bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptomics of single dose and repeated carbon black and ozone inhalation co-exposure highlight progressive pulmonary mitochondrial dysfunction
Authors: Hathaway Quincy A. , Majumder Nairrita , Goldsmith William T. , Kunovac Amina , Pinti Mark V. , Harkema Jack R. , Castranova Vince , Hollander John M. , Hussain Salik 
Published: December 2021

Abstract
Background
Air pollution is a complex mixture of particles and gases, yet current regulations are based on single toxicant levels failing to consider potential interactive outcomes of co-exposures. We examined transcriptomic changes after inhalation co-exposure to a particulate and a gaseous component of air pollution and hypothesized that co-exposure would induce significantly greater impairments to mitochondrial bioenergetics. A whole-body inhalation exposure to ultrafine carbon black (CB), and ozone (O3) was performed, and the impact of single and multiple exposures was studied at relevant deposition levels. C57BL/6 mice were exposed to CB (10 mg/m3) and/or O3 (2 ppm) for 3 h (either a single exposure or four independent exposures). RNA was isolated from lungs and mRNA sequencing performed using the Illumina HiSeq. Lung pathology was evaluated by histology and immunohistochemistry. Electron transport chain (ETC) activities, electron flow, hydrogen peroxide production, and ATP content were assessed.

Results
Compared to individual exposure groups, co-exposure induced significantly greater neutrophils and protein levels in broncho-alveolar lavage fluid as well as a significant increase in mRNA expression of oxidative stress and inflammation related genes. Similarly, a significant increase in hydrogen peroxide production was observed after co-exposure. After single and four exposures, co-exposure revealed a greater number of differentially expressed genes (2251 and 4072, respectively). Of these genes, 1188 (single exposure) and 2061 (four exposures) were uniquely differentially expressed, with 35 mitochondrial ETC mRNA transcripts significantly impacted after four exposures. Both O3 and co-exposure treatment significantly reduced ETC maximal activity for complexes I (− 39.3% and − 36.2%, respectively) and IV (− 55.1% and − 57.1%, respectively). Only co-exposure reduced ATP Synthase activity (− 35.7%) and total ATP content (30%). Further, the ability for ATP Synthase to function is limited by reduced electron flow (− 25%) and translation of subunits, such as ATP5F1, following co-exposure.

Conclusions
CB and O3 co-exposure cause unique transcriptomic changes in the lungs that are characterized by functional deficits to mitochondrial bioenergetics. Alterations to ATP Synthase function and mitochondrial electron flow underly a pathological adaptation to lung injury induced by co-exposure.
A rapid and non-destructive method for spatial–temporal quantification of colonization by Pseudomonas syringae pv. tomato DC3000 in Arabidopsis and tomato
Authors: Furci Leonardo , Pascual-Pardo David , Ton Jurriaan 
Published: December 2021

Abstract
Background
The bacterial leaf pathogen Pseudomonas syringae pv tomato (Pst) is the most popular model pathogen for plant pathology research. Previous methods to study the plant-Pst interactions rely on destructive quantification of Pst colonisation, which can be labour- and time-consuming and does not allow for spatial–temporal monitoring of the bacterial colonisation. Here, we describe a rapid and non-destructive method to quantify and visualise spatial–temporal colonisation by Pst in intact leaves of Arabidopsis and tomato.

Results
The method presented here uses a bioluminescent Pst DC3000 strain that constitutively expresses the luxCDABE operon from Photorhabdus luminescens (Pst::LUX) and requires a common gel documentation (Gel Doc) system with a sensitive CCD/CMOS camera and imaging software (Photoshop or Image J). By capturing bright field and bioluminescence images from Pst::LUX-infected leaves, we imaged the spatiotemporal dynamics of Pst infection. Analysis of bioluminescence from live Pst bacteria over a 5-day time course after spray inoculation of Arabidopsis revealed transition of the bacterial presence from the older leaves to the younger leaves and apical meristem. Colonisation by Pst:LUX bioluminescence was obtained from digital photos by calculating relative bioluminescence values, which is adjusted for bioluminescence intensity and normalised by leaf surface. This method detected statistically significant differences in Pst::LUX colonisation between Arabidopsis genotypes varying in basal resistance, as well as statistically significant reductions in Pst::LUX colonisation by resistance-inducing treatments in both Arabidopsis and tomato. Comparison of relative bioluminescence values to conventional colony counting on selective agar medium revealed a statistically significant correlation, which was reproducible between different Gel Doc systems.

Conclusions
We present a non-destructive method to quantify colonisation by bioluminescent Pst::LUX in plants. Using a common Gel Doc system and imaging software, our method requires less time and labour than conventional methods that are based on destructive sampling of infected leaf material. Furthermore, in contrast to conventional strategies, our method provides additional information about the spatial–temporal patterns of Pst colonisation.
A cis-regulatory-directed pipeline for the identification of genes involved in cardiac development and disease
Authors: Nim Hieu T. , Dang Louis , Thiyagarajah Harshini , Bakopoulos Daniel , See Michael , Charitakis Natalie , Sibbritt Tennille , Eichenlaub Michael P. , Archer Stuart K. , Fossat Nicolas , Burke Richard E. , Tam Patrick P. L. , Warr Coral G. , Johnson Travis K. , Ramialison Mirana 
Published: December 2021

Abstract
Background
Congenital heart diseases are the major cause of death in newborns, but the genetic etiology of this developmental disorder is not fully known. The conventional approach to identify the disease-causing genes focuses on screening genes that display heart-specific expression during development. However, this approach would have discounted genes that are expressed widely in other tissues but may play critical roles in heart development.

Results
We report an efficient pipeline of genome-wide gene discovery based on the identification of a cardiac-specific cis-regulatory element signature that points to candidate genes involved in heart development and congenital heart disease. With this pipeline, we retrieve 76% of the known cardiac developmental genes and predict 35 novel genes that previously had no known connectivity to heart development. Functional validation of these novel cardiac genes by RNAi-mediated knockdown of the conserved orthologs in Drosophila cardiac tissue reveals that disrupting the activity of 71% of these genes leads to adult mortality. Among these genes, RpL14, RpS24, and Rpn8 are associated with heart phenotypes.

Conclusions
Our pipeline has enabled the discovery of novel genes with roles in heart development. This workflow, which relies on screening for non-coding cis-regulatory signatures, is amenable for identifying developmental and disease genes for an organ without constraining to genes that are expressed exclusively in the organ of interest.
Whole body regeneration and developmental competition in two botryllid ascidians
Authors: Nourizadeh Shane , Kassmer Susannah , Rodriguez Delany , Hiebert Laurel S. , De Tomaso Anthony W. 
Published: December 2021

AbstractBackgroundBotryllid ascidians are a group of marine invertebrate chordates that are colonial and grow by repeated rounds of asexual reproduction to form a colony of individual bodies, called zooids, linked by a common vascular network. Two distinct processes are responsible for zooid regeneration. In the first, called blastogenesis, new zooids arise from a region of multipotent epithelium from a pre-existing zooid. In the second, called whole body regeneration (WBR), mobile cells in the vasculature coalesce and are the source of the new zooid. In some botryllid species, blastogenesis and WBR occur concurrently, while in others, blastogenesis is used exclusively for growth, while WBR only occurs following injury or exiting periods of dormancy. In species such asBotrylloides diegensis, injury induced WBR is triggered by the surgical isolation of a small piece of vasculature. However,Botryllus schlosserihas unique requirements that must be met for successful injury induced WBR. Our goal was to understand why there would be different requirements between these two species.ResultsWhile WBR inB. diegensiswas robust, we found that inB. schlosseri, new zooid growth following injury is unlikely due to circulatory cells, but instead a result of ectopic development of tissues leftover from the blastogenic process. These tissues could be whole, damaged, or partially resorbed developing zooids, and we defined the minimal amount of vascular biomass to support ectopic regeneration. We did find a common theme between the two species: a competitive process exists which results in only a single zooid reaching maturity following injury. We utilized this phenomenon and found that competition is reversible and mediated by circulating factors and/or cells.ConclusionsWe propose that WBR does not occur inB. schlosseriand that the unique requirements defined in other studies only serve to increase the chances of ectopic development. This is likely a response to injury as we have discovered a vascular-based reversible competitive mechanism which ensures that only a single zooid completes development. This competition has been described in other species, but the unique response ofB. schlosserito injury provides a new model to study resource allocation and competition within an individual.
The potential for artificial intelligence to predict clinical outcomes in patients who have acquired acute kidney injury during the perioperative period
Authors: Kelly Barry J. , Chevarria Julio , O’Sullivan Barry , Shorten George 
Published: December 2021

AbstractAcute kidney injury (AKI) is a common medical problem in hospitalised patients worldwide that may result in negative physiological, social and economic consequences. Amongst patients admitted to ICU with AKI, over 40% have had either elective or emergency surgery prior to admission. Predicting outcomes after AKI is difficult and the decision on whom to initiate RRT with a goal of renal recovery or predict a long-term survival benefit still poses a challenge for acute care physicians. With the increasing use of electronic healthcare records, artificial intelligence may allow postoperative AKI prognostication and aid clinical management. Patients will benefit if the data can be readily accessed andregulatory, ethical and human factors challenges can be overcome.
Color Doppler ultrasonography of an agitated solution is predictive of accurate catheter placement for a continuous popliteal sciatic nerve block
Authors: Bowens Clifford , Badiola Ignacio J. , Allen Brian Frazer Scott , Canlas Christopher Loredo , Gupta Rajnish Kumar , Jaeger Lisa Michelle , Briggs Eric Russell , Corey John Matthew , Shi Yaping , Schildcrout Jonathan Scott , Malchow Randall John 
Published: December 2021

Abstract
Background
Continuous peripheral nerve catheters (PNCs) have been shown to provide superior postoperative analgesia, decrease opioid consumption, and improve patient satisfaction compared with single injection techniques. In order to achieve success and reliability, accurate catheter positioning is an essential element of PNC placement. An agitated solution of normal saline, D5W, or a local anesthetic solution can be produced by the introduction of air to the injectate, creating air bubbles that can enhance ultrasonographic visualization and possibly improve block success.

Methods
Eighty-three patients were enrolled. Ultrasound-guided continuous popliteal sciatic nerve blocks were performed by positioning the tip of a Tuohy needle between the tibial and common peroneal branches of the sciatic nerve and threading a catheter. An agitated local anesthetic solution was injected through the catheter, viewed with color Doppler ultrasound and video recorded. A peripheral block score (lower score = greater blockade, range 0-14) was calculated based upon the motor and sensory testing at 10, 20, and 30 min after block completion. The color Doppler agitation coverage pattern for the branches of the sciatic nerve was graded as follows: complete (> 50%), partial (> 0%, ≤ 50%), or none (0%).

Results
The degree of nerve blockade at 30 min as judged by median (10th, 90th percentile) peripheral block score was significant for partial or complete color Doppler coverage of the sciatic nerve injectate compared to no coverage [3 (0, 7) vs 8 (4, 14); p < 0.01] and block onset was faster (p = 0.03). The block success was higher in groups with partial or complete coverage of the branches of the sciatic nerve vs no coverage (96% vs 70%; p = 0.02).

Conclusions
Injection of an agitated solution through a popliteal sciatic perineural catheter is predictive of accurate catheter placement when partial or complete coverage of the sciatic nerve branches is visualized with color Doppler ultrasound.

Trial registration
NCT01591603
Ageing and rejuvenation models reveal changes in key microbial communities associated with healthy ageing
Authors: Shin Jongoh , Noh Jung-Ran , Choe Donghui , Lee Namil , Song Yoseb , Cho Suhyung , Kang Eun-Jung , Go Min-Jeong , Ha Seok Kyun , Chang Dong-Ho , Kim Jae-Hoon , Kim Yong-Hoon , Kim Kyoung-Shim , Jung Haiyoung , Kim Myung Hee , Sung Bong-Hyun , Lee Seung-Goo , Lee Dae-Hee , Kim Byoung-Chan , Lee Chul-Ho , Cho Byung-Kwan 
Published: December 2021

Abstract
Background
The gut microbiota is associated with diverse age-related disorders. Several rejuvenation methods, such as probiotic administration and faecal microbiota transplantation, have been applied to alter the gut microbiome and promote healthy ageing. Nevertheless, prolongation of the health span of aged mice by remodelling the gut microbiome remains challenging.

Results
Here, we report the changes in gut microbial communities and their functions in mouse models during ageing and three rejuvenation procedures including co-housing, serum-injection and parabiosis. Our results showed that the compositional structure and gene abundance of the intestinal microbiota changed dynamically during the ageing process. Through the three rejuvenation procedures, we observed that the microbial community and intestinal immunity of aged mice were comparable to those of young mice. The results of metagenomic data analysis underscore the importance of the high abundance of Akkermansia and the butyrate biosynthesis pathway in the rejuvenated mouse group. Furthermore, oral administration of Akkermansia sufficiently ameliorated the senescence-related phenotype in the intestinal systems in aged mice and extended the health span, as evidenced by the frailty index and restoration of muscle atrophy.

Conclusions
In conclusion, the changes in key microbial communities and their functions during ageing and three rejuvenation procedures, and the increase in the healthy lifespan of aged mice by oral administration of Akkermansia. Our results provide a rationale for developing therapeutic strategies to achieve healthy active ageing.
Human microbiota research in Africa: a systematic review reveals gaps and priorities for future research
Authors: Allali Imane , Abotsi Regina E. , Tow Lemese Ah. , Thabane Lehana , Zar Heather J. , Mulder Nicola M. , Nicol Mark P. 
Published: December 2021

Abstract
Background
The role of the human microbiome in health and disease is an emerging and important area of research; however, there is a concern that African populations are under-represented in human microbiome studies. We, therefore, conducted a systematic survey of African human microbiome studies to provide an overview and identify research gaps. Our secondary objectives were: (i) to determine the number of peer-reviewed publications; (ii) to identify the extent to which the researches focused on diseases identified by the World Health Organization [WHO] State of Health in the African Region Report as being the leading causes of morbidity and mortality in 2018; (iii) to describe the extent and pattern of collaborations between researchers in Africa and the rest of the world; and (iv) to identify leadership and funders of the studies.

Methodology
We systematically searched Medline via PubMed, Scopus, CINAHL, Academic Search Premier, Africa-Wide Information through EBSCOhost, and Web of Science from inception through to 1st April 2020. We included studies that characterized samples from African populations using next-generation sequencing approaches. Two reviewers independently conducted the literature search, title and abstract, and full-text screening, as well as data extraction.

Results
We included 168 studies out of 5515 records retrieved. Most studies were published in PLoS One (13%; 22/168), and samples were collected from 33 of the 54 African countries. The country where most studies were conducted was South Africa (27/168), followed by Kenya (23/168) and Uganda (18/168). 26.8% (45/168) focused on diseases of significant public health concern in Africa. Collaboration between scientists from the United States of America and Africa was most common (96/168). The first and/or last authors of 79.8% of studies were not affiliated with institutions in Africa. Major funders were the United States of America National Institutes of Health (45.2%; 76/168), Bill and Melinda Gates Foundation (17.8%; 30/168), and the European Union (11.9%; 20/168).

Conclusions
There are significant gaps in microbiome research in Africa, especially those focusing on diseases of public health importance. There is a need for local leadership, capacity building, intra-continental collaboration, and national government investment in microbiome research within Africa.
Towards emotional responsive mentoring of at-risk students in last-resort programs
Authors: Keijzer Rineke , van der Rijst Roeland , van Schooten Erik , Admiraal Wilfried 
Published: December 2021

AbstractBackgroundMentors guide students in their challenges at school and in life. At-risk students in last-resort programs who are at a high risk of leaving school unqualified are especially in need of highly competent and adaptive mentors. This study therefore aimed to identify mentor qualities as perceived by at-risk students and their mentors that meet students’ needs and mentors’ capabilities.MethodsFace-to-face individual semi-structured interviews were conducted with students and mentors of two specialized programs in the Netherlands. Sensitizing concepts, derived from literature, were used to identify themes. Data analysis was conducted using thematic analyses and was validated by performing an audit.ResultsThe mentor qualities that at-risk students and their mentors reported were classified in three different themes. Mentor tasks consisted of guiding and motivating students and providing them with tangible methods of support. Relationships between mentor and student were based on levels of respect, equality, and bonding. Characteristics of mentors related to empathy, care, and trust.Research implicationsEmotional responsiveness deserves further exploration as it appears to be an underlying concept of being a good mentor. Future research might explore mentor qualities in the context of other last-resort programs for at-risk students.Practical implicationsFindings implicate that mentors have to walk a tightrope between keeping professional distance and being sensitive, suggesting constant attention to their professional development is needed.OriginalityIn the context of last-resort programs, an alternative perspective on mentoring at-risk students is outlined, based on perceptions of both students and mentors.
STAT3 inhibitor mitigates cerebral amyloid angiopathy and parenchymal amyloid plaques while improving cognitive functions and brain networks
Authors: Mehla Jogender , Singh Itender , Diwan Deepti , Nelson James W. , Lawrence Molly , Lee Eunjae , Bauer Adam Q. , Holtzman David M. , Zipfel Gregory J. 
Published: December 2021

AbstractPrevious reports indicate a potential role for signal transducer and activator of transcription 3 (STAT3) in amyloid-β (Aβ) processing and neuritic plaque pathogenesis. In the present study, the impact of STAT3 inhibition on cognition, cerebrovascular function, amyloid pathology, oxidative stress, and neuroinflammation was studied using in vitro and in vivo models of Alzheimer’s disease (AD)-related pathology. For in vitro experiments, human brain vascular smooth muscle cells (HBVSMC) and human brain microvascular endothelial cells (HBMEC) were used, and these cultured cells were exposed to Aβ peptides followed by measurement of activated forms of STAT3 expression and reactive oxygen species (ROS) generation. Further, 6 months old 5XFAD/APOE4 (5XE4) mice and age-matched negative littermates were used for in vivo experiments. These mice were treated with STAT3 specific inhibitor, LLL-12 for 2 months followed by neurobehavioral and histopathological assessment. In vitro experiments showed exposure of cerebrovascular cells to Aβ peptides upregulated activated forms of STAT3 and produced STAT3-mediated vascular oxidative stress. 5XE4 mice treated with the STAT3-specific inhibitor (LLL-12) improved cognitive functions and functional connectivity and augmented cerebral blood flow. These functional improvements were associated with a reduction in neuritic plaques, cerebral amyloid angiopathy (CAA), oxidative stress, and neuroinflammation. Reduction in amyloid precursor protein (APP) processing and attenuation of oxidative modification of lipoprotein receptor related protein-1 (LRP-1) were identified as potential underlying mechanisms. These results demonstrate the broad impact of STAT3 on cognitive functions, parenchymal and vascular amyloid pathology and highlight the therapeutic potential of STAT3 specific inhibition for treatment of AD and CAA.
Science operation plan of Phobos and Deimos from the MMX spacecraft
Authors: Nakamura Tomoki , Ikeda Hitoshi , Kouyama Toru , Nakagawa Hiromu , Kusano Hiroki , Senshu Hiroki , Kameda Shingo , Matsumoto Koji , Gonzalez-Franquesa Ferran , Ozaki Naoya , Takeo Yosuke , Baresi Nicola , Oki Yusuke , Lawrence David J. , Chabot Nancy L. , Peplowski Patrick N. , Barucci Maria Antonietta , Sawyer Eric , Yokota Shoichiro , Terada Naoki , Ulamec Stephan , Michel Patrick , Kobayashi Masanori , Sasaki Sho , Hirata Naru , Wada Koji , Miyamoto Hideaki , Imamura Takeshi , Ogawa Naoko , Ogawa Kazunori , Iwata Takahiro , Imada Takane , Otake Hisashi , Canalias Elisabet , Lorda Laurence , Tardivel Simon , Mary Stéphane , Kunugi Makoto , Mitsuhashi Seiji , Doressoundiram Alain , Merlin Frédéric , Fornasier Sonia , Reess Jean-Michel , Bernardi Pernelle , Imai Shigeru , Ito Yasuyuki , Ishida Hatsumi , Kuramoto Kiyoshi , Kawakatsu Yasuhiro 
Published: December 2021

AbstractThe science operations of the spacecraft and remote sensing instruments for the Martian Moon eXploration (MMX) mission are discussed by the mission operation working team. In this paper, we describe the Phobos observations during the first 1.5 years of the spacecraft’s stay around Mars, and the Deimos observations before leaving the Martian system. In the Phobos observation, the spacecraft will be placed in low-altitude quasi-satellite orbits on the equatorial plane of Phobos and will make high-resolution topographic and spectroscopic observations of the Phobos surface from five different altitudes orbits. The spacecraft will also attempt to observe polar regions of Phobos from a three-dimensional quasi-satellite orbit moving out of the equatorial plane of Phobos. From these observations, we will constrain the origin of Phobos and Deimos and select places for landing site candidates for sample collection. For the Deimos observations, the spacecraft will be injected into two resonant orbits and will perform many flybys to observe the surface of Deimos over as large an area as possible.
Graphical Abstract