bluuebunny/crossref_metadata_2025_split huggingface dataset:
Variable preterm oral microbiome stabilizes and reflects a full-term infant profile within three months
Authors: Selway Caitlin A. , Collins Carmel T. , Makrides Maria , Sullivan Thomas R. ,   N3RO Steering Committee, Gibson Robert A. , Penttila Irmeli , McPhee Andrew , Weyrich Laura S. 
Published: March 2023

Abstract
Background
Preterm infants suffer higher morbidity and mortality rates compared to full-term infants, but little is known about how changes to oral and respiratory tract microbiota may impact disease development.

Methods
Here, very preterm neonates (n = 50) were selected to study oral and respiratory microbiota development during the first few months post-birth, where 26 individuals were diagnosed with BPD and/or sepsis. These infants were compared to 14 healthy full-term infants and 16 adults. Microbiota diversity, composition, and species abundances were calculated from 16S ribosomal RNA gene sequences in buccal swabs and tracheal aspirates at two time points (within a week and 1–3 months post-birth).

Results
Collection time point was the biggest factor to significantly influence the preterm oral microbial diversity and composition. In addition, BPD and sepsis were linked to distinct preterm oral microbiota diversity and composition, and opportunistic pathogens previously associated with these diseases were identified in the initial sample for both healthy preterm neonates and those with the disease. Compared to the full-term infant and adult dataset, preterm infant diversity and composition was initially significantly different, but resembled full-term infant diversity and composition over time.

Conclusion
Overall, consequences of microbiota development need further examination in preterm infant infections and later development.

Impact

Non-gut microbiota research on preterm infants is limited.

At one week post-birth, preterm infants harbor distinct oral microbiota that are not shared with full-term children or adults, eventually becoming similar to full-term infants at 36 weeks postmenstrual age.

DNA from potential opportunistic pathogens was observed in the mouth and lungs of preterm infants within a week of birth, and microbes associated with BPD were identified in the lungs.

Oral microbiota in preterm infants over the first 2–3 months is unique and may be connected to short- and long-term health outcomes in these children.
Necroptosis of macrophage is a key pathological feature in biliary atresia via GDCA/S1PR2/ZBP1/p-MLKL axis
Authors: Yang Shen , Chang Na , Li Weiyang , Yang Ting , Xue Renmin , Liu Jing , Zhang Li , Yao Xingfeng , Chen Yajun , Wang Huanmin , Yang Lin , Huang Jinshi , Li Liying 
Published: March 2023

AbstractBiliary atresia (BA) is a severe inflammatory and fibrosing neonatal cholangiopathy disease characterized by progressive obstruction of extrahepatic bile ducts, resulting in cholestasis and progressive hepatic failure. Cholestasis may play an important role in the inflammatory and fibrotic pathological processes, but its specific mechanism is still unclear. Necroptosis mediated by Z-DNA-binding protein 1 (ZBP1)/phosphorylated-mixed lineage kinase domain-like pseudokinase (p-MLKL) is a prominent pathogenic factor in inflammatory and fibrotic diseases, but its function in BA remains unclear. Here, we aim to determine the effect of macrophage necroptosis in the BA pathology, and to explore the specific molecular mechanism. We found that necroptosis existed in BA livers, which was occurred in liver macrophages. Furthermore, this process was mediated by ZBP1/p-MLKL, and the upregulated expression of ZBP1 in BA livers was correlated with liver fibrosis and prognosis. Similarly, in the bile duct ligation (BDL) induced mouse cholestatic liver injury model, macrophage necroptosis mediated by ZBP1/p-MLKL was also observed. In vitro, conjugated bile acid-glycodeoxycholate (GDCA) upregulated ZBP1 expression in mouse bone marrow-derived monocyte/macrophages (BMDMs) through sphingosine 1-phosphate receptor 2 (S1PR2), and the induction of ZBP1 was a prerequisite for the enhanced necroptosis. Finally, after selectively knocking down of macrophage S1pr2 in vivo, ZBP1/p-MLKL-mediated necroptosis was decreased, and further collagen deposition was markedly attenuated in BDL mice. Furthermore, macrophage Zbp1 or Mlkl specific knockdown also alleviated BDL-induced liver injury/fibrosis. In conclusion, GDCA/S1PR2/ZBP1/p-MLKL mediated macrophage necroptosis plays vital role in the pathogenesis of BA liver fibrosis, and targeting this process may represent a potential therapeutic strategy for BA.
Dying transplanted neural stem cells mediate survival bystander effects in the injured brain
Authors: Han Wei , Meißner Eva-Maria , Neunteibl Stefanie , Günther Madeline , Kahnt Jörg , Dolga Amalia , Xie Cuicui , Plesnila Nikolaus , Zhu Changlian , Blomgren Klas , Culmsee Carsten 
Published: March 2023

SummaryNeural stem and progenitor cell (NSPC) transplants provide neuroprotection in models of acute brain injury, but the underlying mechanisms are not fully understood. Here, we provide evidence that caspase-dependent apoptotic cell death of NSPCs is required for sending survival signals to the injured brain. The secretome of dying NSPCs contains heat-stable proteins, which protect neurons against glutamate-induced toxicity and trophic factor withdrawal in vitro, and from ischemic brain damage in vivo. Our findings support a new concept suggesting a bystander effect of apoptotic NSPCs, which actively promote neuronal survival through the release of a protective “farewell” secretome. Similar protective effects by the secretome of apoptotic NSPC were also confirmed in human neural progenitor cells and neural stem cells but not in mouse embryonic fibroblasts (MEF) or human dopaminergic neurons, suggesting that the observed effects are cell type specific and exist for neural progenitor/stem cells across species.
A maximum-entropy model to predict 3D structural ensembles of chromatin from pairwise distances with applications to interphase chromosomes and structural variants
Authors: Shi Guang , Thirumalai D. 
Published: March 2023

AbstractThe principles that govern the organization of genomes, which are needed for an understanding of how chromosomes are packaged and function in eukaryotic cells, could be deciphered if the three-dimensional (3D) structures are known. Recently, single-cell imaging techniques have been developed to determine the 3D coordinates of genomic loci in vivo. Here, we introduce a computational method (Distance Matrix to Ensemble of Structures, DIMES), based on the maximum entropy principle, with experimental pairwise distances between loci as constraints, to generate a unique ensemble of 3D chromatin structures. Using the ensemble of structures, we quantitatively account for the distribution of pairwise distances, three-body co-localization, and higher-order interactions. The DIMES method can be applied to both small and chromosome-scale imaging data to quantify the extent of heterogeneity and fluctuations in the shapes across various length scales. We develop a perturbation method in conjunction with DIMES to predict the changes in 3D structures from structural variations. Our method also reveals quantitative differences between the 3D structures inferred from Hi-C and those measured in imaging experiments. Finally, the physical interpretation of the parameters extracted from DIMES provides insights into the origin of phase separation between euchromatin and heterochromatin domains.
Magnesium oxide-water compounds at megabar pressure and implications on planetary interiors
Authors: Pan Shuning , Huang Tianheng , Vazan Allona , Liang Zhixin , Liu Cong , Wang Junjie , Pickard Chris J. , Wang Hui-Tian , Xing Dingyu , Sun Jian 
Published: March 2023

AbstractMagnesium Oxide (MgO) and water (H2O) are abundant in the interior of planets. Their properties, and in particular their interaction, significantly affect the planet interior structure and thermal evolution. Here, using crystal structure predictions and ab initio molecular dynamics simulations, we find that MgO and H2O can react again at ultrahigh pressure, although Mg(OH)2 decomposes at low pressure. The reemergent MgO-H2O compounds are: Mg2O3H2 above 400 GPa, MgO3H4 above 600 GPa, and MgO4H6 in the pressure range of 270–600 GPa. Importantly, MgO4H6 contains 57.3 wt % of water, which is a much higher water content than any reported hydrous mineral. Our results suggest that a substantial amount of water can be stored in MgO rock in the deep interiors of Earth to Neptune mass planets. Based on molecular dynamics simulations we show that these three compounds exhibit superionic behavior at the pressure-temperature conditions as in the interiors of Uranus and Neptune. Moreover, the water-rich compound MgO4H6 could be stable inside the early Earth and therefore may serve as a possible early Earth water reservoir. Our findings, in the poorly explored megabar pressure regime, provide constraints for interior and evolution models of wet planets in our solar system and beyond.
Oceanic climate changes threaten the sustainability of Asia’s water tower
Authors: Zhang Qiang , Shen Zexi , Pokhrel Yadu , Farinotti Daniel , Singh Vijay P. , Xu Chong-Yu , Wu Wenhuan , Wang Gang 
Published: March 2023

Abstract
Water resources sustainability in High Mountain Asia (HMA) surrounding the Tibetan Plateau (TP)—known as Asia’s water tower—has triggered widespread concerns because HMA protects millions of people against water stress1,2. However, the mechanisms behind the heterogeneous trends observed in terrestrial water storage (TWS) over the TP remain poorly understood. Here we use a Lagrangian particle dispersion model and satellite observations to attribute about 1 Gt of monthly TWS decline in the southern TP during 2003–2016 to westerlies-carried deficit in precipitation minus evaporation (PME) from the southeast North Atlantic. We further show that HMA blocks the propagation of PME deficit into the central TP, causing a monthly TWS increase by about 0.5 Gt. Furthermore, warming-induced snow and glacial melt as well as drying-induced TWS depletion in HMA weaken the blocking of HMA’s mountains, causing persistent northward expansion of the TP’s TWS deficit since 2009. Future projections under two emissions scenarios verified by satellite observations during 2020–2021 indicate that, by the end of the twenty-first century, up to 84% (for scenario SSP245) and 97% (for scenario SSP585) of the TP could be afflicted by TWS deficits. Our findings indicate a trajectory towards unsustainable water systems in HMA that could exacerbate downstream water stress.
Coastal phytoplankton blooms expand and intensify in the 21st century
Authors: Dai Yanhui , Yang Shangbo , Zhao Dan , Hu Chuanmin , Xu Wang , Anderson Donald M. , Li Yun , Song Xiao-Peng , Boyce Daniel G. , Gibson Luke , Zheng Chunmiao , Feng Lian 
Published: March 2023

AbstractPhytoplankton blooms in coastal oceans can be beneficial to coastal fisheries production and ecosystem function, but can also cause major environmental problems1,2—yet detailed characterizations of bloom incidence and distribution are not available worldwide. Here we map daily marine coastal algal blooms between 2003 and 2020 using global satellite observations at 1-km spatial resolution. We found that algal blooms occurred in 126 out of the 153 coastal countries examined. Globally, the spatial extent (+13.2%) and frequency (+59.2%) of blooms increased significantly (P < 0.05) over the study period, whereas blooms weakened in tropical and subtropical areas of the Northern Hemisphere. We documented the relationship between the bloom trends and ocean circulation, and identified the stimulatory effects of recent increases in sea surface temperature. Our compilation of daily mapped coastal phytoplankton blooms provides the basis for global assessments of bloom risks and benefits, and for the formulation or evaluation of management or policy actions.
H3K4me3 regulates RNA polymerase II promoter-proximal pause-release
Authors: Wang Hua , Fan Zheng , Shliaha Pavel V. , Miele Matthew , Hendrickson Ronald C. , Jiang Xuejun , Helin Kristian 
Published: March 2023

AbstractTrimethylation of histone H3 lysine 4 (H3K4me3) is associated with transcriptional start sites and has been proposed to regulate transcription initiation1,2. However, redundant functions of the H3K4 SET1/COMPASS methyltransferase complexes complicate the elucidation of the specific role of H3K4me3 in transcriptional regulation3,4. Here, using mouse embryonic stem cells as a model system, we show that acute ablation of shared subunits of the SET1/COMPASS complexes leads to a complete loss of all H3K4 methylation. Turnover of H3K4me3 occurs more rapidly than that of H3K4me1 and H3K4me2 and is dependent on KDM5 demethylases. Notably, acute loss of H3K4me3 does not have detectable effects on transcriptional initiation but leads to a widespread decrease in transcriptional output, an increase in RNA polymerase II (RNAPII) pausing and slower elongation. We show that H3K4me3 is required for the recruitment of the integrator complex subunit 11 (INTS11), which is essential for the eviction of paused RNAPII and transcriptional elongation. Thus, our study demonstrates a distinct role for H3K4me3 in transcriptional pause-release and elongation rather than transcriptional initiation.
Orbital period change of Dimorphos due to the DART kinetic impact
Authors: Thomas Cristina A. , Naidu Shantanu P. , Scheirich Peter , Moskovitz Nicholas A. , Pravec Petr , Chesley Steven R. , Rivkin Andrew S. , Osip David J. , Lister Tim A. , Benner Lance A. M. , Brozović Marina , Contreras Carlos , Morrell Nidia , Rożek Agata , Kušnirák Peter , Hornoch Kamil , Mages Declan , Taylor Patrick A. , Seymour Andrew D. , Snodgrass Colin , Jørgensen Uffe G. , Dominik Martin , Skiff Brian , Polakis Tom , Knight Matthew M. , Farnham Tony L. , Giorgini Jon D. , Rush Brian , Bellerose Julie , Salas Pedro , Armentrout William P. , Watts Galen , Busch Michael W. , Chatelain Joseph , Gomez Edward , Greenstreet Sarah , Phillips Liz , Bonavita Mariangela , Burgdorf Martin J. , Khalouei Elahe , Longa-Peña Penélope , Rabus Markus , Sajadian Sedighe , Chabot Nancy L. , Cheng Andrew F. , Ryan William H. , Ryan Eileen V. , Holt Carrie E. , Agrusa Harrison F. 
Published: March 2023

AbstractThe Double Asteroid Redirection Test (DART) spacecraft successfully performed the first test of a kinetic impactor for asteroid deflection by impacting Dimorphos, the secondary of near-Earth binary asteroid (65803) Didymos, and changing the orbital period of Dimorphos. A change in orbital period of approximately 7 min was expected if the incident momentum from the DART spacecraft was directly transferred to the asteroid target in a perfectly inelastic collision1, but studies of the probable impact conditions and asteroid properties indicated that a considerable momentum enhancement (β) was possible2,3. In the years before impact, we used lightcurve observations to accurately determine the pre-impact orbit parameters of Dimorphos with respect to Didymos4–6. Here we report the change in the orbital period of Dimorphos as a result of the DART kinetic impact to be −33.0 ± 1.0 (3σ) min. Using new Earth-based lightcurve and radar observations, two independent approaches determined identical values for the change in the orbital period. This large orbit period change suggests that ejecta contributed a substantial amount of momentum to the asteroid beyond what the DART spacecraft carried.
Distribution of dietary nitrate and its metabolites in rat tissues after 15N-labeled nitrate administration
Authors: Park Ji Won , Piknova Barbora , Walter Peter J. , Cai Hongyi , Upanan Supranee , Thomas Samantha M. , Tunau-Spencer Khalid J. , Schechter Alan N. 
Published: March 2023

AbstractThe reduction pathway of nitrate (NO3−) and nitrite (NO2−) to nitric oxide (NO) contributes to regulating many physiological processes. To examine the rate and extent of dietary nitrate absorption and its reduction to nitrite, we supplemented rat diets with Na15NO3-containing water (1 g/L) and collected plasma, urine and several tissue samples. We found that plasma and urine showed 8.8- and 11.7-fold increases respectively in total nitrate concentrations in 1-day supplementation group compared to control. In tissue samples—gluteus, liver and eyes—we found 1.7-, 2.4- and 4.2-fold increases respectively in 1-day supplementation group. These increases remained similar in 3-day supplementation group. LC–MS/MS analysis showed that the augmented nitrate concentrations were primarily from the exogenously provided 15N-nitrate. Overall nitrite concentrations and percent of 15N-nitrite were also greatly increased in all samples after nitrate supplementation; eye homogenates showed larger increases compared to gluteus and liver. Moreover, genes related to nitrate transport and reduction (Sialin, CLC and XOR) were upregulated after nitrate supplementation for 3 days in muscle (Sialin 2.3-, CLC1 1.3-, CLC3 2.1-, XOR 2.4-fold) and eye (XOR 1.7-fold) homogenates. These results demonstrate that dietary nitrate is quickly absorbed into circulation and tissues, and it can be reduced to nitrite in tissues (and likely to NO) suggesting that nitrate-enriched diets can be an efficient intervention to enhance nitrite and NO bioavailability.
NLRX1 knockdown attenuates pro-apoptotic signaling and cell death in pulmonary hyperoxic acute injury
Authors: Kim Hye Rin , Kim Mi Na , Kim Eun Gyul , Leem Ji Su , Baek Seung Min , Lee Yu Jin , Kim Kyung Won , Kang Min-Jong , Song Tae Won , Sohn Myung Hyun 
Published: March 2023

AbstractHyperoxia is frequently used for treating acute respiratory failure, but it can cause acute lung injury. Nucleotide-binding domain and leucine-rich-repeat-containing family member X1 (NLRX1) is localized in mitochondria and involved in production of reactive oxygen species, inflammation, and apoptosis, which are the features of hyperoxic acute lung injury (HALI). The contribution of NLRX1 to HALI has not previously been addressed. Thus, to investigate the role of NLRX1 in hyperoxia, we generated a murine model of HALI in wild-type (WT) and NLRX1−/− mice by exposure to > 95% oxygen for 72 h. As a result, NLRX1 expression was elevated in mice exposed to hyperoxia. In acute lung injury, levels of inflammatory cells, protein leakage, cell cytotoxicity, and pro-inflammatory cytokines were diminished in NLRX1−/− mice compared to WT mice. In a survival test, NLRX1−/− mice showed reduced mortality under hyperoxic conditions, and apoptotic cell death and caspase expression and activity were also lower in NLRX1−/− mice. Furthermore, levels of the MAPK signaling proteins ERK 1/2, JNK, and p38 were decreased in NLRX1-deficient mice than in WT mice exposed to hyperoxia. The study shows that a genetic deficit in NLRX1 can suppress hyperoxia-induced apoptosis, suggesting that NLRX1 acts as a pivotal regulator of HALI.
Individual personality predicts social network assemblages in a colonial bird
Authors: McCully Fionnuala R. , Rose Paul E. 
Published: March 2023

AbstractAnimal personalities manifest as consistent individual differences in the performance of specific behavioural expressions. Personality research has implications for zoo animal welfare, as it can further our understanding of how captive individuals may differ in their resource use and provide insight into improving individual and group social health. For group living species, personality may enable assortment based on similar behaviour and influence an individual’s interactions with conspecifics (e.g. social support). This research aimed to document how personality traits (aggressive, exploratory, submissive) influenced the social network structure of highly social animals in a captive environment. Data were collected from separate flocks of captive Caribbean (Phoenicopterus ruber) and Chilean flamingos (Phoenicopterus chilensis) to identify relationships between birds and examine opportunities for social support. The flocks associated non-randomly, and in both cases, personality was a substantial predictor of network structure. Personality also predicted key elements of Caribbean flamingo social role (degree, betweenness and average association strength) conflict outcome, and propensity to provide social support, however these patterns were not replicated within the Chilean flamingo network. While both species appear to assort by personality, the broader relationship between personality and social role may vary depending on species and context.
Financial constraint and perceptions of COVID-19
Authors: Trueblood Jennifer S. , Sussman Abigail B. , O’Leary Daniel , Holmes William R. 
Published: March 2023

AbstractIn early March 2020, two crises emerged: the COVID-19 public health crisis and a corresponding economic crisis resulting from business closures and skyrocketing job losses. While the link between socioeconomic status and infectious disease is well-documented, the psychological relationships among economic considerations, such as financial constraint and economic anxiety, and health considerations, such as perceptions of disease spread and preventative actions, is not well understood. Despite past research illustrating the strong link between financial fragility and a wide range of behaviors, surprisingly little research has examined the psychological relationship between the economic crisis and beliefs and behaviors related to the co-occurring health crisis. We show that financial constraint predicts people’s beliefs about both their personal risk of infection and the national spread of the virus as well as their social distancing behavior. In addition, we compare the predictive utility of financial constraint to two other commonly studied factors: political partisanship and local disease severity. We also show that negative affect partially mediates the relationship between financial constraint and COVID-19 beliefs and social distancing behaviors. These results suggest the economic crisis created by COVID-19 spilled over into people’s beliefs about the health crisis and their behaviors.
Fecal contamination of urban parks by domestic dogs and tragedy of the commons
Authors: Mori Kensuke , Rock Melanie , McCormack Gavin , Liccioli Stefano , Giunchi Dimitri , Marceau Danielle , Stefanakis Emmanuel , Massolo Alessandro 
Published: March 2023

AbstractContamination of public parks by dogs is a potential source of conflict among park users, causing “tragedy of the commons” problems. Besides the social conflict, feces can pose serious health risks to both dogs and humans. In this study we analyzed the extent and patterns of the distribution of dog feces in the urban parks of the City of Calgary. We collected dog feces from randomly selected locations in the urban parks. The average density of dog feces by the different dog leash policies of the parks and the distribution pattern of the fecal density within the parks were assessed, and the total contamination of the public parks for the entire city was estimated. We found off-leash parks to be significantly more contaminated than other types of parks. We estimated 127.23 g/ha of dog feces are left unpicked in city parks in total every week. Dog feces were found more often and in greater amount in off-leash parks, and near park entrances and parking lots, than in on-leash parks and away from the park entrances. These results suggest that public park visitors, especially those visiting off-leash parks, are likely to be exposed to large amounts of dog feces. Designation of parks as on-leash and educating dog-owners may be an effective approach for reducing the fecal contamination.