bluuebunny/crossref_metadata_2025_split huggingface dataset:
Coastal Upwelling Combined With the River Plume Regulates Hypoxia in the Changjiang Estuary and Adjacent Inner East China Sea Shelf
Authors: Wei Qinsheng , Yao Peng , Xu Bochao , Zhao Bin , Ran Xiangbin , Zhao Yuhang , Sun Junchuan , Wang Baodong , Yu Zhigang 
Published: November 2021

AbstractThe Changjiang (Yangtze River) Estuary (CE) and adjacent inner East China Sea (ECS) shelf are among the most well‐known hypoxic aquatic environments. However, the coupled effects of coastal upwelling and the river plume on hypoxic dynamics in this region are rarely examined. Based on observations off the CE and Zhejiang coast in the summer of 2018, the dynamic mechanisms were revealed by highlighting the combined role of the river plume and upwelling in regulating hypoxia. The bottom hypoxic water formed in the steep slope on the inner ECS shelf expands upward and seaward. Coastal upwelling and the river plume combine to regulate the primary production regime and hypoxia. The frontal regions in the upper layers are prone to phytoplankton blooms, while the convergent slope generally acts as a hot spot of bottom hypoxic center along cross‐shelf sections. The regional selectivity of hypoxia is responsible for the decoupling between locations of bottom‐water hypoxia and upper‐water phytoplankton patches. The upwelling transports oxygen‐deficient water to the upper layers, resulting in shoreward shoaling of the oxycline. Meanwhile, mainly forced by the seaward expansion of low‐oxygen water protruding from the bottom hypoxia in the sloping region, a pronounced midlayer hypoxic plume forms. Together, upwelling and offshore spreading potentially expand the spatial volume of the hypoxic zone. Vertical secondary circulation and subsequent physical–biogeochemical processes leading to hypoxia are indicated off the CE and Zhejiang coast. Our results demonstrate that the combination of upwelling and the river plume plays an important role in regulating the spatial distribution of coastal and estuarine hypoxia.
Relativistic Electron Model in the Outer Radiation Belt Using a Neural Network Approach
Authors: Chu Xiangning , Ma Donglai , Bortnik Jacob , Tobiska W. Kent , Cruz Alfredo , Bouwer S. Dave , Zhao Hong , Ma Qianli , Zhang Kun , Baker Daniel N. , Li Xinlin , Spence Harlan , Reeves Geoff 
Published: November 2021

AbstractWe present a machine‐learning‐based model of relativistic electron fluxes >1.8 MeV using a neural network approach in the Earth's outer radiation belt. The Outer RadIation belt Electron Neural net model for Relativistic electrons (ORIENT‐R) uses only solar wind conditions and geomagnetic indices as input. For the first time, we show that the state of the outer radiation belt can be determined using only solar wind conditions and geomagnetic indices, without any initial and boundary conditions. The most important features for determining outer radiation belt dynamics are found to be AL, solar wind flow speed and density, and SYM‐H indices. ORIENT‐R reproduces out‐of‐sample relativistic electron fluxes with a correlation coefficient of 0.95 and an uncertainty factor of ∼2. ORIENT‐R reproduces radiation belt dynamics during an out‐of‐sample geomagnetic storm with good agreement to the observations. In addition, ORIENT‐R was run for a completely out‐of‐sample period between March 2018 and October 2019 when the AL index ended and was replaced with the predicted AL index (lasp.colorado.edu/home/personnel/xinlin.li). It reproduces electron fluxes with a correlation coefficient of 0.92 and an out‐of‐sample uncertainty factor of ∼3. Furthermore, ORIENT‐R captured the trend in the electron fluxes from low‐earth‐orbit (LEO) SAMPEX, which is a completely out‐of‐sample data set both temporally and spatially. In sum, the ORIENT‐R model can reproduce transport, acceleration, decay, and dropouts of the outer radiation belt anywhere from short timescales (i.e., geomagnetic storms) and very long timescales (i.e., solar cycle) variations.
Two Cenozoic Extensional Phases in Mallorca and Their Bearing on the Geodynamic Evolution of the Western Mediterranean
Authors: Moragues Lluís , Ruano Patricia , Azañón José Miguel , Garrido Carlos J. , Hidas Karoly , Booth Rea Guillermo 
Published: November 2021

AbstractWe study the structure of the Llevant ranges in Mallorca with special emphasis on the Cenozoic extensional evolution of the island, which we integrate in a new geodynamic model for the Westernmost Mediterranean. Mallorca underwent two Cenozoic rifting phases in the Oligocene and Serravallian, before and after the development of its Foreland Thrust Belt (FTB). The first extensional event produced Oligocene semigrabens (≈29–23 Ma) that were inverted during the Early‐Middle Miocene (19–14 Ma) WNW‐directed FTB development. The second rifting event produced the extensional collapse of the Mallorca FTB during the Serravallian (≈14–11 Ma). This later rifting was polyphasic, with two orthogonal extensional systems, producing first NE‐SW, and then NW‐SE extension. The Oligocene extension affected a major part of the Western Mediterranean, opening the Liguro‐Provençal and other basins after the collapse of the Palaeogene AlKaPeCa orogen, and Mallorca, its former hinterland. Continued plate convergence nucleated a new subduction system in the Early Miocene that initiated along the Ibiza transform, producing the Mallorca WNW‐directed FTB and subduction of the South‐East Iberian passive margin. This process individualized the Betic‐Rif slab and initiated its westward retreat. Serravallian extension occurred at the northern edge of the subduction system coeval to the Algero‐Balearic basin opening. Extension initiated toward the SW direction of slab tearing and later rotated to a NW‐SE direction, probably in response to flexural and isostatic rebound. Through these processes the Alboran domain archipelago was driven toward the southwest until the Late Miocene, contributing to the present isolation of Mallorca from its Betic hinterland.
A secular trend of increasing pubertal BMI change among Swedish adolescents
Authors: Bygdell Maria , Ohlsson Claes , Kindblom Jenny M. 
Published: November 2021

AbstractPubertal BMI change is an independent risk marker of cardiovascular mortality/morbidity. Previous studies demonstrated a secular trend of increased childhood BMI but it is unknown if there is a concomitant secular trend regarding pubertal BMI change. The aim of this study was to describe the trend in pubertal BMI change. We collected heights and weights before and after puberty from school health records and military conscript records for boys born every five years during 1946–1991 (n = 3650, total cohort) and calculated pubertal BMI change (young adult BMI at 20 years of age minus childhood BMI at 8 years of age) for all study participants. A secular trend of increasing pubertal BMI change during the study period was observed. The increase in pubertal BMI change (0.27 kg/m2 per decade [0.22; 0.32]) explained 54% of the secular trend of increasing young adult BMI (0.50 kg/m2 per decade [0.43; 0.57]). We made the novel observation that there is a secular trend of increasing pubertal BMI change. We propose that the secular trend of increasing pubertal BMI change might contribute more than the secular trend of increasing childhood BMI to the adverse cardiovascular health consequences associated with the ongoing obesity epidemic.
Loss of p53 suppresses replication stress-induced DNA damage in ATRX-deficient neuroblastoma
Authors: Akter Jesmin , Katai Yutaka , Sultana Parvin , Takenobu Hisanori , Haruta Masayuki , Sugino Ryuichi P. , Mukae Kyosuke , Satoh Shunpei , Wada Tomoko , Ohira Miki , Ando Kiyohiro , Kamijo Takehiko 
Published: November 2021

AbstractGenetic aberrations are present in the ATRX gene in older high-risk neuroblastoma (NB) patients with very poor clinical outcomes. Its loss-of-function (LoF) facilitates the alternative lengthening of telomeres (ALT) pathway in tumor cells and is strongly linked to replication stress (RS) and DNA damage through G-quadruplex (G4) DNA secondary structures. However, limited information is available on ATRX alteration-related NB tumorigenesis. We herein knocked out (KO) ATRX in MYCN-amplified (NGP) and MYCN single copy (SK-N-AS) NB cells with wild-type (wt) and truncated TP53 at the C terminus, respectively, using CRISPR/Cas9 technologies. The loss of ATRX increased DNA damage and G4 formation related to RS in TP53 wt isogenic ATRX KO NGP cells, but not in SK-N-AS clones. A gene set enrichment analysis (GSEA) showed that the gene sets related to DNA double-strand break repair, negative cell cycle regulation, the G2M checkpoint, and p53 pathway activation were enriched in NGP clones. The accumulation of DNA damage activated the ATM/CHK2/p53 pathway, leading to cell cycle arrest in NGP clones. Interestingly, ATRX loss did not induce RS related to DNA damage response (DDR) in TP53-truncated SK-N-AS cells. p53 inactivation abrogated cell cycle arrest and reduced G4 accumulation in NGP clones. The loss of p53 also induced G4 DNA helicases or Fanconi anemia group D2 protein (FANCD2) with ATRX deficiency, suggesting that ATRX maintained genome integrity and p53 deficiency attenuated RS-induced DNA damage in NB cells featuring inactivated ATRX by regulating DNA repair mechanisms and replication fork stability.
Neonatal sepsis definitions from randomised clinical trials
Authors: Hayes Rían , Hartnett Jack , Semova Gergana , Murray Cian , Murphy Katherine , Carroll Leah , Plapp Helena , Hession Louise , O’Toole Jonathan , McCollum Danielle , Roche Edna , Jenkins Elinor , Mockler David , Hurley Tim , McGovern Matthew , Allen John , Meehan Judith , Plötz Frans B. , Strunk Tobias , de Boode Willem P. , Polin Richard , Wynn James L. , Degtyareva Marina , Küster Helmut , Janota Jan , Giannoni Eric , Schlapbach Luregn J. , Keij Fleur M. , Reiss Irwin K. M. , Bliss Joseph , Koenig Joyce M. , Turner Mark A. , Gale Christopher , Molloy Eleanor J. ,   On behalf of the Infection, Inflammation, Immunology and Immunisation (I4) section of the European Society for Paediatric Research (ESPR)
Published: November 2021

Abstract
Introduction
Neonatal sepsis is a leading cause of infant mortality worldwide with non-specific and varied presentation. We aimed to catalogue the current definitions of neonatal sepsis in published randomised controlled trials (RCTs).

Method
A systematic search of the Embase and Cochrane databases was performed for RCTs which explicitly stated a definition for neonatal sepsis. Definitions were sub-divided into five primary criteria for infection (culture, laboratory findings, clinical signs, radiological evidence and risk factors) and stratified by qualifiers (early/late-onset and likelihood of sepsis).

Results
Of 668 papers screened, 80 RCTs were included and 128 individual definitions identified. The single most common definition was neonatal sepsis defined by blood culture alone (n = 35), followed by culture and clinical signs (n = 29), and then laboratory tests/clinical signs (n = 25). Blood culture featured in 83 definitions, laboratory testing featured in 48 definitions while clinical signs and radiology featured in 80 and 8 definitions, respectively.

Discussion
A diverse range of definitions of neonatal sepsis are used and based on microbiological culture, laboratory tests and clinical signs in contrast to adult and paediatric sepsis which use organ dysfunction. An international consensus-based definition of neonatal sepsis could allow meta-analysis and translate results to improve outcomes.
Viral community analysis in a marine oxygen minimum zone indicates increased potential for viral manipulation of microbial physiological state
Authors: Jurgensen Sophie K , Roux Simon , Schwenck Sarah M , Stewart Frank J , Sullivan Matthew B , Brum Jennifer R 
Published: November 2021

Abstract
Microbial communities in oxygen minimum zones (OMZs) are known to have significant impacts on global biogeochemical cycles, but viral influence on microbial processes in these regions are much less studied. Here we provide baseline ecological patterns using microscopy and viral metagenomics from the Eastern Tropical North Pacific (ETNP) OMZ region that enhance our understanding of viruses in these climate-critical systems. While extracellular viral abundance decreased below the oxycline, viral diversity and lytic infection frequency remained high within the OMZ, demonstrating that viral influences on microbial communities were still substantial without the detectable presence of oxygen. Viral community composition was strongly related to oxygen concentration, with viral populations in low-oxygen portions of the water column being distinct from their surface layer counterparts. However, this divergence was not accompanied by the expected differences in viral-encoded auxiliary metabolic genes (AMGs) relating to nitrogen and sulfur metabolisms that are known to be performed by microbial communities in these low-oxygen and anoxic regions. Instead, several abundant AMGs were identified in the oxycline and OMZ that may modulate host responses to low-oxygen stress. We hypothesize that this is due to selection for viral-encoded genes that influence host survivability rather than modulating host metabolic reactions within the ETNP OMZ. Together, this study shows that viruses are not only diverse throughout the water column in the ETNP, including the OMZ, but their infection of microorganisms has the potential to alter host physiological state within these biogeochemically important regions of the ocean.
Universal activity-based labeling method for ammonia- and alkane-oxidizing bacteria
Authors: Sakoula Dimitra , Smith Garrett J , Frank Jeroen , Mesman Rob J , Kop Linnea F M , Blom Pieter , Jetten Mike S M , van Kessel Maartje A H J , Lücker Sebastian 
Published: November 2021

Abstract
The advance of metagenomics in combination with intricate cultivation approaches has facilitated the discovery of novel ammonia-, methane-, and other short-chain alkane-oxidizing microorganisms, indicating that our understanding of the microbial biodiversity within the biogeochemical nitrogen and carbon cycles still is incomplete. The in situ detection and phylogenetic identification of novel ammonia- and alkane-oxidizing bacteria remain challenging due to their naturally low abundances and difficulties in obtaining new isolates from complex samples. Here, we describe an activity-based protein profiling protocol allowing cultivation-independent unveiling of ammonia- and alkane-oxidizing bacteria. In this protocol, 1,7-octadiyne is used as a bifunctional enzyme probe that, in combination with a highly specific alkyne-azide cycloaddition reaction, enables the fluorescent or biotin labeling of cells harboring active ammonia and alkane monooxygenases. Biotinylation of these enzymes in combination with immunogold labeling revealed the subcellular localization of the tagged proteins, which corroborated expected enzyme targets in model strains. In addition, fluorescent labeling of cells harboring active ammonia or alkane monooxygenases provided a direct link of these functional lifestyles to phylogenetic identification when combined with fluorescence in situ hybridization. Furthermore, we show that this activity-based labeling protocol can be successfully coupled with fluorescence-activated cell sorting for the enrichment of nitrifiers and alkane-oxidizing bacteria from complex environmental samples, enabling the recovery of high-quality metagenome-assembled genomes. In conclusion, this study demonstrates a novel, functional tagging technique for the reliable detection, identification, and enrichment of ammonia- and alkane-oxidizing bacteria present in complex microbial communities.
Structure and stability of symptoms in first episode psychosis: a longitudinal network approach
Authors: Griffiths Siân Lowri , Leighton Samuel P. , Mallikarjun Pavan Kumar , Blake Georgina , Everard Linda , Jones Peter B. , Fowler David , Hodgekins Joanne , Amos Tim , Freemantle Nick , Sharma Vimal , Marshall Max , McCrone Paul , Singh Swaran P. , Birchwood Max , Upthegrove Rachel 
Published: November 2021

AbstractEarly psychosis is characterised by heterogeneity in illness trajectories, where outcomes remain poor for many. Understanding psychosis symptoms and their relation to illness outcomes, from a novel network perspective, may help to delineate psychopathology within early psychosis and identify pivotal targets for intervention. Using network modelling in first episode psychosis (FEP), this study aimed to identify: (a) key central and bridge symptoms most influential in symptom networks, and (b) examine the structure and stability of the networks at baseline and 12-month follow-up. Data on 1027 participants with FEP were taken from the National EDEN longitudinal study and used to create regularised partial correlation networks using the ‘EBICglasso’ algorithm for positive, negative, and depressive symptoms at baseline and at 12-months. Centrality and bridge estimations were computed using a permutation-based network comparison test. Depression featured as a central symptom in both the baseline and 12-month networks. Conceptual disorganisation, stereotyped thinking, along with hallucinations and suspiciousness featured as key bridge symptoms across the networks. The network comparison test revealed that the strength and bridge centralities did not differ significantly between the two networks (C = 0.096153;p = 0.22297). However, the network structure and connectedness differed significantly from baseline to follow-up (M = 0.16405,p = <0.0001; S = 0.74536,p = 0.02), with several associations between psychosis and depressive items differing significantly by 12 months. Depressive symptoms, in addition to symptoms of thought disturbance (e.g. conceptual disorganisation and stereotyped thinking), may be examples of important, under-recognized treatment targets in early psychosis, which may have the potential to lead to global symptom improvements and better recovery.
Cdc25A inhibits autophagy-mediated ferroptosis by upregulating ErbB2 through PKM2 dephosphorylation in cervical cancer cells
Authors: Wang Chen , Zeng Jie , Li Li-Jie , Xue Min , He Si-Li 
Published: November 2021

AbstractCervical cancer is the leading cause of cancer-related deaths in women, and treatment for cervical cancer is very limited. Emerging evidence suggests that targeting ferroptosis is a promising way to treat cancer. Here, we investigated the role of ferroptosis in cervical cancer, with a focus on the Cdc25A/PKM2/ErbB2 axis. Cervical cancer cells were treated with sorafenib to induce ferroptosis. Cellular MDA/ROS/GSH/iron detection assays were used to measure ferroptosis. MTT assays were performed to assess cell viability. qRT-PCR, western blot, and immunostaining assays were performed to measure the levels of proteins. Autophagy was monitored by fluorescence microscopy. Nuclear and cytosolic fractions were isolated to examine the location of PKM2 modifications. Co-IP experiments were conducted to determine the Cdc25A/PKM2 interaction. ChIP assays were performed to measure the binding affinity between H3K9Ac and the ErbB3 promoter, and a dual luciferase assay was performed to examine the transcriptional activity of ErbB2. A nude mouse xenograft model was used to examine the effects of the Cdc25A/ErbB2 axis on tumour growth in vivo. Cdc25A was elevated in human cervical cancer tissues but was reduced during sorafenib-induced ferroptosis of cervical cancer cells. Overexpression of Cdc25A inhibited sorafenib-induced ferroptosis by dephosphorylating nuclear PKM2 and suppressing autophagy. Cdc25A regulated autophagy-induced ferroptosis by increasing ErbB2 levels via the PKM2–pH3T11–H3K9Ac pathway. Cdc25A increased the resistance of cervical cancer to sorafenib, while knockdown of ErbB2 blocked these effects. Cdc25A suppressed autophagy-dependent ferroptosis in cervical cancer cells by upregulating ErbB2 levels through the dephosphorylation of PKM2. These studies revealed that Cdc25A/PKM2/ErbB2 pathway-regulated ferroptosis could serve as a therapeutic target in cervical cancer.
Phacoemulsification combined with micropulse cyclodiode laser in glaucoma patients: efficacy and safety
Authors: Daas Arij , Sherman Thomas , Danieliute Lina , Goyal Saurabh , Amon Andrew , Rodrigues Ian , Karimi Ayesha , Lim Kin Sheng 
Published: November 2021

Abstract
Objective
To evaluate the safety and efficacy of phacoemulsification combined with Micropulse transscleral cyclophotocoagulation (MP-TSCPC) in glaucoma patients.

Methods
This is a retrospective case-note review. The participants were adult patients with diagnoses of glaucoma and cataract who required a further reduction in IOP or a reduction in the number of glaucoma drops. All consecutive patients who underwent cataract surgery (CS) combined with MP-TSCPC laser between October 2018 and July 2019 were included in the study. The effect on visual acuity (VA), intraocular pressure (IOP) and number of anti-glaucoma drops were evaluated at 6 and 12 months in addition to any complications that occurred during any time point of the study.

Results
42 eyes were included in the study. Mean IOP was reduced from 19.5 ± 5.4 mmHg by 22.5% to 15.1 ± 4.6 at 6 months post-operatively and by 19.5% to 15 ± 6.6 mm Hg at 12 months (p < 0.001 at both time points). The number of anti-glaucoma medications also reduced significantly from 2.8 ± 1.3 to 1.6 ± 1.2 at 6 months and to 2.2 ± 1.3 at 12 months (p < 0.001 at both time points). The success rate was 56% at 6 months and 54% at 12 months. 54.7% of our patients who completed 12 months follow up had an improvement or unchanged vision at the last visits.

Conclusion
This is the first study evaluating the effect of cataract surgery combined with MP-TSCPC in glaucoma patients. We demonstrated that this led to a reduction in IOP and the number of anti-glaucoma medications at 6 and 12-month postoperatively. The majority of patients had either stable or better vision at 12 months follow-up.
3D-printed phantoms to quantify accuracy and variability of goniometric and volumetric assessment of Peyronie’s disease deformities
Authors: Walker Dyvon T. , Jiang Tommy , Santamaria Alvaro , Osadchiy Vadim , Daniels Doug , Sturm Renea M. , Mills Jesse N. , Eleswarapu Sriram V. 
Published: November 2021

AbstractCharacterization of Peyronie’s disease (PD) involves manual goniometry and penile length measurement. These techniques neglect volume loss or hourglass deformities. Inter-provider variability complicates accuracy. Using 3D-printed models, we aimed to evaluate measurement accuracy and variability and establish computational assessment workflows. Five digital phantoms were created: 13.0 cm cylinder, 13.0 cm hourglass cylinder, 15.0 cm cylinder with 40° angulation, 12.0 cm straight penis, and 12.9 cm PD penis with 68° angulation and hourglass. Lengths, volumes, and angles were determined computationally. Each phantom was 3D-printed. Ten urology providers determined lengths, angles, and volumes with measuring tape, goniometer, and volume calculator. Provider versus computational measurements were compared to determine accuracy using t-tests or Wilcoxon rank-sum tests. No significant differences were observed between manual assessment of length of penile models and designed length in penile models. Average curvature angles from providers for bent cylinder and PD phantoms were 38.3° ± 3.9° (p = 0.25) and 57.5° ± 7.2° (p = 0.006), respectively. When assessing for volume, hourglass cylinder and bent cylinder showed significant differences between designed volume and provider averages. All assessments of length, angle, and volume showed significant provider variability. Our results suggest manual measurements suffer from inaccuracy and variability. Computational workflows are useful for improved accuracy and volume assessment.