptera: Noctuidae), and we recorded yield at all locations. In the single location trial, yields only separated among hybrids in 3 out of 5 years. In the multiple location trial, yields were variable between both years. We found that Bt hybrids tended to yield higher than non-Bt hybrids overall, but this was influenced by the inclusion of non-Bt hybrids that had a lower overall genetic yield potential in the environments we tested them in. In both tests, when hybrids were analyzed during each year, both Bt and non-Bt hybrids were among the statistically highest yielders. Our study demonstrates the importance of comparing multiple Bt and non-Bt hybrids to draw yield comparisons. This highlights the need for corn seed company breeders to put effort into improving yield for non-Bt hybrids. Hopefully this effort will translate into increased planting of non-Bt refuge corn for growers in the US Cotton Belt.
Complement or insult: the emerging link between complement cascade deficiencies and pathology of myeloid malignancies
Authors: Oakes Alissa , Liu Yuchen , Dubielecka Patrycja M
Published: June 2024

The complement cascade is an ancient and highly conserved arm of the immune system. The accumulating evidence highlights elevated activity of the complement cascade in cancer microenvironment and emphasizes its effects on the immune, cancer, and cancer stroma cells, pointing to a role in inflammation-mediated etiology of neoplasms. The role the cascade plays in development, progression, and relapse of solid tumors is increasingly recognized, however its role in hematological malignancies, especially those of myeloid origin, has not been thoroughly assessed and remains obscure. As the role of inflammation and autoimmunity in development of myeloid malignancies is becoming recognized, in this review we focus on summarizing the links that have been identified so far for complement cascade involvement in the pathobiology of myeloid malignancies. Complement deficiencies are primary immunodeficiencies that cause an array of clinical outcomes including an increased risk of a range of infectious as well as local or systemic inflammatory and thrombotic conditions. Here, we discuss the impact that deficiencies in complement cascade initiators, mid- and terminal-components and inhibitors have on the biology of myeloid neoplasms. The emergent conclusions indicate that the links between complement cascade, inflammatory signaling, and the homeostasis of hematopoietic system exist, and efforts should continue to detail the mechanistic involvement of complement cascade in the development and progression of myeloid cancers.
Private Woodland Owner Perceptions of Threat and Efficacy Shape Management Responses for Climate Change Adaptation
Authors: Breigenzer Peter , Leahy Jessica , Rogers Nicole Suzanne , Wason Jay W
Published: June 2024

Private woodland owners (PWOs) face an increasing number of considerations for climate change adaptation and mitigation activities in their forest management. Evidence suggests there may be a disconnect between PWOs’ climate change perceptions and behaviors, which can limit implementation. We conducted seventeen semistructured interviews in Maine to develop a typological framework of PWOs based on their perceptions of climate-induced threats and efficacy. Our results produced three types of PWOs: the steady-as-they-go landowner (low perceived threat), the science-driven landowner (high perceived threat; high efficacy), and the seeking-support landowner (high perceived threat; low efficacy). Although all three types of PWOs regularly implemented resistance and resilience practices, their attitudes toward transition practices (i.e., assisted migration) diverged based on their perceptions of threat and efficacy. This typological framework can be used when targeting communications to PWOs regarding the overlap between climate adaptive management and traditional best management practices.

Study Implications: PWOs in our study recognized climate-related impacts while implementing diverse forest management practices to meet both climate-related and non-climate-related objectives. The divergent attitudes toward transition practices exhibited by our three PWO types highlight the notion that adaptive practices can be both intentional and incidental. Our findings suggest that outreach efforts should understand PWO perceptions of climate change threats and their feelings of efficacy in responding to such threats. When combined with knowledge about the overlap between traditional best management practices and new climate-adaptive strategies, extension and outreach efforts can tailor their messaging to fit the appropriate audience.