bluuebunny/crossref_metadata_2025 huggingface dataset:
Combining Satellite‐Derived PM2.5 Data and a Reduced‐Form Air Quality Model to Support Air Quality Analysis in US Cities
Authors: Gallagher Ciaran L. , Holloway Tracey , Tessum Christopher W. , Jackson Clara M. , Heck Colleen
Published: May 2023

Air quality models can support pollution mitigation design by simulating policy scenarios and conducting source contribution analyses. The Intervention Model for Air Pollution (InMAP) is a powerful tool for equitable policy design as its variable resolution grid enables intra‐urban analysis, the scale of which most environmental justice inquiries are levied. However, InMAP underestimates particulate sulfate and overestimates particulate ammonium formation, errors that limit the model's relevance to city‐scale decision‐making. To reduce InMAP's biases and increase its relevancy for urban‐scale analysis, we calculate and apply scaling factors (SFs) based on observational data and advanced models. We consider both satellite‐derived speciated PM2.5 from Washington University and ground‐level monitor measurements from the U.S. Environmental Protection Agency, applied with different scaling methodologies. Relative to ground‐monitor data, the unscaled InMAP model fails to meet a normalized mean bias performance goal of <±10% for most of the PM2.5 components it simulates (pSO4: −48%, pNO3: 8%, pNH4: 69%), but with city‐specific SFs it achieves the goal benchmarks for every particulate species. Similarly, the normalized mean error performance goal of <35% is not met with the unscaled InMAP model (pSO4: 53%, pNO3: 52%, pNH4: 80%) but is met with the city‐scaling approach (15%–27%). The city‐specific scaling method also improves the R2 value from 0.11 to 0.59 (ranging across particulate species) to the range of 0.36–0.76. Scaling increases the percent pollution contribution of electric generating units (EGUs) (nationwide 4%) and non‐EGU point sources (nationwide 6%) and decreases the agriculture sector's contribution (nationwide −6%).
Hertz-rate metropolitan quantum teleportation
Authors: Shen Si , Yuan Chenzhi , Zhang Zichang , Yu Hao , Zhang Ruiming , Yang Chuanrong , Li Hao , Wang Zhen , Wang You , Deng Guangwei , Song Haizhi , You Lixing , Fan Yunru , Guo Guangcan , Zhou Qiang
Published: May 2023

Quantum teleportation can transfer an unknown quantum state between distant quantum nodes, which holds great promise in enabling large-scale quantum networks. To advance the full potential of quantum teleportation, quantum states must be faithfully transferred at a high rate over long distance. Despite recent impressive advances, a high-rate quantum teleportation system across metropolitan fiber networks is extremely desired. Here, we demonstrate a quantum teleportation system which transfers quantum states carried by independent photons at a rate of 7.1 ± 0.4 Hz over 64-km-long fiber channel. An average single-photon fidelity of ≥90.6 ± 2.6% is achieved, which exceeds the maximum fidelity of 2/3 in classical regime. Our result marks an important milestone towards quantum networks and opens the door to exploring quantum entanglement based informatic applications for the future quantum internet.
Dose-response relationships of LSD-induced subjective experiences in humans
Authors: Hirschfeld Tim , Prugger Johanna , Majić Tomislav , Schmidt Timo T.
Published: May 2023

Lysergic acid diethylamide (LSD) is a potent classic serotonergic psychedelic, which facilitates a variety of altered states of consciousness. Here we present the first meta-analysis establishing dose-response relationship estimates of the altered states of consciousness induced by LSD. Data extracted from articles identified by a systematic literature review following PRISMA guidelines were obtained from the Altered States Database. The psychometric data comprised ratings of subjective effects from standardized and validated questionnaires: the Altered States of Consciousness Rating Scale (5D-ASC, 11-ASC) and the Mystical Experience Questionnaire (MEQ30). We performed meta-regression analyses using restricted cubic splines for data from studies with LSD doses of up to 200 μg base. Most scales revealed a sigmoid-like increase of effects, with a plateauing at around 100 μg. The most strongly modulated factors referred to changes in perception and illusory imagination, followed by positively experienced ego-dissolution, while only small effects were found for Anxiety and Dread of Ego Dissolution. The considerable variability observed in most factors and scales points to the role of non-pharmacological factors in shaping subjective experiences. The established dose-response relationships may be used as general references for future experimental and clinical research on LSD to compare observed with expected subjective effects and to elucidate phenomenological differences between psychedelics.
The association between gut microbiota and postoperative delirium in patients
Authors: Zhang Yiying , Baldyga Kathryn , Dong Yuanlin , Song Wenyu , Villanueva Mirella , Deng Hao , Mueller Ariel , Houle Timothy T. , Marcantonio Edward R. , Xie Zhongcong
Published: May 2023

Postoperative delirium is a common postoperative complication in older patients, and its pathogenesis and biomarkers remain largely undetermined. The gut microbiota has been shown to regulate brain function, and therefore, it is vital to explore the association between gut microbiota and postoperative delirium. Of 220 patients (65 years old or older) who had a knee replacement, hip replacement, or laminectomy under general or spinal anesthesia, 86 participants were included in the data analysis. The incidence (primary outcome) and severity of postoperative delirium were assessed for two days. Fecal swabs were collected from participants immediately after surgery. The 16S rRNA gene sequencing was used to assess gut microbiota. Principal component analyses along with a literature review were used to identify plausible gut microbiota, and three gut bacteria were further studied for their associations with postoperative delirium. Of the 86 participants [age 71.0 (69.0–76.0, 25–75% percentile of quartile), 53% female], 10 (12%) developed postoperative delirium. Postoperative gut bacteria Parabacteroides distasonis was associated with postoperative delirium after adjusting for age and sex (Odds Ratio [OR] 2.13, 95% Confidence Interval (CI): 1.09–4.17, P = 0.026). The association between delirium and both Prevotella (OR: 0.59, 95% CI: 0.33–1.04, P = 0.067) and Collinsella (OR: 0.57, 95% CI: 0.27–1.24, P = 0.158) did not meet statistical significance. These findings suggest that there may be an association between postoperative gut microbiota, specifically Parabacteroides distasonis, and postoperative delirium. However, further research is needed to confirm these findings and better understand the gut-brain axis’s role in postoperative outcomes.
Rapid neuroplasticity changes and response to intravenous ketamine: a randomized controlled trial in treatment-resistant depression
Authors: Kopelman Jared , Keller Timothy A. , Panny Benjamin , Griffo Angela , Degutis Michelle , Spotts Crystal , Cruz Nicolas , Bell Elizabeth , Do-Nguyen Kevin , Wallace Meredith L. , Mathew Sanjay J. , Howland Robert H. , Price Rebecca B.
Published: May 2023

Intravenous ketamine is posited to rapidly reverse depression by rapidly enhancing neuroplasticity. In human patients, we quantified gray matter microstructural changes on a rapid (24-h) timescale within key regions where neuroplasticity enhancements post-ketamine have been implicated in animal models. In this study, 98 unipolar depressed adults who failed at least one antidepressant medication were randomized 2:1 to a single infusion of intravenous ketamine (0.5 mg/kg) or vehicle (saline) and completed diffusion tensor imaging (DTI) assessments at pre-infusion baseline and 24-h post-infusion. DTI mean diffusivity (DTI-MD), a putative marker of microstructural neuroplasticity in gray matter, was calculated for 7 regions of interest (left and right BA10, amygdala, and hippocampus; and ventral Anterior Cingulate Cortex) and compared to clinical response measured with the Montgomery-Asberg Depression Rating Scale (MADRS) and the Quick Inventory of Depressive Symptoms-Self-Report (QIDS-SR). Individual differences in DTI-MD change (greater decrease from baseline to 24-h post-infusion, indicative of more neuroplasticity enhancement) were associated with larger improvements in depression scores across several regions. In the left BA10 and left amygdala, these relationships were driven primarily by the ketamine group (group * DTI-MD interaction effects:p = 0.016–0.082). In the right BA10, these associations generalized to both infusion arms (p = 0.007). In the left and right hippocampus, on the MADRS only, interaction effects were observed in the opposite direction, such that DTI-MD change was inversely associated with depression change in the ketamine arm specifically (group * DTI-MD interaction effects:p = 0.032–0.06). The acute effects of ketamine on depression may be mediated, in part, by acute changes in neuroplasticity quantifiable with DTI.
Cost-effectiveness analysis of molecular testing in minimally invasive samples to detect endometrial cancer in women with postmenopausal bleeding
Authors: Peremiquel-Trillas Paula , Gómez David , Martínez José Manuel , Fernández-González Sergi , Frias-Gomez Jon , Paytubi Sonia , Pelegrina Beatriz , Pineda Marta , Brunet Joan , Ponce Jordi , Matias-Guiu Xavier , Bosch Xavier , de Sanjosé Silvia , Bruni Laia , Alemany Laia , Costas Laura , Díaz Mireia
Published: May 2023

Introduction

New approaches are being developed to early detect endometrial cancer using molecular biomarkers. These approaches offer high sensitivities and specificities, representing a promising horizon to develop early detection strategies.

Objective

To evaluate the effectiveness and cost-effectiveness of introducing molecular testing to detect endometrial cancer in women with postmenopausal bleeding compared to the current strategy using the national healthcare service perspective.

Methods

A Markov model was developed to assess the two early detection strategies. The model predicts the number of hysterectomies, lifetime expectancy, quality-adjusted life-years, endometrial cancer prevalence and incidence, mortality from endometrial cancer and the lifetime cost of screening, diagnosis, and treatment. Strategies were compared using the incremental cost-effectiveness ratio.

Results

The molecular strategy reduces 1.9% of the overall number of hysterectomies and the number of undetected cancer cases by 65%. Assuming a molecular test cost of 310€, the molecular strategy has an incremental cost of -32,952€ per QALY gained, being more effective and less expensive than the current strategy.

Conclusions

The introduction of molecular testing to diagnose endometrial cancer in women presenting postmenopausal bleeding provides more health benefit at a lower cost, and therefore has the potential to be cost-effective.
Targeting pyroptosis as a preventive and therapeutic approach for stroke
Authors: Long Junpeng , Sun Yang , Liu Shasha , Yang Songwei , Chen Chen , Zhang Zhao , Chu Shifeng , Yang Yantao , Pei Gang , Lin Meiyu , Yan Qian , Yao Jiao , Lin Yuting , Yi Fan , Meng Lei , Tan Yong , Ai Qidi , Chen Naihong
Published: May 2023

Stroke has caused tremendous social stress worldwide, yet despite decades of research and development of new stroke drugs, most have failed and rt-PA (Recombinant tissue plasminogen activator) is still the accepted treatment for ischemic stroke. the complexity of the stroke mechanism has led to unsatisfactory efficacy of most drugs in clinical trials, indicating that there are still many gaps in our understanding of stroke. Pyroptosis is a programmed cell death (PCD) with inflammatory properties and are thought to be closely associated with stroke. Pyroptosis is regulated by the GSDMD of the gasdermin family, which when cleaved by Caspase-1/Caspase-11 into N-GSDMD with pore-forming activity can bind to the plasma membrane to form small 10–20 nm pores, which would allow the release of inflammatory factors IL-18 and IL-1β before cell rupture, greatly exacerbating the inflammatory response. The pyroptosis occurs mainly in the border zone of cerebral infarction, and glial cells, neuronal cells and brain microvascular endothelial cells (BMECs) all undergo pyroptosis after stroke, which largely exacerbates the breakdown of the blood-brain barrier (BBB) and thus aggravates brain injury. Therefore, pyroptosis may be a good direction for the treatment of stroke. In this review, we focus on the latest mechanisms of action of pyroptosis and the process by which pyroptosis regulates stroke development. We also suggest potential therapeutic stroke drugs that target the pyroptosis pathway, providing additional therapeutic strategies for the clinical management of stroke.
Current perspectives on mesenchymal stromal cell therapy for graft versus host disease
Authors: Kadri Nadir , Amu Sylvie , Iacobaeus Ellen , Boberg Erik , Le Blanc Katarina
Published: May 2023

Graft versus host disease (GvHD) is the clinical condition in which bone marrow-derived mesenchymal stromal cells (MSCs) have been most frequently studied. In this review, we summarize the experience from clinical trials that have paved the way to translation. While MSC-based therapy has shown an exceptional safety profile, identifying potency assays and disease biomarkers that reliably predict the capacity of a specific MSC batch to alleviate GvHD has been difficult. As GvHD diagnosis and staging are based solely on clinical criteria, individual patients recruited in the same clinical trial may have vastly different underlying biology, obscuring trial outcomes and making it difficult to determine the benefit of MSCs in subgroups of patients. An accumulating body of evidence indicates the importance of considering not only the cell product but also patient-specific biomarkers and/or immune characteristics in determining MSC responsiveness. A mode of action where intravascular MSC destruction is followed by monocyte-efferocytosis-mediated skewing of the immune repertoire in a permissive inflammatory environment would both explain why cell engraftment is irrelevant for MSC efficacy and stress the importance of biologic differences between responding and nonresponding patients. We recommend a combined analysis of clinical outcomes and both biomarkers of disease activity and MSC potency assays to identify patients with GvHD who are likely to benefit from MSC therapy.
Measures of multiple deprivation and visual field loss in glaucoma clinics in England: lessons from big data
Authors: Rathore Mehal , Shweikh Yusrah , Kelly Stephen R. , Crabb David P.
Published: May 2023

Background/Objectives

To examine the association between multiple deprivation with late diagnosis and rapid worsening of glaucoma in patients in English hospital eye services (HES).

Methods

602,439 visual fields (VFs) were extracted from five regionally different glaucoma clinics in England. Mean Deviation (MD) worse than −12 dB was used as a surrogate definition for advanced VF loss at diagnosis in patients with ≥2 reliable VF records. MD loss worse than -1 dB per year was used to define rapid VF progression in patients with ≥6 VFs. Patient data were stratified into deciles of the Index of Multiple Deprivation (IMD) from residential postcodes.

Results

There was an association between IMD and advanced VF loss at diagnosis in 44,956 patients with 18% (293/1608) and 11% (771/6929) in the most and least deprived IMD decile, respectively. Age-corrected odds ratio (OR) for having advanced VF loss at entry into HES was 1.42 (95% confidence interval [CI] 1.21–1.67) and 0.75 (95% CI: 0.66–0.85) in the most and least deprived IMD decile respectively (reference = fifth decile). In 15,094 patients with follow up data (median [interquartile range] of 6.9 [4.5, 10.0] years), the proportion having rapid VF progression did not differ across the IMD spectrum.

Conclusion

Large-scale VF data from clinics indicates that glaucoma severity at presentation to English HES is associated with levels of multiple deprivation. We found no evidence to suggest likelihood of having rapid VF progression during follow-up is associated with IMD; this hints at equity of glaucoma care and outcomes once patients are in English HES.
Engineering a new-to-nature cascade for phosphate-dependent formate to formaldehyde conversion in vitro and in vivo
Authors: Nattermann Maren , Wenk Sebastian , Pfister Pascal , He Hai , Lee Seung Hwan , Szymanski Witold , Guntermann Nils , Zhu Fayin , Nickel Lennart , Wallner Charlotte , Zarzycki Jan , Paczia Nicole , Gaißert Nina , Franciò Giancarlo , Leitner Walter , Gonzalez Ramon , Erb Tobias J.
Published: May 2023

Formate can be envisioned at the core of a carbon-neutral bioeconomy, where it is produced from CO2 by (electro-)chemical means and converted into value-added products by enzymatic cascades or engineered microbes. A key step in expanding synthetic formate assimilation is its thermodynamically challenging reduction to formaldehyde. Here, we develop a two-enzyme route in which formate is activated to formyl phosphate and subsequently reduced to formaldehyde. Exploiting the promiscuity of acetate kinase and N-acetyl-γ-glutamyl phosphate reductase, we demonstrate this phosphate (Pi)-based route in vitro and in vivo. We further engineer a formyl phosphate reductase variant with improved formyl phosphate conversion in vivo by suppressing cross-talk with native metabolism and interface the Pi route with a recently developed formaldehyde assimilation pathway to enable C2 compound formation from formate as the sole carbon source in Escherichia coli. The Pi route therefore offers a potent tool in expanding the landscape of synthetic formate assimilation.
Widening the landscape of transcriptional regulation of green algal photoprotection
Authors: Arend Marius , Yuan Yizhong , Ruiz-Sola M. Águila , Omranian Nooshin , Nikoloski Zoran , Petroutsos Dimitris
Published: May 2023

Availability of light and CO2, substrates of microalgae photosynthesis, is frequently far from optimal. Microalgae activate photoprotection under strong light, to prevent oxidative damage, and the CO2 Concentrating Mechanism (CCM) under low CO2, to raise intracellular CO2 levels. The two processes are interconnected; yet, the underlying transcriptional regulators remain largely unknown. Employing a large transcriptomic data compendium of Chlamydomonas reinhardtii’s responses to different light and carbon supply, we reconstruct a consensus genome-scale gene regulatory network from complementary inference approaches and use it to elucidate transcriptional regulators of photoprotection. We show that the CCM regulator LCR1 also controls photoprotection, and that QER7, a Squamosa Binding Protein, suppresses photoprotection- and CCM-gene expression under the control of the blue light photoreceptor Phototropin. By demonstrating the existence of regulatory hubs that channel light- and CO2-mediated signals into a common response, our study provides an accessible resource to dissect gene expression regulation in this microalga.
Anatomical and functional maturation of the mid-gestation human enteric nervous system
Authors: Dershowitz Lori B. , Li Li , Pasca Anca M. , Kaltschmidt Julia A.
Published: May 2023

Immature gastrointestinal motility impedes preterm infant survival. The enteric nervous system controls gastrointestinal motility, yet it is unknown when the human enteric nervous system matures enough to carry out vital functions. Here we demonstrate that the second trimester human fetal enteric nervous system takes on a striped organization akin to the embryonic mouse. Further, we perform ex vivo functional assays of human fetal tissue and find that human fetal gastrointestinal motility matures in a similar progression to embryonic mouse gastrointestinal motility. Together, this provides critical knowledge, which facilitates comparisons with common animal models to advance translational disease investigations and testing of pharmacological agents to enhance gastrointestinal motility in prematurity.
TRPV1 inhibition overcomes cisplatin resistance by blocking autophagy-mediated hyperactivation of EGFR signaling pathway
Authors: Oh Se Jin , Lim Ji Yeon , Son Min Kyu , Ahn Jun Hyeok , Song Kwon-Ho , Lee Hyo-Jung , Kim Suyeon , Cho Eun Ho , Chung Joon-Yong , Cho Hanbyoul , Kim Hyosun , Kim Jae-Hoon , Park Jooyoung , Choi Jungmin , Hwang Sun Wook , Kim Tae Woo
Published: May 2023

Cisplatin resistance along with chemotherapy-induced neuropathic pain is an important cause of treatment failure for many cancer types and represents an unmet clinical need. Therefore, future studies should provide evidence regarding the mechanisms of potential targets that can overcome the resistance as well as alleviate pain. Here, we show that the emergence of cisplatin resistance is highly associated with EGFR hyperactivation, and that EGFR hyperactivation is arisen by a transcriptional increase in the pain-generating channel, TRPV1, via NANOG. Furthermore, TRPV1 promotes autophagy-mediated EGF secretion via Ca2+ influx, which activates the EGFR-AKT signaling and, consequentially, the acquisition of cisplatin resistance. Importantly, TRPV1 inhibition renders tumors susceptible to cisplatin. Thus, our findings indicate a link among cisplatin resistance, EGFR hyperactivation, and TRPV1-mediated autophagic secretion, and implicate that TRPV1 could be a crucial drug target that could not only overcome cisplatin resistance but also alleviate pain in NANOG+ cisplatin-resistant cancer.
Viral subversion of selective autophagy is critical for biogenesis of virus replication organelles
Authors: Lan Yun , van Leur Sophie Wilhelmina , Fernando Julia Ayano , Wong Ho Him , Kampmann Martin , Siu Lewis , Zhang Jingshu , Li Mingyuan , Nicholls John M. , Sanyal Sumana
Published: May 2023

Infection by many (+)RNA viruses is accompanied by ER-expansion and membrane remodelling to form viral replication organelles, followed by assembly and secretion of viral progenies. We previously identified that virus-triggered lipophagy was critical for flaviviral assembly, and is driven by the lipid droplet associated protein Ancient ubiquitin protein 1 (Aup1). A ubiquitin conjugating protein Ube2g2 that functions as a co-factor for Aup1 was identified as a host dependency factor in our study. Here we characterized its function: Ube2g2-deficient cells displayed a dramatic reduction in virus production, which could be rescued by reconstituting the wild-type but not the catalytically deficient (C89K) mutant of Ube2g2, suggesting that its enzymatic activity is necessary. Ube2g2 deficiency did not affect entry of virus particles but resulted in a profound loss in formation of replication organelles, and production of infectious progenies. This phenomenon resulted from its dual activity in (i) triggering lipophagy in conjunction with Aup1, and (ii) degradation of ER chaperones such as Herpud1, SEL1L, Hrd1, along with Sec62 to restrict ER-phagy upon Xbp1-IRE1 triggered ER expansion. Our results therefore underscore an exquisite fine-tuning of selective autophagy by flaviviruses that drive host membrane reorganization during infection to enable biogenesis of viral replication organelles.
A protective, single-visit TB vaccination regimen by co-administration of a subunit vaccine with BCG
Authors: Dijkman Karin , Lindenstrøm Thomas , Rosenkrands Ida , Søe Rikke , Woodworth Joshua S. , Lindestam Arlehamn Cecilia S. , Mortensen Rasmus
Published: May 2023

The only licensed tuberculosis (TB) vaccine, Bacillus Calmette Guerin (BCG), fails to reliably protect adolescents and adults from pulmonary TB, resulting in ~1.6 million deaths annually. Protein subunit vaccines have shown promise against TB in clinical studies. Unfortunately, most subunit vaccines require multiple administrations, which increases the risk of loss to follow-up and necessitates more complex and costly logistics. Given the well-documented adjuvant effect of BCG, we hypothesized that BCG co-administration could compensate for a reduced number of subunit vaccinations. To explore this, we developed an expression-optimized version of our H107 vaccine candidate (H107e), which does not cross-react with BCG. In the CAF®01 adjuvant, a single dose of H107e induced inferior protection compared to three H107e/CAF®01 administrations. However, co-administering a single dose of H107e/CAF®01 with BCG significantly improved protection, which was equal to BCG co-administered with three H107e/CAF®01 doses. Importantly, combining BCG with a single H107e/CAF®01 dose also increased protection in previously BCG-primed animals. Overall, a single dose of H107e/CAF®01 with BCG induced long-lived immunity and triggered BCG-specific Th17 responses. These data support co-administration of BCG and subunit vaccines in both BCG naïve and BCG-primed individuals as an improved TB vaccine strategy with reduced number of vaccination visits.
Mitotic clustering of pulverized chromosomes from micronuclei
Authors: Lin Yu-Fen , Hu Qing , Mazzagatti Alice , Valle-Inclán Jose Espejo , Maurais Elizabeth G. , Dahiya Rashmi , Guyer Alison , Sanders Jacob T. , Engel Justin L. , Nguyen Giaochau , Bronder Daniel , Bakhoum Samuel F. , Cortés-Ciriano Isidro , Ly Peter
Published: May 2023

Complex genome rearrangements can be generated by the catastrophic pulverization of missegregated chromosomes trapped within micronuclei through a process known as chromothripsis1–5. As each chromosome contains a single centromere, it remains unclear how acentric fragments derived from shattered chromosomes are inherited between daughter cells during mitosis6. Here we tracked micronucleated chromosomes with live-cell imaging and show that acentric fragments cluster in close spatial proximity throughout mitosis for asymmetric inheritance by a single daughter cell. Mechanistically, the CIP2A–TOPBP1 complex prematurely associates with DNA lesions within ruptured micronuclei during interphase, which poises pulverized chromosomes for clustering upon mitotic entry. Inactivation of CIP2A–TOPBP1 caused acentric fragments to disperse throughout the mitotic cytoplasm, stochastically partition into the nucleus of both daughter cells and aberrantly misaccumulate as cytoplasmic DNA. Mitotic clustering facilitates the reassembly of acentric fragments into rearranged chromosomes lacking the extensive DNA copy-number losses that are characteristic of canonical chromothripsis. Comprehensive analysis of pan-cancer genomes revealed clusters of DNA copy-number-neutral rearrangements—termed balanced chromothripsis—across diverse tumour types resulting in the acquisition of known cancer driver events. Thus, distinct patterns of chromothripsis can be explained by the spatial clustering of pulverized chromosomes from micronuclei.
A multi-omic resource of wheat seed tissues for nutrient deposition and improvement for human health
Authors: Zhi Jingjing , Zeng Jian , Wang Yaqiong , Zhao Hongyan , Wang Guoli , Guo Jing , Wang Yuesheng , Chen Mingjie , Yang Guangxiao , He Guangyuan , Chen Xiaoyuan , Chang Junli , Li Yin
Published: May 2023

As a globally important staple crop, wheat seeds provide us with nutrients and proteins. The trend of healthy dietary has become popular recently, emphasizing the consumption of whole-grain wheat products and the dietary benefits. However, the dynamic changes in nutritional profiles of different wheat seed regions (i.e., the embryo, endosperm and outer layers) during developmental stages and the molecular regulation have not been well studied. Here, we provide this multi-omic resource of wheat seeds and describe the generation, technical assessment and preliminary analyses. This resource includes a time-series RNA-seq dataset of the embryo, endosperm and outer layers of wheat seeds and their corresponding metabolomic dataset, covering the middle and late stages of seed development. Our RNA-seq experiments profile the expression of 63,708 genes, while the metabolomic data includes the abundance of 984 metabolites. We believe that this was the first reported transcriptome and metabolome dataset of wheat seeds that helps understand the molecular regulation of the deposition of beneficial nutrients and hence improvements for nutritional and processing quality traits.
Sustained year-round oceanographic measurements from Rothera Research Station, Antarctica, 1997–2017
Authors: Venables Hugh , Meredith Michael P. , Hendry Katharine R. , ten Hoopen Petra , Peat Helen , Chapman Alice , Beaumont Jennifer , Piper Rayner , Miller Andrew J. , Mann Paul , Rossetti Helen , Massey Ali , Souster Terri , Reeves Simon , Fenton Mairi , Heiser Sabrina , Pountney Sam , Reed Sarah , Waring Zoë , Clark Marlon , Bolton Emma , Mathews Ryan , London Hollie , Clement Alice , Stuart Emma , Reichardt Aurelia , Brandon Mark , Leng Melanie , Arrowsmith Carol , Annett Amber , Henley Sian F. , Clarke Andrew
Published: May 2023

Oceanographic changes adjacent to Antarctica have global climatic and ecological impacts. However, this is the most challenging place in the world to obtain marine data due to its remoteness and inhospitable nature, especially in winter. Here, we present more than 2000 Conductivity-Temperature-Depth (CTD) profiles and associated water sample data collected with (almost uniquely) full year-round coverage from the British Antarctic Survey Rothera Research Station at the west Antarctic Peninsula. Sampling is conducted from a small boat or a sled, depending on the sea ice conditions. When conditions allow, sampling is twice weekly in summer and weekly in winter, with profiling to nominally 500 m and with discrete water samples taken at 15 m water depth. Daily observations are made of the sea ice conditions in the area. This paper presents the first 20 years of data collection, 1997-2017. This time series represents a unique and valuable resource for investigations of the high-latitude ocean’s role in climate change, ocean/ice interactions, and marine biogeochemistry and carbon drawdown.
Genome-wide analysis of heavy metal ATPases (HMAs) in Poaceae species and their potential role against copper stress in Triticum aestivum
Authors: Batool Tuba Sharf , Aslam Roohi , Gul Alvina , Paracha Rehan Zafar , Ilyas Mahnoor , De Abreu Kathryn , Munir Faiza , Amir Rabia , Williams Lorraine E.
Published: May 2023

Plants require copper for normal growth and development and have evolved an efficient system for copper management based on transport proteins such as P1B-ATPases, also known as heavy metal ATPases (HMAs). Here, we report HMAs in eleven different Poaceae species, including wheat. Furthermore, the possible role of wheat HMAs in copper stress was investigated. BlastP searches identified 27 HMAs in wheat, and phylogenetic analysis based on the Maximum Likelihood method demonstrated a separation into four distinct clades. Conserved motif analysis, domain identification, gene structure, and transmembrane helices number were also identified for wheat HMAs using computational tools. Wheat seedlings grown hydroponically were subjected to elevated copper and demonstrated toxicity symptoms with effects on fresh weight and changes in expression of selected HMAs TaHMA7, TaHMA8, and TaHMA9 were upregulated in response to elevated copper, suggesting a role in wheat copper homeostasis. Further investigations on these heavy metal pumps can provide insight into strategies for enhancing crop heavy metal tolerance in the face of heavy metal pollution.
Muscle quality determined by computed tomography predicts short-term and long-term survival after liver transplantation
Authors: Molwitz Isabel , Recklies Franziska , Stark Maria , Horvatits Thomas , Salamon Johannes , Huber Samuel , Fischer Lutz , Adam Gerhard , Lohse Ansgar W. , Sterneck Martina , Horvatits Karoline
Published: May 2023

Sarcopenia, the loss of muscle mass and quality, contributes to worse clinical outcome in patients with end-stage liver disease, but its impact on short- and long-term survival remains insufficiently understood. The aim of this study was to evaluate the development of computed tomography (CT) muscle parameters and their impact on short-term and long-term survival after liver transplantation. This retrospective study included patients with liver transplantation between 2011 and 2015 and a pre-transplant CT scan. Clinical characteristics, CT muscle mass and density were assessed pre-transplant, and in available CT scans at short-term (11 months) and long-term follow-up (56 months). Overall, 93/152 (61%) patients (109 male, 55 ± 10 years) suffered from sarcopenia pre-transplant. In short- (n = 50) and long-term follow-up (n = 52) the muscle mass (− 2.65 cm2/m2 95% CI [− 4.52, − 0.77], p = 0.007; − 2.96 cm2/m2 [− 4.7, − 1.23], p = 0.001, respectively), and muscle density (− 3 HU [− 6, − 1], p = 0.007; − 2 HU [− 4, 0], p = 0.069) decreased. Myosteatosis was associated with a higher post-transplant mortality (survival probability: 3 months 72% vs. 95%, 1 year 63% vs. 90%, 5 years 54% vs. 84%, p = 0.001), while muscle mass was not. In conclusion, muscle mass and quality did not improve after transplant. Muscle quality predicts short- and long-term survival and could help to identify a patient’s risk profile.
Assessing cohesion and diversity in the collaboration network of the SALURBAL project
Authors: Baquero Sofía , Montes Felipe , Stankov Ivana , Sarmiento Olga L. , Medina Pablo , Slesinski S. Claire , Diez-Canseco Francisco , Kroker-Lobos Maria F. , Caiaffa Waleska Teixeira , Vives Alejandra , Alazraqui Marcio , Barrientos-Gutiérrez Tonatiuh , Roux Ana V. Diez
Published: May 2023

The SALURBAL (Urban Health in Latin America) Project is an interdisciplinary multinational network aimed at generating and disseminating actionable evidence on the drivers of health in cities of Latin America. We conducted a temporal multilayer network analysis where we measured cohesion over time using network structural properties and assessed diversity within and between different project activities according to participant attributes. Between 2017 and 2020 the SALURBAL network comprised 395 participants across 26 countries, 23 disciplines, and 181 institutions. While the cohesion of the SALURBAL network fluctuated over time, overall, an increase was observed from the first to the last time point of our analysis (clustering coefficient increased [0.83–0.91] and shortest path decreased [1.70–1.68]). SALURBAL also exhibited balanced overall diversity within project activities (0.5–0.6) by designing activities for different purposes such as capacity building, team-building, research, and dissemination. The network’s growth was facilitated by the creation of new diverse collaborations across a range of activities over time, while maintaining the diversity of existing collaborations (0.69–0.75 between activity diversity depending on the attribute). The SALURBAL experience can serve as an example for multinational research projects aiming to build cohesive networks while leveraging heterogeneity in countries, disciplines, career stage, and across sectors.
Temporal dynamics of the Rubber Hand Illusion
Authors: Finotti Gianluca , Garofalo Sara , Costantini Marcello , Proffitt Dennis R.
Published: May 2023

It is widely accepted that the representation of the body is not fixed and immutable, but rather flexible and constantly updated based on a continuous stream of multisensory information. This mechanism can be very useful to adapt to several situations, but it would not be adaptive if the body representation was too malleable or if it wasn’t capable of restoring its integrity after a transient modification. Here we used the Rubber Hand Illusion (RHI) to investigate how quickly the body representation can be modified. Previous studies have investigated the timing of the onset and offset of the illusion, however, they did not assess a fine temporal resolution. Here, we used a potentiometer to record a moment-by-moment rating of the feeling of owning the RH for two minutes during the visuo-tactile stimulation and two minutes following the stimulation. Our results suggest that the feeling of Ownership is already established during the first 19 s of stimulation then it continues to grow, but at a much slower pace. The feeling of Ownership disappears within 66 s from the end of the stimulation. This work sheds new light on the temporal dynamics of the RHI and the malleability of the body self-consciousness.
AT 1 inhibition mediated neuroprotection after experimental traumatic brain injury is dependent on neutrophils in male mice
Authors: Timaru-Kast Ralph , Coronel-Castello Shila P. , Krämer Tobias J. , Hugonnet André V. , Schäfer Michael K. E. , Sebastiani Anne , Thal Serge C.
Published: May 2023

After traumatic brain injury (TBI) cerebral inflammation with invasion of neutrophils and lymphocytes is a crucial factor in the process of secondary brain damage. In TBI the intrinsic renin-angiotensin system is an important mediator of cerebral inflammation, as inhibition of the angiotensin II receptor type 1 (AT1) reduces secondary brain damage and the invasion of neutrophil granulocytes into injured cerebral tissue. The current study explored the involvement of immune cells in neuroprotection mediated by AT1 inhibition following experimental TBI. Four different cohorts of male mice were examined, investigating the effects of neutropenia (anti-Ly6G antibody mediated neutrophil depletion; C57BL/6), lymphopenia (RAG1 deficiency, RAG1−/−), and their combination with candesartan-mediated AT1 inhibition. The present results showed that reduction of neutrophils and lymphocytes, as well as AT1 inhibition in wild type and RAG1−/− mice, reduced brain damage and neuroinflammation after TBI. However, in neutropenic mice, candesartan did not have an effect. Interestingly, AT1 inhibition was found to be neuroprotective in RAG1−/− mice but not in neutropenic mice. The findings suggest that AT1 inhibition may exert neuroprotection by reducing the inflammation caused by neutrophils, ultimately leading to a decrease in their invasion into cerebral tissue.
A nursing care-sensitive patient satisfaction measure in older patients
Authors: Goes Margarida , Oliveira Henrique , Lopes Manuel , Fonseca César , Pinho Lara , Marques Maria
Published: May 2023

As a novelty, this article proposes the empirical operationalization of an indicator sensitive to nursing care called patient satisfaction based on functional capacity and quality of life assessments. This was a descriptive cross-sectional study with a sample of 351 individuals aged 65 and older residing in the community. Data acquisition was performed using the structured interview method, employing a core set of 25 codes taken from the International Classification of Functioning, Disability, and Health and the WHOQOL-BREF instrument of the World Health Organization. Confirmatory factor analysis was used to infer the reliability and construct validity of the proposed model, involving three latent factors: functional capacity, quality of life, and patient satisfaction with nursing care received. The proposed model showed good reliability and construct validity, although it failed regarding discriminant validity between latent factors. The greatest statistically significant predictor of the patient satisfaction latent factor was the quality of life latent factor ($$\beta =0.89;p<0.001$$

β
=
0.89
;
p
<
0.001

), followed by the functional capacity latent factor ($$\beta =-0.77;p<0.001$$

β
=
-
0.77
;
p
<
0.001

). The findings seem to suggest that patient satisfaction is an indicator that may be quantitatively measurable, with functional capacity and quality of life considered very significant predictors of patient satisfaction with the nursing care experience.
Resting-state oscillations reveal disturbed excitation–inhibition ratio in Alzheimer’s disease patients
Authors: van Nifterick Anne M. , Mulder Danique , Duineveld Denise J. , Diachenko Marina , Scheltens Philip , Stam Cornelis J. , van Kesteren Ronald E. , Linkenkaer-Hansen Klaus , Hillebrand Arjan , Gouw Alida A.
Published: May 2023

An early disruption of neuronal excitation–inhibition (E–I) balance in preclinical animal models of Alzheimer’s disease (AD) has been frequently reported, but is difficult to measure directly and non-invasively in humans. Here, we examined known and novel neurophysiological measures sensitive to E–I in patients across the AD continuum. Resting-state magnetoencephalography (MEG) data of 86 amyloid-biomarker-confirmed subjects across the AD continuum (17 patients diagnosed with subjective cognitive decline, 18 with mild cognitive impairment (MCI) and 51 with dementia due to probable AD (AD dementia)), 46 healthy elderly and 20 young control subjects were reconstructed to source-space. E–I balance was investigated by detrended fluctuation analysis (DFA), a functional E/I (fE/I) algorithm, and the aperiodic exponent of the power spectrum. We found a disrupted E–I ratio in AD dementia patients specifically, by a lower DFA, and a shift towards higher excitation, by a higher fE/I and a lower aperiodic exponent. Healthy subjects showed lower fE/I ratios (< 1.0) than reported in previous literature, not explained by age or choice of an arbitrary threshold parameter, which warrants caution in interpretation of fE/I results. Correlation analyses showed that a lower DFA (E–I imbalance) and a lower aperiodic exponent (more excitation) was associated with a worse cognitive score in AD dementia patients. In contrast, a higher DFA in the hippocampi of MCI patients was associated with a worse cognitive score. This MEG-study showed E–I imbalance, likely due to increased excitation, in AD dementia, but not in early stage AD patients. To accurately determine the direction of shift in E–I balance, validations of the currently used markers and additional in vivo markers of E–I are required.
Unexpected silicon localization in calcium carbonate exoskeleton of cultured and fossil coccolithophores
Authors: Bordiga M. , Lupi C. , Langer G. , Gianoncelli A. , Birarda G. , Pollastri S. , Bonanni V. , Bedolla D. E. , Vaccari L. , Gariani G. , Cerino F. , Cabrini M. , Beran A. , Zuccotti M. , Fiorentino G. , Zanoni M. , Garagna S. , Cobianchi M. , Di Giulio A.
Published: May 2023

Coccolithophores, marine calcifying phytoplankton, are important primary producers impacting the global carbon cycle at different timescales. Their biomineral structures, the calcite containing coccoliths, are among the most elaborate hard parts of any organism. Understanding the morphogenesis of coccoliths is not only relevant in the context of coccolithophore eco-physiology but will also inform biomineralization and crystal design research more generally. The recent discovery of a silicon (Si) requirement for crystal shaping in some coccolithophores has opened up a new avenue of biomineralization research. In order to develop a mechanistic understanding of the role of Si, the presence and localization of this chemical element in coccoliths needs to be known. Here, we document for the first time the uneven Si distribution inHelicosphaera cartericoccoliths through three synchrotron-based techniques employing X-ray Fluorescence and Infrared Spectromicroscopy. The enrichment of Si in specific areas of the coccoliths point to a targeted role of this element in the coccolith formation. Our findings mark a key step in biomineralization research because it opens the door for a detailed mechanistic understanding of the role Si plays in shaping coccolith crystals.
Association of maternal depression and hypothyroidism with infant gastroschisis: a population-based cohort study in Canada
Authors: Liu Shiliang , Claude Hughes , Yong Shin Jie , Chen Dunjin
Published: May 2023

Gastroschisis has increased globally over recent decades, and this increase has not been explained by identified risk factors. We conducted a population-based study of infants born in Canada, 2004–2020. We used “winter” months (i.e., September through June) and northern areas of residence as indicators of less sunlight/less active lifestyle, while“summer”(i.e., July and August) and southern areas were considered as reference. Rate of gastroschisis for infants conceived inwinter(3.4 per 10,000) was higher than for infants conceived insummer(2.2 per 10,000;p < 0.001). Exposure towinter, and northern area, hypothyroidism, substance or tobacco uses and depressive disorder were initially identified as risk factors for gastroschisis. There was a significant interaction between women < 24 years of age and 2-month conception intervals (rate ratio (RR): 1.42 (95% confidence interval [CI] 1.19–1.70). The association of maternal depression (mean ratio 2.19, 95% CI 0.87–3.50,p = 0.001) with infant gastroschisis was mediated by hypothyroidism (mean ratio 1.04, 95% CI 1.01–1.07,p < 0.001), whereas substance use, hypothyroidism, tobacco smoking and gestational diabetes showed 5.5-, 3.1-, 2.7-, and 1.2-fold associations, respectively, with maternal depression. In contrast to thesummerconception interval of low gastroschisis risk, an elevated risk of gastroschisis spans the other ten months in association with higher levels of stress adaptation, thermoregulation and metabolism, reproduction, and growth effector hormones. Our findings suggest that periconception depression with mediation by hypothyroidism, may play a causal role in offspring gastroschisis.
Assessing the climate change mitigation potential from food waste composting
Authors: Pérez Tibisay , Vergara Sintana E. , Silver Whendee L.
Published: May 2023

Food waste is a dominant organic constituent of landfills, and a large global source of greenhouse gases. Composting food waste presents a potential opportunity for emissions reduction, but data on whole pile, commercial-scale emissions and the associated biogeochemical drivers are lacking. We used a non-invasive micrometeorological mass balance approach optimized for three-dimensional commercial-scale windrow compost piles to measure methane (CH4), nitrous oxide (N2O), and carbon dioxide (CO2) emissions continuously during food waste composting. Greenhouse gas flux measurements were complemented with continuous oxygen (O2) and temperature sensors and intensive sampling for biogeochemical processes. Emission factors (EF) ranged from 6.6 to 8.8 kg CH4–C/Mg wet food waste and were driven primarily by low redox and watering events. Composting resulted in low N2O emissions (0.01 kg N2O–N/Mg wet food waste). The overall EF value (CH4 + N2O) for food waste composting was 926 kgCO2e/Mg of dry food waste. Composting emissions were 38–84% lower than equivalent landfilling fluxes with a potential net minimum savings of 1.4 MMT CO2e for California by year 2025. Our results suggest that food waste composting can help mitigate emissions. Increased turning during the thermophilic phase and less watering overall could potentially further lower emissions.