bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractAvailability 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

AbstractImmature 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

AbstractCisplatin 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

AbstractInfection 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

AbstractThe 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

AbstractComplex 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

AbstractAs 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

AbstractOceanographic 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

AbstractPlants 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

AbstractSarcopenia, 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

AbstractThe 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

AbstractIt 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

AbstractAfter 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

AbstractAs 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

AbstractAn 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.